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PennLINC / xcpEngine

Official public repository for the XCP Engine. This tool is deprecated in favor of XCP-D and ASLPrep.
MIT License
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Wrong brain masking #277

Closed egarza closed 4 years ago

egarza commented 4 years ago

Describe the bug I was checking my xcpEngine output, mainly the residual nifti 4D files for the last sanity check. No Errors. Everything was ran from an fmriprep output.

To me the residual images for most subject showed much less brain than obtained and in some cases the normalization seemed to be the culprit, but others were a puzzle. Here I attach the example.

Screenshot from 2020-01-10 16-34-05 (In red you can see the MNI 2mm template, in gray the residual 4D fMRI from xcpOutput sub_ses_std.nii.gz).

Brain masks were fine in fmrprep, so I went to check the masks in the xcp prestats folder. That's when I realized the masks were wrong mask.nii.gz. The orientation was correct but the mask was not centered, hence when the referenceVolumeBrain.nii.gz was created using fslmaths, it cut much of the brain, which was made worse in the normalization.

Screenshot from 2020-01-10 16-32-26 (mask.nii.gz in red, preprocessed.nii.gz file in gray)

Screenshot from 2020-01-10 16-33-10 (referenceVolumeBrain.nii.gz in red, referenceVolume.nii.gz file in gray)

I don't know what the problem may be in terms of the pipeline, however it is perhaps that the use of AFNI for resampling (3dresample) prior to brain extracting with FSL may be screwing up the geometry of the mask. This could be resolved by copying the geometry of the images to the mask.

Any help is appreciated.

