Hi Molly, Can you please send me the listing of files in the mri directories of one of the subjects? (i.e., /media/ubuntu/cxy/FreesT1/output.long/[SOME_SUBJECT]/mri Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yang Molly <mollyyang1...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 19, 2020 at 13:56 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] quantifyHAsubregions.sh does not work External Email - Use Caution Hi experts, When I tried to gathered the volumes of hippocampus subregions from all subjects by using the commend " quantifyHAsubregions.sh", the command did not work well. There's no error message in the terminal but no file was made after that command. My data was longitudinal data, so I did the longitudinal segment used “segmentHA_T1_long.sh”. Therefore, the exact command I run for results collection was "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt", I also tried to provide the subject directory explicitly as fourth argument like "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt /media/ubuntu/cxy/FreesT1/output.long”. The results was same, there was no file. All my subjects were pre-processed and segmentations using freesurfer version 7.1.0 on ubuntu 16.04. I attached screenshot of my terminal window and the script of quantifyHAsubregions.sh in my computer as below. Do you have any suggestions on how I could figure out this problem? Or other method to gather the results? Thanks a lot!! Molly
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