The WU-Minn Human Connectome Project (HCP) releases imaging data collected on subjects on a regular basis. Details on what data is included in each release are available in the Reference Manual for that release on the HCP documentation page. On this wiki page, we document known updates, data issues, bugs, and known missing files in the data distributed with each release (including those distributed in Connectome in a box for each release) and plans to fix or patch each bug. Date added is listed at the beginning of entries.
The following runs from 169444 are unusable due to major acquisition artifacts and instability. The following runs in the released data are affected and should not be used:
rfMRI_REST1_7T_PA
tfMRI_RETBAR1_7T_AP
tfMRI_RETBAR2_7T_PA
tfMRI_RETCCW_7T_AP
tfMRI_RETCON_7T_PA
tfMRI_RETCW_7T_PA
tfMRI_RETEXP_7T_AP
Data from the remaining 7T fMRI runs for this subject (and all other 3T and 7T data) are usable.
No planned Fix: These data are released and we do not plan to remove them from ConnectomeDB or AWS S3. We recommend excluding these runs from your analyses.
3T Functional MRI data from a batch of 25 subjects were incorrectly processed, with all "RL" runs (right-left phase encoding) being processed with the wrong phase encoding direction. Not only are the preprocessing results for the RL functional runs themselves incorrect, but the MSM-All registration for these subjects, which is dependent on the correct preprocessing outputs, is also incorrect. Therefore any analyses using the MSM-All aligned data from these subjects would be affected. Further, 7 of these subjects also have 7T data, so analyses of 7T data that use MSM-All aligned data would be affected as well (since the MSM-All registration applied to the 7T data was based on the 3T data). No Test-Retest subjects were affected.
The 3T "LR" (left to right phase encoding) runs for these subjects were processed correctly, but we recommend using both runs in analyses to mitigate phase encoding bias. The MSM-Sulc data for the 3T LR functional runs and 7T functional data are not misaligned, but we don't recommend using MSM-Sulc aligned data for cross subject analyses.
Recommendations:
Due to the incorrect preprocessing of half the runs, we recommend excluding these subjects from any further analyses of the 3T functional data.
7T preprocessed Functional data (all runs) were processed correctly and can be used. However, due to the non-optimally aligned MSM-All surfaces, if you are performing cross-subject analyses using the 7T functional data, your options are to either: (1) exclude these subjects from your analysis, (2) confirm that the MSM-All registration in these subjects is still reasonable*, or (3) use the MSM-Sulc registered surfaces instead for all subjects (not recommended).
3T and 7T preprocessed Diffusion data for these subjects was not affected by the functional preprocessing error and can be used. However, due to the non-optimally aligned MSM-All surfaces, if you are performing cross-subject diffusion analyses involving surfaces, your options are to either: (1) exclude these subjects from your analysis, (2) confirm that the MSM-All registration in these subjects is still reasonable*, or (3) use the MSM-Sulc registered surfaces instead for all subjects (not recommended).
*One may determine that the MSM-All registration is reasonable in the affected subjects by:
- Comparing affected subjects' MSMAll myelin maps ${StudyFolder}/${Subject}/MNINonLinear/${Subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar to the group template available for download in https://github.com/Washington-University/HCPpipelines/blob/master/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii
- Looking at the affected subjects' MSMAll areal distortion maps ${StudyFolder}/${Subject}/MNINonLinear/${Subject}.ArealDistortion_MSMAll.164k_fs_LR.dscalar.nii
Affected subjects, with 7T subjects noted:
103010
113417
116423
120010
121719
127226
130114 7T
143830
169040 7T
185038
189652
202820
204218
329844
385046 7T
401422 7T
462139
469961
644246 7T
688569
723141
908860
943862 7T
969476
971160 7T
Subject 168139 has an anatomical anomaly, as noted in HCP Subjects with Identified Quality Control Issues (QC_Issue measure codes explained), a large posterior fossa subarachnoid cyst. The cyst was large enough in this case to cause the EPI to T1w alignment to fail severely in the fMRI Volume part of functional preprocessing, and causes all subsequent preprocessing results to be unusable. The following runs in the released data are affected and should not be used:
tfMRI_EMOTION_LR
tfMRI_GAMBLING_LR
tfMRI_GAMBLING_RL
tfMRI_LANGUAGE_LR
tfMRI_LANGUAGE_RL
tfMRI_MOTOR_LR
tfMRI_MOTOR_RL
tfMRI_RELATIONAL_LR
tfMRI_RELATIONAL_RL
tfMRI_SOCIAL_LR
tfMRI_SOCIAL_RL
tfMRI_WM_LR
tfMRI_WM_RL
Data from the remaining fMRI runs for this subject (all resting state and tfMRI_EMOTION_RL) are usable.
No planned Fix: These data are released and we do not plan to remove them from ConnectomeDB or AWS S3. We recommend excluding these runs from your analyses.
For a variety of reasons, some fMRI runs for particular subjects were released in the S1200 data release, but should not be used. The following runs are affected and should not be used:
196952 tfMRI_WM_LR
748662 tfMRI_SOCIAL_RL
809252 tfMRI_SOCIAL_RL
Data from the remaining fMRI runs for these subjects (all resting state and other tfMRI runs) are usable.
No planned Fix: These data are released and we do not plan to remove them from ConnectomeDB or AWS S3. We recommend excluding these runs from your analyses.
The following released runs display incomplete brain coverage due to misplaced acquisition Field of View (FOV). We recommend exclusion of these data from analyses.
