Hi all
I am running Freesurfer 7.4
I am trying to extract QSM values at different cortical depths, and obtain statistics for the 400 Schaefer regions.
my code is
mri_vol2surf --mov [QSM coregistered to orig_nu.mgz ] \
--regheader $sub \
--hemi lh \
--surf white \
--o outputsurf.mgh \
--projfrac 0.2
mri_segstats --annot subjid lh 400Parcels_Yeo2011_17Networks \
--i outputsurf.mgh \
--sum outputstats.stats
I get the following errors
Reading annotation $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot
error: No such file or directory
error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match
... trying local annot
error: No such file or directory
error: # elements (137017) in $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot and # vertices (137601) don't match
The annot file is there, I checked, and that's verified by the fact that apparently it knows how many vertices are there. Moreover, it totally worked when I tried this command to extract anatomical stats from the same parcel
mris_anatomical_stats -a $SUBJECTS_DIR/$sub/label/lh.400Parcels_Yeo2011_17Networks.annot -f $SUBJECTS_DIR/$sub/stats/$hemi.$parc.stats $sub $hemi
Do you have any idea of what is going on?
The volume [QSM coregistered to orig_nu.mgz ] was created by applying the QSM 2 T1 rigid transform with ants antsApplyTransform, with orig_nu.mgz as reference volume, which provided a new QSM volume that looks aligned to orig_nu.mgz and on the same grid. It is not a problem of this file since I tried producing an mgh file with orig_nu.mgz as --mov volume and the error persists.