Thank you

Eduardo

Cohort file

id0,id1,img
sub-001,ses-t0,sub-001/anat/sub-001_desc-preproc_T1w.nii.gz
sub-001,ses-t1,sub-001/anat/sub-001_desc-preproc_T1w.nii.gz
sub-002,ses-t0,sub-002/anat/sub-002_desc-preproc_T1w.nii.gz
sub-002,ses-t14,sub-002/anat/sub-002_desc-preproc_T1w.nii.gz
sub-002,ses-t1,sub-002/anat/sub-002_desc-preproc_T1w.nii.gz
sub-002,ses-t2,sub-002/anat/sub-002_desc-preproc_T1w.nii.gz
sub-002,ses-t3,sub-002/anat/sub-002_desc-preproc_T1w.nii.gz
sub-003,ses-t0,sub-003/anat/sub-003_desc-preproc_T1w.nii.gz
sub-003,ses-t1,sub-003/anat/sub-003_desc-preproc_T1w.nii.gz
sub-003,ses-t2,sub-003/anat/sub-003_desc-preproc_T1w.nii.gz
sub-003,ses-t3,sub-003/anat/sub-003_desc-preproc_T1w.nii.gz
sub-004,ses-t0,sub-004/anat/sub-004_desc-preproc_T1w.nii.gz
sub-004,ses-t1,sub-004/anat/sub-004_desc-preproc_T1w.nii.gz
sub-004,ses-t2,sub-004/anat/sub-004_desc-preproc_T1w.nii.gz
sub-004,ses-t3,sub-004/anat/sub-004_desc-preproc_T1w.nii.gz
sub-005,ses-t0,sub-005/anat/sub-005_desc-preproc_T1w.nii.gz
sub-006,ses-t0,sub-006/anat/sub-006_desc-preproc_T1w.nii.gz
sub-006,ses-t14,sub-006/anat/sub-006_desc-preproc_T1w.nii.gz
sub-006,ses-t1,sub-006/anat/sub-006_desc-preproc_T1w.nii.gz
sub-007,ses-t0,sub-007/anat/sub-007_desc-preproc_T1w.nii.gz
sub-007,ses-t1,sub-007/anat/sub-007_desc-preproc_T1w.nii.gz
sub-007,ses-t2,sub-007/anat/sub-007_desc-preproc_T1w.nii.gz
sub-007,ses-t3,sub-007/anat/sub-007_desc-preproc_T1w.nii.gz
sub-008,ses-t0,sub-008/anat/sub-008_desc-preproc_T1w.nii.gz
sub-008,ses-t14,sub-008/anat/sub-008_desc-preproc_T1w.nii.gz
sub-008,ses-t1,sub-008/anat/sub-008_desc-preproc_T1w.nii.gz
sub-008,ses-t2,sub-008/anat/sub-008_desc-preproc_T1w.nii.gz
sub-008,ses-t3,sub-008/anat/sub-008_desc-preproc_T1w.nii.gz
sub-009,ses-t0,sub-009/anat/sub-009_desc-preproc_T1w.nii.gz
sub-010,ses-t0,sub-010/anat/sub-010_desc-preproc_T1w.nii.gz
sub-010,ses-t14,sub-010/anat/sub-010_desc-preproc_T1w.nii.gz
sub-010,ses-t1,sub-010/anat/sub-010_desc-preproc_T1w.nii.gz
sub-011,ses-t0,sub-011/anat/sub-011_desc-preproc_T1w.nii.gz
sub-011,ses-t1,sub-011/anat/sub-011_desc-preproc_T1w.nii.gz
sub-012,ses-t0,sub-012/anat/sub-012_desc-preproc_T1w.nii.gz
sub-012,ses-t14,sub-012/anat/sub-012_desc-preproc_T1w.nii.gz
sub-012,ses-t1,sub-012/anat/sub-012_desc-preproc_T1w.nii.gz
sub-013,ses-t0,sub-013/anat/sub-013_desc-preproc_T1w.nii.gz
sub-013,ses-t14,sub-013/anat/sub-013_desc-preproc_T1w.nii.gz
sub-013,ses-t1,sub-013/anat/sub-013_desc-preproc_T1w.nii.gz
sub-015,ses-t0,sub-015/anat/sub-015_desc-preproc_T1w.nii.gz
sub-015,ses-t1,sub-015/anat/sub-015_desc-preproc_T1w.nii.gz
sub-015,ses-t2,sub-015/anat/sub-015_desc-preproc_T1w.nii.gz
sub-016,ses-t0,sub-016/anat/sub-016_desc-preproc_T1w.nii.gz
sub-016,ses-t1,sub-016/anat/sub-016_desc-preproc_T1w.nii.gz
sub-017,ses-t0,sub-017/anat/sub-017_desc-preproc_T1w.nii.gz
sub-017,ses-t1,sub-017/anat/sub-017_desc-preproc_T1w.nii.gz
sub-018,ses-t0,sub-018/anat/sub-018_desc-preproc_T1w.nii.gz
sub-018,ses-t1,sub-018/anat/sub-018_desc-preproc_T1w.nii.gz
sub-019,ses-t0,sub-019/anat/sub-019_desc-preproc_T1w.nii.gz
sub-019,ses-t1,sub-019/anat/sub-019_desc-preproc_T1w.nii.gz
sub-020,ses-t0,sub-020/anat/sub-020_desc-preproc_T1w.nii.gz
sub-020,ses-t1,sub-020/anat/sub-020_desc-preproc_T1w.nii.gz
sub-020,ses-t2,sub-020/anat/sub-020_desc-preproc_T1w.nii.gz
sub-020,ses-t3,sub-020/anat/sub-020_desc-preproc_T1w.nii.gz
sub-021,ses-t0,sub-021/anat/sub-021_desc-preproc_T1w.nii.gz
sub-021,ses-t1,sub-021/anat/sub-021_desc-preproc_T1w.nii.gz