144428 tfMRI_MOTOR_RL
144428 tfMRI_GAMBLING_LR
144428 tfMRI_MOTOR_LR
168139 tfMRI_EMOTION_LR
186545 tfMRI_SOCIAL_LR
186545 tfMRI_SOCIAL_RL
186545 tfMRI_RELATIONAL_LR
186545 tfMRI_RELATIONAL_RL
186545 tfMRI_EMOTION_LR
186545 tfMRI_EMOTION_RL
192237 tfMRI_MOTOR_RL
223929 tfMRI_RELATIONAL_LR
320826 tfMRI_EMOTION_RL
644044 tfMRI_RELATIONAL_LR
644044 tfMRI_RELATIONAL_RL
644044 tfMRI_EMOTION_LR
644044 tfMRI_EMOTION_RL
822244 tfMRI_GAMBLING_LR
822244 tfMRI_MOTOR_RL
870861 tfMRI_GAMBLING_LR
870861 tfMRI_MOTOR_LR
870861 tfMRI_MOTOR_RL
947668 tfMRI_GAMBLING_LR
947668 tfMRI_GAMBLING_RL
947668 tfMRI_MOTOR_RL
Data from the remaining fMRI runs for these subjects (all resting state and other tfMRI runs) are usable.
No planned Fix: These data are released and we do not plan to remove them from ConnectomeDB or AWS S3. We recommend excluding these runs from your analyses.
Age and Gender-adjusted T-scores for the Achenbach Self Report behavioral survey have been mislabeled/misdefined as Age and Gender adjusted Percentile scores as variable names and in Data Dictionary descriptions since these scores were released for the 500 Subjects data release. The affected scores are:
Current Correct
ASR_Anxd_Pct ASR_Anxd_T
ASR_Witd_Pct ASR_Witd_T
ASR_Soma_Pct ASR_Soma_T
ASR_Thot_Pct ASR_Thot_T
ASR_Attn_Pct ASR_Attn_T
ASR_Aggr_Pct ASR_Aggr_T
ASR_Rule_Pct ASR_Rule_T
ASR_Intr_Pct ASR_Intr_T
DSM_Depr_Pct DSM_Depr_T
DSM_Anxi_Pct DSM_Anxi_T
DSM_Somp_Pct DSM_Somp_T
DSM_Avoid_Pct DSM_Avoid_T
DSM_Adh_Pct DSM_Adh_T
DSM_Antis_Pct DSM_Antis_T
Completed Fix: Labels and definitions of T-Scores for the ASR Syndrome and DSM-Oriented Scales were updated with the rerelease of the 7T HCP functional data in April 2018.
Between HCP data collection for subjects released in the 500 Subjects Release and 900 Subjects Release, NIH Toolbox changed how the Words In Noise (WIN) audition test was administered to subjects (through computer speakers in v1 to through earphones in v2). Due to how our internal database was recording the scores for WIN v1 and WIN v2 separately, only the v1 scores have been correctly released in ConnectomeDB under the "Noise_Comp" variable, the WIN Computed score. Subjects tested with WIN v2 (most subjects newly released in S900 and S1200 releases) erroneously have either no score listed or a score of -99. NIH Toolbox has verified that the v1 and v2 WIN scoring has been normed to be directly comparable, so we plan to combine the v1/v2 scores for release as the single "Noise_Comp" variable.
Completed Fix:Words In Noise v2 scores were added to the "Noise_Comp" variable released with the rerelease of the 7T HCP functional data in April 2018.
For many previously-released participants (specifically, subjects initially released up to and including the "500 Subjects Release"), some "In-scanner performance" EMOTION variables were swapped in behavioral data .csv files downloaded from ConnectomeDB (either from the quick downloads section of the S1200 project page or from the subject dashboard). Specifically, the Emotion_Task_Acc and Emotion_Task_Face_Acc variables were swapped, and the Emotion_Task_Median_RT and Emotion_Task_Face_Median_RT variables were swapped. The following data were not affected: .csv files for individual scan runs (obtained via Connectome-in-a-Box or downloaded .zip packages), and values for participants that were first released in the 900 Subjects Release and subsequent releases.
Completed Fix: The EMOTION variables in ConnectomeDB .csv files were corrected as of July 28, 2017. The EMOTION task accuracy and reaction time variables for all affected participants are correct in spreadsheets downloaded after this date.
A bug in the 7T fMRIVolume pipeline caused all Anterior->Posterior (AP phase-encoding direction) runs in the 7T fMRI data on all subjects to be unwarped using the incorrect direction, causing registration and all subsequent processing results to be incorrect. Since the unwarping is a very early processing step, all AP run 7T fMRI data is affected, including all preprocessed and FIX-cleaned resting state, retinotopy, and movie-watching data. All 7T fMRI data should not be used. Therefore, we have made this data unavailable for download in ConnectomeDB until fixed by reprocessing. Unprocessed 7T fMRI and all 7T diffusion MRI data is unaffected by this issue and is still available for download.
Completed Fix: All 7T fMRI data was reprocessed with the bug fixed and rereleased in ConnectomeDB in April 2018. (7T data, including the correction to the fMRI data, uploaded to HCP Amazon AWS S3 bucket for first time in Nov 2021).
Two versions of the image reconstruction algorithm were used for the fMRI data (both task and resting-state) over the course of the Young-Adult HCP: version "r177" for subjects scanned early (Q1 through mid-Q3) and version "r227" for subjects scanned after that (mid-Q3 onward). The reconstruction version has a notable signature on the fMRI data that can make a large difference in fMRI data analysis. Users wanting to use only data with the same reconstruction algorithm in their analyses can filter data on the ConnectomeDB dashboard by fMRI reconstruction version (in the Study Completion category, "fMRI_3T_ReconVrs"). See Ramifications of Image Reconstruction Version Differences for more details. On ConnectomeDB, we also provide separate Resources for Group Average Functional Connectivity ("dense connectomes") and Parcellation+Timeseries+Netmats ("PTN") files based on both all subjects ("r177+r227") and just the "r227" subjects.
