[Freesurfer] Error in Analyze: Couldn't open PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file.
External Email - Use Caution 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, Fabiola ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC command not found
External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all the patients, I tried to open qdec for the analysis by typing qdec and the answer is "command not found". Could you help me, please? Many thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Universidade de São Paulo Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Total Brain volume normalization
External Email - Use Caution Hello Free Surfer developers, >From my understanding, the volumes provided in the aseg.stats document is not >corrected by the head size. In order to do that, it is recommended to use the ITV and the label ID's: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53 However, I need the corrected volume of the Brain Segmentation Volume without Ventricles, the Total gray matter volume, Left hemisphere cerebral white matter volume, and Right hemisphere cerebral white matter volume, none of which have a label ID. Is there any way to obtain these corrected volumes in free surfer itself? Thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Faculdade de Medicina do Hospital das Clínicas da USP Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
