I am trying to use fsfast to analyze task-based functional data output by fmriprep. The subcorticals seem to be working, but I am having trouble with the surfaces. One thing I have noticed before running any fsfast code, when I load the surfaces output by fmriprep into freeview (overlaid onto the fsaverage ?h.inflated) both the *space-fsaverage_hemi-L_bold.func.gii and *space-fsaverage_hemi-R_bold.func.gii get overlaid onto the rh.inflated surface, instead of the L_bold.func.gii getting overlaid onto lh.inflated. I don't know if this points to some issue with my fmriprep output that may be causing dowstream problems.
I have taken the func.gii in fsaverage space from fmriprep, converted them to nifiti and smoothed them using the following code adapted from code posted here: https://github.com/nipreps/fmriprep/issues/994
#*************************************************************** # convert surface files, smooth, and reinforce tr declare -a hemis=("l" "r") for hemi in "${hemis[@]}" do out_stem=fmcpr.sm${fwhm}.fsaverage.${hemi}h in_stem=${fmp_stem}_space-fsaverage_hemi-${hemi^}_bold.func mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage \ --sval ${fmriprepFunc_dir}/${in_stem}.gii \ --tval ${run_dir}/${out_stem}.nii.gz \ --fwhm-trg ${fwhm} --hemi ${hemi}h mri_convert ${run_dir}/${out_stem}.nii.gz ${run_dir}/${out_stem}.nii.gz -tr ${tr} done #***************************************************************
When running this, I get what appear to be warnings:
** DA[0] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) ** DA[1] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) ** DA[2] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET)
There are one of these for each TR in my data. Full output attached as convertAndSmoothOutput.txt
Next I am running mkanalysis-sess with the following:
#******************************************************************************* #!/bin/bash
# Script for converting fmriprep outputs to fsfast structure for first levels # This converts files to fsaverage surface spaces and mni305 volume spaces
conds="1,CX 2,eCS+1 3,eCS+2 4,eCS-atCS+1 5,eCS-atCS+2 6,lCS+1 7,lCS+2 8,lCS-atCS+1 9,lCS-atCS+2 10,NOShock_1 11,omittedSck_1 12,shock" fwhms="5"
# source freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
# set matlab path export MATLAB='/usr/local/bin/matlab' set MATLAB
# full path to recons folder export SUBJECTS_DIR="/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/freesurfer"
for fwhm in ${fwhms}; do for side in l r; do mkanalysis-sess \ -no-mask \ -paradigm events.txt \ -tpexclude tpef.txt \ -nuisreg MotConfounds.txt 12 \ -mni305 -analysis cond_fsavSurf_${side}_sm${fwhm} -per-run -polyfit 2 \ -event-related -TR 2.56 -fsd cond -refeventdur 6 \ -spmhrf 0 -nconditions 12 -force \ -funcstem fmcpr.sm${fwhm}.fsaverage.${side}h.nii.gz
for i in ${conds} ; do condNum=${i%,*}; cond=${i#*,}; mkcontrast-sess -contrast ${cond} -analysis cond_fsavSurf_${side}_sm${fwhm} \ -a ${condNum} done #*******************************************************************************
output attached in mkanalysisSurfOutput.txt
When I then run selxavg3-sess on the data with:
#******************************************************************************* #!/bin/bash
fsfastD="/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast" regions="fsavSurf_l" fwhms="5" conds="cond"
# source freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
for fwhm in ${fwhms}; do for region in ${regions}; do for cond in ${conds}; do selxavg3-sess -no-preproc -s sub-101KI_ses-bld1 \ -d ${fsfastD} \ -analysis ${cond}_${region}_sm${fwhm} done done done #*******************************************************************************
I get the following error:
#******************************************************************************* Smoothing ACF /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only: Segmentation fault voxelvolume 1 mm3 Loading mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz Search region is 163842 voxels = 163842.000000 mm3 Smoothing input by fwhm=20.000000, gstd=8.493218
ERROR: /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only
ans =
139
ERROR: fast_selxavg3() failed\n #*******************************************************************************
the full output is attached as selxavg3Output.txt
Any idea on what is causing selxavg3 to crash?
Thanks!