With the S1200 release, a subject data measure (QC_Issue) has been added to ConnectomeDB to flag subjects with notable issues found in the HCP Quality Control process. The issues are notable, but were not considered severe enough to exclude the subject's imaging data from release. We are sharing these findings of issues to alert users and allow them to decide whether to include or exclude these subjects in their own analyses. More details can be found here: HCP Subjects with Identified Quality Control Issues (QC_Issue measure codes explained)
Nineteen subjects from the S1200 Release (including two originally released in S500+MEG2 and eleven originally released in the S900 Release) do not have gradient-recalled echo (GRE) field maps accompanying their structural (T1 and T2) scans.
Affected Subjects:
102614
111009
111514
115017
121416
130821
138332
179952
299760
300618
392750
406432
429040
633847
662551
679770
688569
693461
815247
The field maps for these subjects were not collected or are unusable. Field maps are not required for HCP structural processing (in contrast to fMRI processing, where field maps are required). However, the lack of field maps prevents us from performing readout distortion correction on the structurals and will have these two effects:
Issue Cannot be Fixed
The following variables appear twice (duplicate):
FS_L_Cerebellum_Cort_Vol
FS_L_Cerebellum_Cort_Vox
FS_L_Cerebellum_Cort_Mean
FS_L_Cerebellum_Cort_Std
FS_L_Cerebellum_Cort_Range
FS_L_Cerebellum_Cort_Min
FS_L_Cerebellum_Cort_Max
For each of these, the “duplicate” appears in the position where the value for the “R” side value should be located and comparing actual values against the aseg.stats, indicates that the values in the columns that should be “R” are indeed from the right side, so the error appears to be solely in the column labels for those columns.
Planned Fix: The column labels for these Expanded FreeSurfer Data variables will be reset to "R" versions.
FIX processing for the rfMRI_REST1_RL RETEST run of subject 341834 was never successfully completed so this data is not available in the release.
No planned Fix. Due to other priorities, we will not be generating this data. Users needing this data can run the HCP FIX pipeline on the functional processing results.In version 3.4.1 of the HCPpipelines (used to process the structural data for HCP-YA S1200 release), there was a bug in the FreeSurferHiResPial.sh script that caused the lh.curv.pial and rh.curv.pial files (curvature of the pial surface) to be written out incorrectly. Therefore those two files should not be used.
Instead, use the {lh,rh}.curv.pial.T2.two files that are also contained in the {Subject_ID}/T1w/{Subject_ID}/surf directory of the “Structural Extended Packages”
No planned Fix. Due to the minor nature of the bug, that it can be easily worked around, and the age of ConnectomeDB, we do not plan to fix this in the released data.
The preprocessing results for the tfMRI_WM_RL run are incomplete for subject 668361, despite our collecting complete tfMRI_WM_RL data for this subject.
These directories/files are missing from the 668361/MNINonLinear/Results/tfMRI_WM_RL directory:
/EVs
/RibbonVolumeToSurfaceMapping
Movement_*.txt files
*TAB.txt files
brainmask_fs.2.nii.gz
tfMRI_WM_LR.nii.gz
tfMRI_WM_LR_Atlas.dtseries.nii
tfMRI_WM_LR_Jacobian.nii.gz
tfMRI_WM_LR_SBRef.nii.gz
tfMRI_WM_LR_hp200_s4_level1.fsf
Planned Fix: The tfMRI_WM_RL run will be reprocessed and the missing files regenerated to update the 668361 WM tfMRI preproc package and the 668361 data in AWS S3.
Due to a late stage error in the running of the functional preprocessing pipeline for some subjects newly released with the S1200, *TAB.txt and *Physio_log.txt files are missing in the {Subject_ID}/MNINonLinear/Results/tfMRI_{TASK}_{RUN} directories for ALL tasks completed and the *Physio_log.txt files are missing in the {Subject_ID}/MNINonLinear/Results/rfMRI_{REST?}_{RUN} directory.
The missing files do exist for these subjects in {Subject_ID}/unprocessed/3T/tfMRI_{TASK}_{RUN}/LINKED_DATA/EPRIME, {Subject_ID}/unprocessed/3T/tfMRI_{TASK}_{RUN}/LINKED_DATA/PHYSIO, and {Subject_ID}/rfMRI_{REST?}_{RUN}/LINKED_DATA/PHYSIO directories, so there was a problem with the transfer to the preprocessed directories.
Affected subjects:
116423
120010
121719
127226
130114
143830
202820
385046
401422
462139
469961
644246
723141
943862
969476
971160
Because this issue is isolated to subjects newly released with S1200, this DOES NOT affect earlier release data distributed by HCP.
Planned Fix: The missing *TAB.txt and *Physio_log.txt files will be transferred to the appropriate preprocessing {Subject_ID}/MNINonLinear/Results directories, the affected rfMRI and tfMRI preprocessing packages will be updated in ConnectomeDB, and AWS S3 will be updated.
7T Preprocessed fMRI AP run data (Resting State, Retinotopy, and Movie-watching Task) unwarped using the incorrect direction in the fMRIVolume pipeline for all 7T Subjects
A bug in the 7T fMRIVolume pipeline caused all Anterior->Posterior (AP phase-encoding direction) runs in the 7T fMRI data on all subjects to be unwarped using the incorrect direction, causing registration and all subsequent processing results to be incorrect. Since the unwarping is a very early processing step, all AP run 7T fMRI data is affected, including all preprocessed and FIX-cleaned resting state, retinotopy, and movie-watching data. All 7T fMRI data should not be used. Therefore, we have made this data unavailable for download in ConnectomeDB until fixed by reprocessing. Unprocessed 7T fMRI and all 7T diffusion MRI data is unaffected by this issue and is still available for download.