sub-022,ses-t0,sub-022/anat/sub-022_desc-preproc_T1w.nii.gz
sub-022,ses-t14,sub-022/anat/sub-022_desc-preproc_T1w.nii.gz
sub-022,ses-t1,sub-022/anat/sub-022_desc-preproc_T1w.nii.gz
sub-022,ses-t2,sub-022/anat/sub-022_desc-preproc_T1w.nii.gz
sub-022,ses-t3,sub-022/anat/sub-022_desc-preproc_T1w.nii.gz
sub-023,ses-t0,sub-023/anat/sub-023_desc-preproc_T1w.nii.gz
sub-023,ses-t1,sub-023/anat/sub-023_desc-preproc_T1w.nii.gz
sub-023,ses-t2,sub-023/anat/sub-023_desc-preproc_T1w.nii.gz
sub-023,ses-t3,sub-023/anat/sub-023_desc-preproc_T1w.nii.gz
sub-024,ses-t0,sub-024/anat/sub-024_desc-preproc_T1w.nii.gz
sub-024,ses-t1,sub-024/anat/sub-024_desc-preproc_T1w.nii.gz
sub-024,ses-t2,sub-024/anat/sub-024_desc-preproc_T1w.nii.gz
sub-024,ses-t3,sub-024/anat/sub-024_desc-preproc_T1w.nii.gz
sub-025,ses-t0,sub-025/anat/sub-025_desc-preproc_T1w.nii.gz
sub-025,ses-t1,sub-025/anat/sub-025_desc-preproc_T1w.nii.gz
sub-025,ses-t2,sub-025/anat/sub-025_desc-preproc_T1w.nii.gz
sub-025,ses-t3,sub-025/anat/sub-025_desc-preproc_T1w.nii.gz
sub-026,ses-t0,sub-026/anat/sub-026_desc-preproc_T1w.nii.gz
sub-026,ses-t1,sub-026/anat/sub-026_desc-preproc_T1w.nii.gz
sub-027,ses-t0,sub-027/anat/sub-027_desc-preproc_T1w.nii.gz
sub-027,ses-t14,sub-027/anat/sub-027_desc-preproc_T1w.nii.gz
sub-027,ses-t1,sub-027/anat/sub-027_desc-preproc_T1w.nii.gz
sub-027,ses-t2,sub-027/anat/sub-027_desc-preproc_T1w.nii.gz
sub-027,ses-t3,sub-027/anat/sub-027_desc-preproc_T1w.nii.gz
sub-028,ses-t0,sub-028/anat/sub-028_desc-preproc_T1w.nii.gz
sub-029,ses-t0,sub-029/anat/sub-029_desc-preproc_T1w.nii.gz
sub-030,ses-t0,sub-030/anat/sub-030_desc-preproc_T1w.nii.gz
sub-030,ses-t14,sub-030/anat/sub-030_desc-preproc_T1w.nii.gz
sub-030,ses-t1,sub-030/anat/sub-030_desc-preproc_T1w.nii.gz
sub-031,ses-t0,sub-031/anat/sub-031_desc-preproc_T1w.nii.gz
sub-031,ses-t1,sub-031/anat/sub-031_desc-preproc_T1w.nii.gz
sub-031,ses-t2,sub-031/anat/sub-031_desc-preproc_T1w.nii.gz
sub-032,ses-t0,sub-032/anat/sub-032_desc-preproc_T1w.nii.gz
sub-032,ses-t1,sub-032/anat/sub-032_desc-preproc_T1w.nii.gz
sub-032,ses-t2,sub-032/anat/sub-032_desc-preproc_T1w.nii.gz
sub-032,ses-t3,sub-032/anat/sub-032_desc-preproc_T1w.nii.gz
sub-033,ses-t0,sub-033/anat/sub-033_desc-preproc_T1w.nii.gz
sub-033,ses-t1,sub-033/anat/sub-033_desc-preproc_T1w.nii.gz
sub-034,ses-t0,sub-034/anat/sub-034_desc-preproc_T1w.nii.gz
sub-034,ses-t1,sub-034/anat/sub-034_desc-preproc_T1w.nii.gz
sub-034,ses-t2,sub-034/anat/sub-034_desc-preproc_T1w.nii.gz
sub-035,ses-t0,sub-035/anat/sub-035_desc-preproc_T1w.nii.gz
sub-036,ses-t0,sub-036/anat/sub-036_desc-preproc_T1w.nii.gz
sub-036,ses-t14,sub-036/anat/sub-036_desc-preproc_T1w.nii.gz
sub-036,ses-t1,sub-036/anat/sub-036_desc-preproc_T1w.nii.gz
sub-036,ses-t2,sub-036/anat/sub-036_desc-preproc_T1w.nii.gz
sub-036,ses-t3,sub-036/anat/sub-036_desc-preproc_T1w.nii.gz
sub-037,ses-t0,sub-037/anat/sub-037_desc-preproc_T1w.nii.gz
sub-037,ses-t1,sub-037/anat/sub-037_desc-preproc_T1w.nii.gz
sub-039,ses-t0,sub-039/anat/sub-039_desc-preproc_T1w.nii.gz
sub-039,ses-t1,sub-039/anat/sub-039_desc-preproc_T1w.nii.gz
sub-039,ses-t2,sub-039/anat/sub-039_desc-preproc_T1w.nii.gz
sub-040,ses-t0,sub-040/anat/sub-040_desc-preproc_T1w.nii.gz
sub-041,ses-t0,sub-041/anat/sub-041_desc-preproc_T1w.nii.gz
sub-041,ses-t1,sub-041/anat/sub-041_desc-preproc_T1w.nii.gz
sub-041,ses-t2,sub-041/anat/sub-041_desc-preproc_T1w.nii.gz
sub-042,ses-t0,sub-042/anat/sub-042_desc-preproc_T1w.nii.gz
sub-042,ses-t1,sub-042/anat/sub-042_desc-preproc_T1w.nii.gz
