Hello,
In my task design xcpengine file for my data, the task module is looking for the boldtoMNI.nii.gz file and then files in a freesurfer folder inside a subject folder. However, the freesurfer folder is outside my subject ID folder. Does anyone have any guidance or able to provide any insight on why this may be the case and what I can do?
I’m including what I see in my log below:
`Computing registration from header.
Using /data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/mri/orig.mgz as target reference.
mghRead(/data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/mri/orig.mgz, -1): could not open file
MRISread(/data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/surf/lh.sphere): could not open file
No such file or directory
/opt/freesurfer/bin/mris_convert: could not read surface file /data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/surf/lh.sphere
No such file or directory
srcvol = /data/xcpOut/sub-021/ses-1/task/boldtoMNI.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
WARNING: niiRead(): unknown time units 0 in /data/xcpOut/sub-021/ses-1/task/boldtoMNI.nii.gz
INFO: using NIfTI-1 qform
Done loading volume
Computing registration from header.
Using /data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/mri/orig.mgz as target reference.
mghRead(/data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/mri/orig.mgz, -1): could not open file
MRISread(/data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/surf/rh.sphere): could not open file
No such file or directory
/opt/freesurfer/bin/mris_convert: could not read surface file /data/fmriprep_out/sub-021/ses-1/…/…/freesurfer/fsaverage/surf/rh.sphere
No such file or directory
While running:
/xcpEngine/thirdparty/workbench/bin_rh_linux64/…/exe_rh_linux64/wb_command -cifti-create-dense-scalar /data/xcpOut/sub-021/ses-1/task/sub-021_ses-1_res4D.dscalar.nii -left-metric /data/xcpOut/sub-021/ses-1/task/sub-021_ses-1_res4d_lh.func.gii -right-metric /data/xcpOut/sub-021/ses-1/task/sub-021_ses-1_res4d_rh.func.gii
ERROR: NAME OF FILE: sub-021_ses-1_res4d_lh.func.gii
PATH TO FILE: /data/xcpOut/sub-021/ses-1/task
File does not exist.`