Completed Fix: All 7T fMRI data was reprocessed with the bug fixed and rereleased in ConnectomeDB in April 2018. (7T data, including the correction to the fMRI data, uploaded to HCP Amazon AWS S3 bucket for first time in Nov 2021).
Age and Gender-adjusted T-scores for the Achenbach Self Report behavioral survey have been mislabeled/misdefined as Age and Gender adjusted Percentile scores as variable names and in Data Dictionary descriptions since these scores were released for the 500 Subjects data release. The affected scores are:
Current Correct
ASR_Anxd_Pct ASR_Anxd_T
ASR_Witd_Pct ASR_Witd_T
ASR_Soma_Pct ASR_Soma_T
ASR_Thot_Pct ASR_Thot_T
ASR_Attn_Pct ASR_Attn_T
ASR_Aggr_Pct ASR_Aggr_T
ASR_Rule_Pct ASR_Rule_T
ASR_Intr_Pct ASR_Intr_T
DSM_Depr_Pct DSM_Depr_T
DSM_Anxi_Pct DSM_Anxi_T
DSM_Somp_Pct DSM_Somp_T
DSM_Avoid_Pct DSM_Avoid_T
DSM_Adh_Pct DSM_Adh_T
DSM_Antis_Pct DSM_Antis_T
Completed Fix: Labels and definitions of T-Scores for the ASR Syndrome and DSM-Oriented Scales were updated with the rerelease of the 7T HCP functional data in April 2018.
Between HCP data collection for subjects released in the 500 Subjects Release and 900 Subjects Release, NIH Toolbox changed how the Words In Noise (WIN) audition test was administered to subjects (through computer speakers in v1 to through earphones in v2). Due to how our internal database was recording the scores for WIN v1 and WIN v2 separately, only the v1 scores have been correctly released in ConnectomeDB under the "Noise_Comp" variable, the WIN Computed score. Subjects tested with WIN v2 (most subjects newly released in S900 and S1200 releases) erroneously have either no score listed or a score of -99. NIH Toolbox has verified that the v1 and v2 WIN scoring has been normed to be directly comparable, so we plan to combine the v1/v2 scores for release as the single "Noise_Comp" variable.
Completed Fix: Words In Noise v2 scores were added to the "Noise_Comp" variable released with the rerelease of the 7T HCP functional data in April 2018.
For many previously-released participants (specifically, subjects initially released up to and including the "500 Subjects Release"), some "In-scanner performance" EMOTION variables were swapped in behavioral data .csv files downloaded from ConnectomeDB (either from the quick downloads section of the S900 project page or from the subject dashboard). Specifically, the Emotion_Task_Acc and Emotion_Task_Face_Acc variables were swapped, and the Emotion_Task_Median_RT and Emotion_Task_Face_Median_RT variables were swapped. The following data were not affected: .csv files for individual scan runs (in Connectome-in-a-Box or downloaded .zip packages), and values for participants that were first released in the 900 Subjects Release and 1200 Subjects Release.
Completed Fix: The EMOTION variables in ConnectomeDB .csv files were corrected as of July 28, 2017. The EMOTION task accuracy and reaction time variables for all affected participants are correct in spreadsheets downloaded after this date.
Diffusion data removed for Subjects 130922 and 150423 [RESOLVED with S1200 Release]
Two subjects had some or all previously released diffusion scans which were deemed to be unusable and removed from the released data with the S1200 Release. For subject 130922, originally part of the Q3 release, the DWI_dir95_RL diffusion scan (only) was determined to be unusable. For subject150423, originally part of the Q1 release, only two diffusion scans were completed and that is not enough for useful analysis, therefore all diffusion data was removed.
Completed Fix: As of the S1200 Release, the DWI_dir95_RL diffusion scan for subject 130922 and all diffusion data for subject 150423 were removed from the released data. The affected preprocessed dMRI data for these subjects from previous releases should not be used (whether obtained via Connectome in a Box or downloaded online).
Image reconstruction algorithm versions
Two versions of the image reconstruction algorithm applied to dMRI and fMRI data have been used in HCP to date: version r177 for subjects scanned in Q1 through mid-Q3, version r227 for subjects scanned mid-Q3 and after. We were able to retroactively recon all dMRI data using the newer r227 version. However, for the fMRI data, this was not possible and data reconstructed with both r177 and r227 versions remain in ConnectomeDB. The reconstruction version makes a notable signature on the data that can make a large difference in fMRI data analysis. Users wanting to use only data with the same reconstruction algorithm applied in their analyses can filter data on the ConnectomeDB dashboard by fMRI reconstruction version (in the Study Completion category). See Ramifications of Image Reconstruction Version Differences for more details.
An artifact (characterized by a striped spatial pattern in image intensity around orbitofrontal susceptibility areas) caused by intermittent technical problems with the 32 channel head coil has been found in a limited number of fMRI scan session (24 rfMRI scans in 18 subjects; 6 tfMRI scans in 6 subjects) that were obtained during the summer of 2013. We have opted to release these data for public use with the expectation that investigators will review the data, before and after their chosen pre-processing steps, to decide whether this artifact might affect their data analysis. See Intermittent orbitofrontal artifact affecting some fMRI scans for details, including a list of affected subjects/scans and example images.
The preprocessing results for the tfMRI_WM_RL run are incomplete for subject 668361, despite our collecting complete tfMRI_WM_RL data for this subject.
