Dear FreeSurfer experts:
I am processing in qdec 25 subjects (each with 3 MRIs studies) and I have this terminal output:
Error in Analyze: Couldn't open
PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file.
I have executed the following qcache command for each subject:
long_mris_slopes --qdec qdecfile --meas thickness --hemi
> lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time
> months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR
All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh.
However, the file that qdec asks for - is missing in all the bases subjects.
I have also created a qdec/.Qdecrc file in the qdec directory that contains the following lines:
MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc
Could you please help out?
I have found another person with exactly the same problem in the freesurfer forum and the person assisting him, couldn't explain why this happen. Just went around about a bunch of other things that could be and didnt solve the guy's problem.
I honestly found the tutorials for longitudinal analysis in the website very frustrating and poorly explained. Even in regard to the .Qdecrc file that we need to create, it wasn't clear to me what extension it was and if we were only suppose to copy paste the following in any terminal editor:
EASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc
Thanks,