sub-042,ses-t14,sub-042/anat/sub-042_desc-preproc_T1w.nii.gz
sub-043,ses-t0,sub-043/anat/sub-043_desc-preproc_T1w.nii.gz
sub-043,ses-t1,sub-043/anat/sub-043_desc-preproc_T1w.nii.gz
sub-045,ses-t0,sub-045/anat/sub-045_desc-preproc_T1w.nii.gz
sub-045,ses-t1,sub-045/anat/sub-045_desc-preproc_T1w.nii.gz
sub-045,ses-t14,sub-045/anat/sub-045_desc-preproc_T1w.nii.gz
sub-046,ses-t0,sub-046/anat/sub-046_desc-preproc_T1w.nii.gz
sub-046,ses-t1,sub-046/anat/sub-046_desc-preproc_T1w.nii.gz
sub-046,ses-t14,sub-046/anat/sub-046_desc-preproc_T1w.nii.gz
sub-047,ses-t0,sub-047/anat/sub-047_desc-preproc_T1w.nii.gz
sub-047,ses-t1,sub-047/anat/sub-047_desc-preproc_T1w.nii.gz
sub-047,ses-t14,sub-047/anat/sub-047_desc-preproc_T1w.nii.gz
sub-048,ses-t0,sub-048/anat/sub-048_desc-preproc_T1w.nii.gz
sub-048,ses-t1,sub-048/anat/sub-048_desc-preproc_T1w.nii.gz
sub-049,ses-t0,sub-049/anat/sub-049_desc-preproc_T1w.nii.gz
sub-049,ses-t1,sub-049/anat/sub-049_desc-preproc_T1w.nii.gz
sub-050,ses-t0,sub-050/anat/sub-050_desc-preproc_T1w.nii.gz
sub-050,ses-t1,sub-050/anat/sub-050_desc-preproc_T1w.nii.gz
sub-052,ses-t0,sub-052/anat/sub-052_desc-preproc_T1w.nii.gz
sub-052,ses-t1,sub-052/anat/sub-052_desc-preproc_T1w.nii.gz
sub-053,ses-t0,sub-053/anat/sub-053_desc-preproc_T1w.nii.gz
sub-053,ses-t1,sub-053/anat/sub-053_desc-preproc_T1w.nii.gz
sub-054,ses-t0,sub-054/anat/sub-054_desc-preproc_T1w.nii.gz
sub-054,ses-t1,sub-054/anat/sub-054_desc-preproc_T1w.nii.gz
id0,id1,img,antsct
sub-001,ses-t0,fmriprep/output/fmriprep/sub-001/ses-t0/func/sub-001_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-001/ses-t0/struc
sub-001,ses-t1,fmriprep/output/fmriprep/sub-001/ses-t1/func/sub-001_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-001/ses-t1/struc
sub-002,ses-t0,fmriprep/output/fmriprep/sub-002/ses-t0/func/sub-002_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-002/ses-t0/struc
sub-002,ses-t14,fmriprep/output/fmriprep/sub-002/ses-t14/func/sub-002_ses-t14_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-002/ses-t14/struc
sub-002,ses-t1,fmriprep/output/fmriprep/sub-002/ses-t1/func/sub-002_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-002/ses-t1/struc
sub-002,ses-t2,fmriprep/output/fmriprep/sub-002/ses-t2/func/sub-002_ses-t2_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-002/ses-t2/struc
sub-002,ses-t3,fmriprep/output/fmriprep/sub-002/ses-t3/func/sub-002_ses-t3_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-002/ses-t3/struc
sub-003,ses-t0,fmriprep/output/fmriprep/sub-003/ses-t0/func/sub-003_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-003/ses-t0/struc
sub-003,ses-t1,fmriprep/output/fmriprep/sub-003/ses-t1/func/sub-003_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-003/ses-t1/struc
sub-003,ses-t2,fmriprep/output/fmriprep/sub-003/ses-t2/func/sub-003_ses-t2_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-003/ses-t2/struc
sub-003,ses-t3,fmriprep/output/fmriprep/sub-003/ses-t3/func/sub-003_ses-t3_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-003/ses-t3/struc
sub-004,ses-t0,fmriprep/output/fmriprep/sub-004/ses-t0/func/sub-004_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-004/ses-t0/struc
sub-004,ses-t1,fmriprep/output/fmriprep/sub-004/ses-t1/func/sub-004_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-004/ses-t1/struc
sub-004,ses-t2,fmriprep/output/fmriprep/sub-004/ses-t2/func/sub-004_ses-t2_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-004/ses-t2/struc