These directories/files are missing from the 668361/MNINonLinear/Results/tfMRI_WM_RL directory:
/EVs
/RibbonVolumeToSurfaceMapping
Movement_*.txt files
*TAB.txt files
brainmask_fs.2.nii.gz
tfMRI_WM_LR.nii.gz
tfMRI_WM_LR_Atlas.dtseries.nii
tfMRI_WM_LR_Jacobian.nii.gz
tfMRI_WM_LR_SBRef.nii.gz
tfMRI_WM_LR_hp200_s4_level1.fsf
Planned Fix: The tfMRI_WM_RL run will be reprocessed and the missing files regenerated to update the 668361 WM tfMRI preproc package and the 668361 data in AWS S3.
The T1w and T2w structural data quality was reassessed and subjects 121719 & 169040 were deemed of sufficient quality to release all available imaging data with the S1200 Release.
Completed Fix: All available imaging data for subjects 121719 & 169040 was released with the S1200 Release.
Thirteen subjects from the S900 Release (including two originally released in the S500+MEG2 Release) do not have gradient-recalled echo (GRE) field maps accompanying their structural (T1 and T2) scans.
Affected Subjects:
111009
111514
115017
121416
130821
179952
300618
392750
406432
429040
633847
662551
679770
693461
The field maps for these subjects were not collected or are unusable. Field maps are not required for HCP structural processing (in contrast to fMRI processing, where field maps are required). However, the lack of field maps prevents us from performing readout distortion correction on the structurals and will have these two effects:
We anticipate that a limited number of subjects that will be included in upcoming HCP releases will also have this issue. Those subjects will be identified on this Issues wiki in the appropriate release section.
Age and Gender-adjusted T-scores for the Achenbach Self Report behavioral survey have been mislabeled/misdefined as Age and Gender adjusted Percentile scores as variable names and in Data Dictionary descriptions since these scores were released for the 500 Subjects data release. The affected scores are:
Current Correct
ASR_Anxd_Pct ASR_Anxd_T
ASR_Witd_Pct ASR_Witd_T
ASR_Soma_Pct ASR_Soma_T
ASR_Thot_Pct ASR_Thot_T
ASR_Attn_Pct ASR_Attn_T
ASR_Aggr_Pct ASR_Aggr_T
ASR_Rule_Pct ASR_Rule_T
ASR_Intr_Pct ASR_Intr_T
DSM_Depr_Pct DSM_Depr_T
DSM_Anxi_Pct DSM_Anxi_T
DSM_Somp_Pct DSM_Somp_T
DSM_Avoid_Pct DSM_Avoid_T
DSM_Adh_Pct DSM_Adh_T
DSM_Antis_Pct DSM_Antis_T
Completed Fix: Labels and definitions of T-Scores for the ASR Syndrome and DSM-Oriented Scales were updated with the rerelease of the 7T HCP functional data in April 2018.
For many previously-released participants (specifically, subjects initially released up to and including the "500 Subjects Release"), some "In-scanner performance" EMOTION variables were swapped in behavioral data .csv files downloaded from ConnectomeDB (either from the quick downloads section of the S500 project page or from the subject dashboard). Specifically the Emotion_Task_Acc and Emotion_Task_Face_Acc variables were swapped, and the Emotion_Task_Median_RT and Emotion_Task_Face_Median_RT variables were swapped. The following data were not affected: .csv files for individual scan runs (in Connectome-in-a-Box or downloaded .zip packages), and values for participants that were first released in the 900 Subjects Release and 1200 Subjects Release. (**)
(**) Technically, the small set of 15 subjects that were first released in the "S500+MEG2" Release were also not affected by this problem.
Completed Fix: The EMOTION variables in ConnectomeDB .csv files were corrected as of July 28, 2017. The EMOTION task accuracy and reaction time variables for all participants are correct in spreadsheets downloaded after this date.
An artifact (characterized by a striped spatial pattern in image intensity around orbitofrontal susceptibility areas) caused by intermittent technical problems with the 32 channel head coil has been found in a limited number of fMRI scan session (24 rfMRI scans in 18 subjects; 6 tfMRI scans in 6 subjects) that were obtained during the summer of 2013. We have opted to release these data for public use with the expectation that investigators will review the data, before and after their chosen pre-processing steps, to decide whether this artifact might affect their data analysis. See Intermittent orbitofrontal artifact affecting some fMRI scans for details, including a list of affected subjects/scans and example images.
Two versions of the image reconstruction algorithm applied to dMRI and fMRI data have been used in HCP to date: version r177 for subjects scanned in Q1 through mid-Q3, version r227 for subjects scanned mid-Q3 and after. We were able to retroactively recon all dMRI data using the newer r227 version. However, for the fMRI data, this was not possible and data reconstructed with both r177 and r227 versions remain in ConnectomeDB. The reconstruction version makes a notable signature on the data that can make a large difference in fMRI data analysis. Users wanting to use only data with the same reconstruction algorithm applied in their analyses can filter data on the ConnectomeDB dashboard by fMRI reconstruction version (in the Study Completion category). See Ramifications of Image Reconstruction Version Differences for more details.
In preparation for the HCP 900 subjects data release, we identified previously unknown timing errors in the in the processed physiological log files (e.g., rfMRI_REST1_RL_Physio_log.txt). These errors have resulted in variable offsets in timing, sometimes amounting to hundreds of milliseconds. The timing errors affected rsfMRI, tfMRI, and pulse oximetry data that was collected during diffusion MRI scans. Due to limitations in computational resources, it was not possible to correct the physio files in the packages being released. Therefore, the physio log files in those packages should not be used.
Completed Fix: The corrected processed physiological log files were released for all subjects with the 900 Subjects Release in December 2015.
