Hi all,
I’ve run my participants through fmriprep and xcpEngine. I’m now trying to take the output from the preprocessing pipeline and project the functional signal onto the surface volume constructed with freesurfer. I’m getting a warning when I run mri_vol2surf and I was wondering if anyone knows what to do about this. I’ll post the error and the code below it. I’m sure I must be missing something, but any input would be great!
Error:
srcvol = /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/xcpEngine/data/sub-ADS1915/ses-wave2/sub-ADS1915_ses-wave2.nii.gz
srcreg = sub-ADS1915_from-T1w_to-fsnative_mode-image_xfm.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = sub-ADS1915
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 1
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
Input reg is register.dat
WARNING: the voxel resolution in the source volume (3.281,3.281,5) differs
from that listed in the registration file (0.9,0.9,0.449219)
-------- original matrix -----------
-0.99937 0.03390 -0.01006 -0.00226;
-0.01006 0.00046 0.99995 -0.01735;
-0.03390 -0.99943 0.00012 -0.00481;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Reading surface /projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer/sub-ADS1915/surf/lh.white
Code:
freesurfer=/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/freesurfer
fmriprep=/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/fmriprep
xcp=/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/xcpEngine
subj=sub-ADS1915
wave=ses-wave2
outdir=/projects/adapt_lab/shared/ADS/data/BIDS_data/derivatives/rsfMRI_processed/${subj}/${wave}
source /projects/adapt_lab/shared/ADS/Scripts/sMRI/SetUpFreeSurfer.sh
cd ${fmriprep}/${subj}/anat
cp ${freesurfer}/${subj}/masks/gordon333/lh.gordon333.annot ${freesurfer}/${subj}/label
mkdir -p ${outdir}
lta_convert --initk ${subj}_from-T1w_to-fsnative_mode-image_xfm.txt \
--outlta ${subj}_from-T1w_to-fsnative_mode-image_xfm.lta \
--outreg ${subj}_from-T1w_to-fsnative_mode-image_xfm.dat \
--src ${subj}_desc-preproc_T1w.nii.gz \
--trg ${freesurfer}/${subj}/mri/T1.mgz \
--subject ${subj}
mri_vol2surf --mov ${xcp}/data/${subj}/${wave}/${subj}_${wave}.nii.gz \
--out ${outdir}/lh.${subj}_${wave}_xcp.mgh \
--reg ${subj}_from-T1w_to-fsnative_mode-image_xfm.dat \
--hemi lh \
--projfrac 0.5 \
--interp nearest \
--trgsubject ${subj} \
--reshape