sub-004,ses-t3,fmriprep/output/fmriprep/sub-004/ses-t3/func/sub-004_ses-t3_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-004/ses-t3/struc
sub-005,ses-t0,fmriprep/output/fmriprep/sub-005/ses-t0/func/sub-005_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-005/ses-t0/struc
sub-006,ses-t0,fmriprep/output/fmriprep/sub-006/ses-t0/func/sub-006_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-006/ses-t0/struc
sub-006,ses-t14,fmriprep/output/fmriprep/sub-006/ses-t14/func/sub-006_ses-t14_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-006/ses-t14/struc
sub-006,ses-t1,fmriprep/output/fmriprep/sub-006/ses-t1/func/sub-006_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-006/ses-t1/struc
sub-007,ses-t0,fmriprep/output/fmriprep/sub-007/ses-t0/func/sub-007_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-007/ses-t0/struc
sub-007,ses-t1,fmriprep/output/fmriprep/sub-007/ses-t1/func/sub-007_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-007/ses-t1/struc
sub-007,ses-t2,fmriprep/output/fmriprep/sub-007/ses-t2/func/sub-007_ses-t2_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-007/ses-t2/struc
sub-007,ses-t3,fmriprep/output/fmriprep/sub-007/ses-t3/func/sub-007_ses-t3_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-007/ses-t3/struc
sub-008,ses-t0,fmriprep/output/fmriprep/sub-008/ses-t0/func/sub-008_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-008/ses-t0/struc
sub-008,ses-t14,fmriprep/output/fmriprep/sub-008/ses-t14/func/sub-008_ses-t14_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-008/ses-t14/struc
sub-008,ses-t1,fmriprep/output/fmriprep/sub-008/ses-t1/func/sub-008_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-008/ses-t1/struc
sub-008,ses-t2,fmriprep/output/fmriprep/sub-008/ses-t2/func/sub-008_ses-t2_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-008/ses-t2/struc
sub-008,ses-t3,fmriprep/output/fmriprep/sub-008/ses-t3/func/sub-008_ses-t3_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-008/ses-t3/struc
sub-009,ses-t0,fmriprep/output/fmriprep/sub-009/ses-t0/func/sub-009_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-009/ses-t0/struc
sub-010,ses-t0,fmriprep/output/fmriprep/sub-010/ses-t0/func/sub-010_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-010/ses-t0/struc
sub-010,ses-t14,fmriprep/output/fmriprep/sub-010/ses-t14/func/sub-010_ses-t14_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-010/ses-t14/struc
sub-010,ses-t1,fmriprep/output/fmriprep/sub-010/ses-t1/func/sub-010_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-010/ses-t1/struc
sub-011,ses-t0,fmriprep/output/fmriprep/sub-011/ses-t0/func/sub-011_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-011/ses-t0/struc
sub-011,ses-t1,fmriprep/output/fmriprep/sub-011/ses-t1/func/sub-011_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-011/ses-t1/struc
sub-012,ses-t0,fmriprep/output/fmriprep/sub-012/ses-t0/func/sub-012_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-012/ses-t0/struc
sub-012,ses-t14,fmriprep/output/fmriprep/sub-012/ses-t14/func/sub-012_ses-t14_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-012/ses-t14/struc
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sub-054,ses-t0,fmriprep/output/fmriprep/sub-054/ses-t0/func/sub-054_ses-t0_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-054/ses-t0/struc
sub-054,ses-t1,fmriprep/output/fmriprep/sub-054/ses-t1/func/sub-054_ses-t1_task-rest_space-T1w_desc-preproc_bold.nii.gz,xcpOut/sub-054/ses-t1/struc