Subject 142626 removed from ConnectomeDB [RESOLVED with S900 Release]
Subject 142626, released in the 500 Subjects Release (June 2014), has been found to have the same identity as another subject in the HCP study. Thus, we have removed all data for subject 142626 from ConnectomeDB. For any ongoing analyses, we recommend that if possible you exclude subject 142626 from your analyses.
Note: we have not removed the duplicate subject’s dataset, which is comparable in quality to other released subjects, from ConnectomeDB or from ongoing HCP analyses. However, for reasons of confidentiality, we are electing to not reveal the subject number for the duplicate subject. If the subject number of the duplicate subject is found by other investigators using HCP data, we request that you to keep this information confidential.
Subject 142626 was originally released in the 500 Subjects Release and have been available in ConnectomeDB and through Connectome in a Box (CinaB) and Amazon S3 since then.
Completed Fix: All data from subject 142626 has been removed from ConnectomeDB, CinaB, and Amazon S3 as of November 6, 2015 and will no longer be distributed by HCP.
A problem with the middle stages of the v3.1 (500 Subjects) preprocessing of diffusion data released for subject 103515 has been found. The file size for the Diffusion data for this subject is only about 400Mb, which is much smaller than the normal size, and should not be used. (In particular, while the NIFTI header indicates the correct dimensions, frames 83 onward are corrupted in that they contain a single intensity throughout the brain).
Completed Fix: Diffusion data for subject 103515 was completely reprocessed and the fixed version was available as part of the 900 Subjects Release. The preprocessed dMRI for this subject from the 500 Subjects release should not be used (whether obtained via Connectome in a Box or downloaded online). The reprocessed files will be included in 900 Subjects Connectome in a Box versions and in the 900 Subjects update to the HCP Amazon S3 bucket.
A significant amount of head motion in the SBRef scan collected for the SOCIAL_LR task for S500 subject 748662 corrupted data for the entire scan. Therefore, the S500 released data for SOCIAL_LR of 748662 (including the unprocessed, minimally preprocessed, and level 2, cross run analyzed data) should not be used.
We are in the process of removing the corrupt data from ConnectomeDB. SOCIAL tfMRI data for this subject downloaded from June 6, 2014-October 31, 2014 (or distributed in Connectome in a Box drives dated 20140805 or earlier) will contain the corrupted data and should not be used.
Completed Fix: The corrupt SOCIAL_LR tfMRI data for subject 748662 has been permanently removed from ConnectomeDB as of 10/31/2014. These files need to be removed from 500 Subjects Connectome in a Box dated 20140805 or earlier. These files have been removed in 500 Subjects Connectome in a Box versions dated 20141203 and later.
A problem with the early stages of the v3.1 (500 Subjects) preprocessing of diffusion data released for subject 173132 has been found. Diffusion data for this subject downloaded from June 6, 2014-October 31, 2014 (or distributed in Connectome in a Box drives dated 20140805 or earlier) should not be used.
Completed Fix: Diffusion data for subject 173132 has been completely reprocessed and the fixed version is available in ConnectomeDB as of 10/31/14. These files will need to be replaced for 500 Subjects Connectome in a Box dated 20140805 or earlier. The reprocessed files are included in 500 Subjects Connectome in a Box versions dated 20141203 and later.
The issue is that some CSV importers ignore double-quotation marks (" "), which by CSV standard practice are used to handle single fields that contain commas or carriage returns. Our CSV files contain a small number of fields that contain commas within the field. These single fields are being split into multiple fields by CSV importers/code that ignore the standard, resulting in added and misaligned data columns. This issue affects all CSVs (both Open Access and Restricted Access versions) downloaded from ConnectomeDB from Q1 (March 2013) until November 2014.
Completed Fix: As of the MEG2 release (Nov 26, 2014) the commas were removed from the few data fields that contain these in the HCP dataset to fix this issue for future downloaded CSVs.
Users who would like this script for current use can download it by clicking this link: prepare_level2_feat_analysis.sh
Please also see the Advice for FEAT Analysis of HCP task fMRI data for more information on performing tfMRI analysis on HCP data.
Note: Users can also download task analysis data packages containing the results of individual subject, cross-run ("level 2") fMRI grayordinates analysis in FSL for each HCP task at various smoothing levels. Analogous "level2" data packages for volume-based tfMRI processing are available at 4mm smoothing. Please see the HCP 500 Subjects Data Release Reference Manual for more details.
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140925
154936
180129
211417
355542
390645
424229
586460
599671
644044
729254
733548
Completed Fix: We have updated the Color Vision/Eye tested information for these subjects in ConnectomeDB as of June 12, 2014. Restricted Access users that downloaded the restricted dataprior to that date should update their restricted data accordingly.
Completed Fix: We have updated the family structure information for this subject in ConnectomeDB as of July 3, 2014. Restricted Access users that include this subject in their analyses will need to check the demographic data in DB and update downloaded restricted data accordingly.
Two versions of the image reconstruction algorithm applied to dMRI and fMRI data have been used in HCP to date: version r177 for subjects scanned in Q1 through mid-Q3, version r227 for subjects scanned mid-Q3 and after. We were able to retroactively recon all dMRI data using the newer r227 version. However, for the fMRI data, this was not possible and data reconstructed with both r177 and r227 versions remain in ConnectomeDB. The reconstruction version makes a notable signature on the data that can make a large difference in fMRI data analysis. Users wanting to use only data with the same reconstruction algorithm applied in their analyses can filter data on the ConnectomeDB dashboard by fMRI reconstruction version (in the Study Completion category). See Ramifications of Image Reconstruction Version Differences for more details.
Subjects 209733 and 528446 removed from ConnectomeDB
Second-level QC on all subjects has revealed two Q2 subjects with structural brain abnormalities, specifically gray matter heterotopia. The abnormalities significantly affect functional and structural connectivity in these subjects, beyond what is considered normal variation. Therefore, we recommend that data from subjects 209733 and 528446 NOT be used in analyses.
Subjects 209733 and 528446 were originally released in Q2 and have been available in ConnectomeDB and through Connectome in a Box since then. Both subjects were included in the Unrelated 40, Unrelated 80, and Related 120 groups until the 500 subject release (June 6, 2014).
Completed Fix: All data from subjects 209733 and 528446 have been removed from ConnectomeDB as of the 500 subject release and will no longer be distributed by HCP.
The diffusion preprocessing output file containing the structural volume sampled at the same resolution as the diffusion data (necessary for analysis) was inadvertently left out of the dMRI data packages released for Q3:
e.g. ${StudyFolder}/${SubjectID}/T1w/T1w_acpc_dc_restore_1.25.nii.gz
Completed Fix: The dMRI data packages have been rebuilt with this file and as of 1/28/2014 are available via download from ConnectomeDB.
Users can also generate this file for previously downloaded or Connectome in a Box (CINAB) data, using the following FSL commands:
#Generate 1.25mm structural space for resampling the diffusion data into
${FSLDIR}/bin/flirt -interp spline -in T1w_acpc_dc_restore -ref T1w_acpc_dc_restore -applyisoxfm 1.25 -out T1w_acpc_dc_restore_1.25
${FSLDIR}/bin/applywarp --rel --interp=spline -i T1w_acpc_dc_restore -r T1w_acpc_dc_restore_1.25 -o T1w_acpc_dc_restore_1.25
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Functional data for one subject, 727654, needs to be reconstructed with the newer reconstruction method. Because of this, functional data for this subject should not be used in analyses.
As a reminder, do not mix preprocessed data from different data releases in your analyses. The data in Q1, Q2+Q3, and the 500 Subjects Releases were run through different versions of the HCP pipelines, with differences significant enough that preprocessed data should not be compared across releases.
Data for all these subjects should be part of the next "new subject" data release coming in Spring 2015.
Completed Fix: We replaced the Working Memory EVs with new versions set to onset at the cue before the block, and last until the end of the final trial in the block. The "Measure" variable names were modified to be consistent with those of the other tasks. These changes are available as part of the March 2014 data patch.
Completed Fix: We corrected the Target accuracies in the stats files. The "Measure" variable names were modified to be consistent with those of the other tasks. These changes are available as part of the March 2014 data patch.
Improved formatting and additional variables in all tfMRI Stats files
Completed update: The following improvements to all tfMRI Stats files are available as part of the March 2014 data patch:
Change to csv format to make processing behavioral files simpler.
Consistency in variable naming and formatting across Stats files.
Attempt to provide additional performance metrics for the specific conditions being used in the imaging analyses.
Users who would like this script for current use can download it by clicking this link: prepare_level2_feat_analysis.sh
Please also see the Advice for FEAT Analysis of HCP task fMRI data for more information on performing tfMRI analysis on HCP data.
Note: With the Q3 and 500 Subjects release, users can also download task analysis data packages containing the results of individual subject, cross-run ("level 2") fMRI grayordinates analysis for each HCP task at various smoothing levels. Analogous "level2" data packages for volume-based tfMRI processing at 4mm smoothing were made available as of March 2014 and also were part of the 500 Subjects released. Please see the HCP Q3 Data Release Reference Manual or the HCP 500 Subjects Data Release Reference Manual for more details.
${StudyFolder}/156233/MNINonLinear/Results/tfMRI_GAMBLING_RL/Movement_Regressors.txt
${StudyFolder}/156233/MNINonLinear/Results/tfMRI_SOCIAL_LR/Movement_Regressors.txt
${StudyFolder}/165840/MNINonLinear/Results/tfMRI_WM_LR/Movement_Regressors.txt
${StudyFolder}/366446/MNINonLinear/Results/tfMRI_WM_RL/Movement_Regressors.txt
Users who have the Q1+Q2 data: A zipped archive is available containing all of the fixed files for all Q1+Q2 subjects and a python script for patching existing download or Connectome in a box data, which places the fixed files in the HCP directory structure (details in the HCP Q2 Data Release Reference Manual and the associated directory structure Appendix III). Download the Q1/Q2 data patch script here (requires ConnectomeDB login).
Second-level QC on all subjects has revealed two Q2 subjects with structural brain abnormalities, specifically gray matter heterotopia. The abnormalities significantly affect functional and structural connectivity in these subjects, beyond what is considered normal variation. Therefore, we recommend that data from subjects 209733 and 528446 NOT be used in analyses.
Subjects 209733 and 528446 were originally released in Q2 and have been available in ConnectomeDB and through Connectome in a Box since then. Both subjects were included in the Unrelated 40, Unrelated 80, and Related 120 groups until the 500 subject release (June 6, 2014).
Completed Fix: All data from subjects 209733 and 528446 were removed from ConnectomeDB as of the 500 subject release and will no longer be distributed by HCP.
For one Q1+Q2 subject, DICOM to NIFTI failed to output correct number of volumes or lines in some tfMRI Relational data files:
${StudyFolder}/138231/MNINonLinear/Results/tfMRI_RELATIONAL_LR/*
Subject/scan affected: file type Issue:
138231/tfMRI_RELATIONAL_LR 4D volume volumes should be 232 instead of 106
138231/tfMRI_RELATIONAL_LR all movement regressor files lines should be 232 instead of 106
138231/tfMRI_RELATIONAL_LR Physio_log.txt triggers should be 232 instead of 105
Surface files for this subject will also be affected.
Completed Fix: DICOM2NIFTI was rerun and files are fixed as of the Q3 release (September 2013).
Users should either: 1) replace unprocessed and processed versions Q1+Q2 Relational data for subject 138231 by re-downloading the Relational packages (both unproc and preproc) for subject 138231, or 2) download and run the Q1/Q2 release patch script available here (requires ConnectomeDB login).
tfMRI Social EV *.txt files incomplete
For some Q1+Q2 subjects, EV files for the Social tfMRI task were missing an entry for one or more blocks, and thus those EV files are inaccurate and incomplete. Specifically, there was a bug in the EV creation script used for the Q1 and Q2 releases for the SOCIAL task such that blocks were omitted from the EV file if the subject didn't respond during that block.
e.g. ${StudyFolder}/${SubjectID}/MNINonLinear/Results/tfMRI_SOCIAL_RL/EVs/*.txt
Subjects/affected directories with this bug: Q1+Q2 Subjects with Shortened tfMRI Social EV *.txt Files
Completed Fix: These bugs have resolved for the Q3 release (September 2013).
Users should run the Q1/Q2 data patch script to correct all these incomplete files (download available here) (requires ConnectomeDB login).
150423/tfMRI_GAMBLING_RL tfMRI_GAMBLING_RL_hp200_s4_level1.fsf npts should be 232 instead of 253
150423/tfMRI_RELATIONAL_LR tfMRI_RELATIONAL_LR_hp200_s4_level1.fsf npts should be 193 instead of 232
329440/tfMRI_GAMBLING_RL tfMRI_GAMBLING_RL_hp200_s4_level1.fsf npts should be 202 instead of 253
250427/tfMRI_WM_RL tfMRI_WM_RL_hp200_s4_level1.fsf file missing
250427/tfMRI_GAMBLING_RL tfMRI_GAMBLING_RL_hp200_s4_level1.fsf file missing
Completed fix: These bugs have resolved for the Q3 release (September 2013).
Users should run the Q1/Q2 data patch script to correct all these incomplete files (download available here) (requires ConnectomeDB login).
There is a bug in the Q1+Q2 aparc.a2009s+aseg.nii.gz files (both in the T1w/ and MNINonLinear/ directories as shown below) for all subjects, such that all of cortex is labelled as 14175, which is wm_rh_S_temporal_transverse. The current files are corrupted in every subject and not usable for any analyses.
${StudyFolder}/${SubjectID}/T1w/aparc.a2009s+aseg.nii.gz
${StudyFolder}/${SubjectID}/MNINonLinear/aparc.a2009s+aseg.nii.gz
Completed fix: These aparc files have been regenerated in Q1/Q2 subjects from pipeline intermediates and all Q1/Q2 packages have been updated with this change for Q3. The bug has been fixed in the PostFreeSurfer pipeline and Q3 subjects' data should not have this issue.
Users should run the Q1/Q2 data patch script to correct all these incomplete files (download available here) (requires ConnectomeDB login).
In all minimally preprocessed fMRI data mapped to grayordinate surface vertices, e.g. 136833/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_Atlas.dtseries.nii, there are some empty vertices (timeseries = 0s) very near the medial wall. This is because the FreeSurfer defined medial wall sometimes extends outside the atlas medial wall used to define the grayordinates space. Due to a bug in the PostFreeSurfer Pipeline, these vertices were set to zero because the affected subject's specific medial wall ROI was larger than the atlas medial wall ROI. This bug appears in approximately half the subjects' right and/or left hemispheres (too many to list here).
This bug should not create a problem for most users because the empty vertices should always be located around the medial wall (where the data is not very good anyway). However, the zero values could cause some algorithms to crash if they can't cope with zeros in CIFTI/surface data.The tfMRI analysis pipeline is not affected by this bug and the issue is fixed in the analyzed task data. FIX is not negatively affected by this, but the bug remains in the fix cleaned timeseries.
Planned Fix: This bug is not trivial to fix for all Q1, Q2, and Q3 subjects without running all these subjects through a new version of the minimally preprocessing pipelines (specifically the PostFreeSurfer pipeline, see Glasser et al. 2013 for details), which will take a substantial amount of computing time. To date (August 2013), we have not decided exactly when we will do this.
Users who need to fix the files before we make the permanent fix, a relatively simple DIY fix of affected files is available using the command "-cifti-dilate" in wb_command.
e.g. ${StudyFolder}/${SubjectID}/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_ Physio_log.txt
Subjects missing files *_Physio_log.txt : Q1+Q2 Subjects Missing fMRI Physio_log Files
Planned fix: In some of these cases where there is missing data, there was a problem with the data collection that is recoverable (e.g., in the physiological data, a gap in the timing between the trigger pulse and pulse/respiratory signal); in other cases, the data was not collected or is otherwise unrecoverable.
For those subjects whose physiological data is recoverable, the data is being extracted and will be released with a patch script to place them in the appropriate directory structure.
e.g. ${StudyFolder}/${SubjectID}/MNINonLinear/Results/tfMRI_WM_RL/REC_run1_TAB.txt
Subjects missing one or both REC_run1_TAB.txt, REC_run2_TAB.txt files: Q1+Q2 Subjects Missing tfMRI Recognition Memory E-Prime Data Files
Planned fix: For those subjects whose recognition memory data is recoverable, the data is being extracted and will be released with a patch script to place them in the appropriate directory structure.
Near Completed fix: For all but the last two subjects, 131924 and 677968, the data has been recovered and will be released as part of the Q3 release in the ConnectomeDB. For the two remaining subjects, we have sent paper forms for them to refill their responses to the questions asked at their subject visit, which we will add to ConnectomeDB once they are received.
Users who have the Q1+Q2 data should re-download the fixed behavioral data for all subjects available here or on the ConnectomeDB splash page.