Hi Fabiola,
QDEC is not supported any longer since a while. Also these 2-stage longitudinal statistics are not maintained and have been superseded by our Linear Mixed Effects tools (Matlab) https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
About your error: Is “sub_01” the name of the base directory?
Also what FreeSurfer version are you using? These scripts have probably not been maintained or tested on anything higher than version 6.0. So it could be that they don’t work on 7.* Or it could be that there is an error in your qdecfile. You can try processing one subject with FreeSurfer 6.0 adjusting the qdefile to only this subject and running again with the scripts in 6.0. Or you could switch to LME (recommended).
The .Qdecrc is for running QDEC afterwards, so it has nothing to do with this error. (But again QDEC is also not supported any longer, sadly).
Best, Martin
On 21. Sep 2021, at 22:35, Fabiola Macruz <fabiolamacruz@hotmail.commailto:fabiolamacruz@hotmail.com> wrote:
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,
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