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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.
Thank you for your help
Simone Cauzzo