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Hi Juan,
Thank you for the reply.
The files in the mri directory includes: antsdn.brain.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz aparc.DKTatlas+aseg.mgz aseg.auto.mgz aseg.auto_noCCseg.mgz aseg.fused.mgz aseg.mgz aseg.presurf.hypos.mgz aseg.presurf.mgz aseg_sub011base.mgz brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brainmask_sub011base.mgz brain.mgz filled.mgz lh.amygNucVolumes-T1.long.v21.txt lh.hippoAmygLabels-T1.long.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v21.CA.mgz lh.hippoAmygLabels-T1.long.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v21.FS60.mgz lh.hippoAmygLabels-T1.long.v21.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v21.HBT.mgz lh.hippoAmygLabels-T1.long.v21.mgz lh.hippoSfVolumes-T1.long.v21.txt lh.ribbon.mgz mri_nu_correct.mni.log mri_nu_correct.mni.log.bak norm.mgz nu.mgz orig orig.mgz orig_nu.log orig_nu.mgz rawavg.mgz rh.amygNucVolumes-T1.long.v21.txt rh.hippoAmygLabels-T1.long.v21.CA.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v21.CA.mgz rh.hippoAmygLabels-T1.long.v21.FS60.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v21.FS60.mgz rh.hippoAmygLabels-T1.long.v21.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v21.HBT.mgz rh.hippoAmygLabels-T1.long.v21.mgz rh.hippoSfVolumes-T1.long.v21.txt rh.ribbon.mgz ribbon.mgz segment.dat T1.mgz talairach.invalid.mgz talairach.label_intensities.txt talairach.status.mgz transforms wm.asegedit.mgz wm.mgz wmparc.mgz wm.seg.mgz
Please also see the screenshot of mri directory in the attachment.
Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu 于2020年8月20日周四 上午2:19写道：
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
