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)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yang Molly <mollyyang1006@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