Design File

Anatomical

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete task-free functional connectivity pipeline.
# You may execute the analysis specified in this design file by
# calling (in any bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * GLOBAL VARIABLES are used at all stages of all analyses.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the analysis
#                  stage during which they are used.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are sometimes array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=struc-ACCELERATOR
design=/mnt/MD1200B/egarza/sfernandezl/AddimexTMS/sourcedata/xcpEngine/designs/anat-antsct.dsn
sequence=anatomical
standard=MNI%1x1x1

###################################################################
# PIPELINE
###################################################################

pipeline=struc,roiquant,qcanat

###################################################################
# 1 STRUC
###################################################################

struc_denoise_anat[1]=0
struc_prior_weight[1]=0.25
struc_posterior_formulation[1]='Socrates[1]'
struc_keepBEImages[1]=0
struc_floating_point[1]=0
struc_random_seed[1]=0
struc_bspline[1]=0
struc_fit[1]=0.3
struc_quick[1]=0
struc_seg_priors[1]=1
struc_rerun[1]=0
struc_cleanup[1]=1
struc_process[1]=ACT

###################################################################
# 2 ROIQUANT
###################################################################

roiquant_atlas[2]=all
roiquant_vol[2]=1
roiquant_rerun[2]=1
roiquant_cleanup[2]=1

###################################################################
# 3 QCANAT
###################################################################

qcanat_gm[3]=Y
qcanat_gm_val[3]=2,4
qcanat_wm[3]=Y
qcanat_wm_val[3]=3
qcanat_csf[3]=Y
qcanat_csf_val[3]=1
qcanat_cort[3]=Y
qcanat_cort_val[3]=4
qcanat_rerun[3]=0
qcanat_cleanup[3]=1

Functional

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the module that
#                  calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are typically array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  loc alised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=fc_$(whoami)
design=/mnt/MD1200B/egarza/sfernandezl/AddimexTMS/sourcedata/xcpEngine/designs/fc-36p_scrub.dsn
sequence=anatomical
standard=MNI%1x1x1

###################################################################
# PIPELINE
###################################################################

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc

###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP

###################################################################
# 2 CONFOUND2
###################################################################

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=1
confound2_censor_contig[2]=1
confound2_framewise[2]=fds:0.25,dv:2
confound2_rerun[2]=1
confound2_cleanup[2]=1

###################################################################
# 3  REGRESS
###################################################################

regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_smo[3]=6
regress_sptf[3]=uniform
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=1
regress_cleanup[3]=1
regress_process[3]=DMT-TMP-REG

###################################################################
# 4 FCON
###################################################################

fcon_atlas[4]=power264
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_window[4]=10
fcon_pad[4]=FALSE
fcon_rerun[4]=1
fcon_cleanup[4]=1

###################################################################
# 5 REHO
###################################################################

reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=uniform
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1

###################################################################
# 6 ALFF
###################################################################

alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=uniform
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1

###################################################################
# 7 ROIQUANT
###################################################################

roiquant_atlas[7]=aal116
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=1
norm_cleanup[8]=1

