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Oh, I'm sorry for the careless mistake. It works!
Thank you for your patience.
_______________________________________________OK I think I got it: you wrote hippoSF instead of hippoSf (lower case f)
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: Thursday, August 20, 2020 at 04:54
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] quantifyHAsubregions.sh does not work
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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
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