quantifyHAsubregions.sh does not work

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Yang Molly

19 Aug 2020 19 Aug '20

1:54 p.m.

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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

Attachments:

attachment.html (text/html — 7.1 KB)
quantifyHAsubregions.sh (application/octet-stream — 2.3 KB)
20200820014058.png (image/png — 499.5 KB)

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Iglesias Gonzalez, Juan E.

19 Aug 19 Aug

2:18 p.m.

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-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,

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

Yang Molly

20 Aug 20 Aug

4:52 a.m.

External Email - Use Caution

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)

http://www.jeiglesias.com

*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

Iglesias Gonzalez, Juan E.

10:43 a.m.

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) http://www.jeiglesias.com

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

External Email - Use Caution Hi Juan,

Thank you for the reply.

Please also see the screenshot of mri directory in the attachment.

Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto: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) http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yang Molly <mollyyang1006@gmail.commailto:mollyyang1006@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 19, 2020 at 13:56 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] quantifyHAsubregions.sh does not work

External Email - Use Caution Hi experts,

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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Yang Molly

10:46 p.m.

External Email - