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Comment: Reverted from v. 183

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1200 Subjects Release (March 1, 2017)

Major Issues 

  • 35/94/2020 3T Functional Preprocessing Error of all 3T "RL" fMRI runs in 25 Subjects (7 are also 7T Subjects)

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).

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  • Subject 169444 preprocessed data from several 7T fMRI runs unusable

    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.

  • 3/9/2020:  3T Functional Preprocessing Error of all 3T "RL" fMRI runs in 25 Subjects (7 are also 7T Subjects)

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 diffusion analyses involving surfacesanalyses 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:

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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)

  • Subjects without Field Maps for Structural scans

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:

    •  Some minor differences in the susceptibility regions (superior orbitofrontal and inferior temporal gyrus regions) of myelin maps produced by the HCP Structural pipeline.
    •  Tissue volumes in these regions may also be slightly different.

Issue Cannot be Fixed

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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)

  • Subjects without Field Maps for Structural scans

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:

    •  Some minor differences in the susceptibility regions (superior orbitofrontal and inferior temporal gyrus regions) of myelin maps produced by the HCP Structural pipeline.
    •  Tissue volumes in these regions may also be slightly different.

Issue Cannot be Fixed

Minor Issues & Updates

    • 2/12/2021: Some variable names in the “Expanded FreeSurfer Data” are mislabelled as left hemisphere values rather than right hemisphere values

      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.

    • Retest 341834 rfMRI_REST1_RL missing FIX results

      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 FixDue 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.
    • Bug affecting lh.curv.pial and rh.curv.pial in Structural Extended Packages

      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.

    • Missing tfMRI_WM_RL preprocessing files for Subject 668361

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