Hi Ken,
Hmm, not sure. Does it give a reason why it cannot be loaded? Could be read permissions, could be corrupted.
Generally the commands look good. You could also try to check the subject SPC on the base-template surface. Those files should also be there in the base dir.
Best, Martin
On 31. Aug 2020, at 04:02, KennethSPrice KennethSPrice@protonmail.com wrote:
Hello Freesurfers!
I am working through the longitudinal tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
To keep it simple, I ran longitudinal processing on 2 timepoints for one subject. My qdec file had only two entries. I would like to look at pct difference in thickness for one subject. I ran
long_mris_slopes --qdec qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
When I run the overlay I get an error saying that "the overlay cannot be loaded", although the file exists.
freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5
First of all, is this method sound in order to visualize pct change in thickness for one subject? If so, why is the overlay not loading?
Best, Ken
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