##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=aal116
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message No Errors

Runtime Information Singularity was used in an HCP

Additional context Add any other context about the problem here.

a3sha2 commented 4 years ago

Hi @egarza You dont need to run struc pipeline if you already run the fmriprep https://xcpengine.readthedocs.io/config/cohort.html#functional-processing. xcp will use anatomical output of fmriprep. masking problem during functional processing is likely to be from fmriprep or struc. Xcp only produces reference volume brain by multiply the mask and reference volume (both from fmriprep).
and you can let be standard=MNI%2x2x2 for functional processing can you pull for new docker/singulairty image?

egarza commented 4 years ago

Hi @a3sha2

Thanks for the answer. The fmriprep masks are fine, they only are wrong after being copied for xcpEngine. You think the problem is running the struct pipeline as well?

I'm confused about these lines:

3dresample -orient RPI -inset /mnt/MD1200B/egarza/sfernandezl/AddimexTMS/derivatives/fmriprep/output/fmriprep/sub-033/ses-t0/func/sub-033_ses-t0_task-rest_space-T1w_desc-brain_mask.nii.gz -prefix sub-033_ses-t0_imgmask.nii.gz -overwrite

fslmaths sub-033_ses-t0_imgmask.nii.gz -mul sub-033_ses-t0_structmask.nii.gz /mnt/MD1200B/egarza/sfernandezl/AddimexTMS/derivatives/xcpOut/sub-033/ses-t0/prestats/sub-033_ses-t0_mask.nii.gz

Why is 3dresample being used? Because the files I get in xcp prestat (brain mask and volume) do not coincide, which is making the whole problem. If they only multiplied the mask and reference volume there shouldn't be problems. I can upload the files if you need to check, the fmriprep and xcp prestats.

I can get the new images if you think that is the problem, we are using one version from September (xcpengine-2019-09-03.img).

Thanks

Eduardo

a3sha2 commented 4 years ago

this first line of code: 3dresample -orient RPI -inset /mnt/MD1200B/egarza/sfernandezl/AddimexTMS/derivatives/fmriprep/output/fmriprep/sub-033/ses-t0/func/sub-033_ses-t0_task-rest_space-T1w_desc-brain_mask.nii.gz -prefix sub-033_ses-t0_imgmask.nii.gz -overwrite was added so that structural, functional derivatives and template all have the same orientation RPI. if you check , the fmriprep writes out the outputs in LPI format. XCP ensures that both structural and functional have the same orientation as template and consistent.

the second line : fslmaths sub-033_ses-t0_imgmask.nii.gz -mul sub-033_ses-t0_structmask.nii.gz /mnt/MD1200B/egarza/sfernandezl/AddimexTMS/derivatives/xcpOut/sub-033/ses-t0/prestats/sub-033_ses-t0_mask.nii.gz multiply both structural mask and bold mask. Sometime the bold mask generated by fmriprep include some part of the necks and outside brain and the structural mask is always look good with fsl bet. Though there is improvement in fmriprep with afni skullstrip. Also, there is improvement in the latest version of xcp handling this steps.

Please pull for new (:latest) xcpengine docker or singularity image and let us know. Thanks you very much

egarza commented 4 years ago

Hi again,

I ran some subjects using the newest fmriprep image and got the same result. Then I ran it again without running the struc pipeline and got some errors from ANTs.

Because I ran everything with fmriprep, I should instead run it without rerunning the prestats, right? I had the prestats_rerun = 1.

###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=0
prestats_cleanup[1]=1
prestats_process[1]=FMP

I'm reruning with 0 and see if it makes a difference.

Eduardo

egarza commented 4 years ago

Hi,

I keep getting the same results. Finally I downloaded the latest fmriprep and the latest xcpEngine and I'm rerunning subjects to see if that was the problem.

I'll keep you posted.

Eduardo

a3sha2 commented 4 years ago

can you post ants error pls

egarza commented 4 years ago

Hi,

I reran the analysis using the latest fmriprep and xcpEngine and that worked. Now I don't see this error and the normalization is perfect.

Therefore, the problem was solved in the newest versions.

Thank you

Eduardo

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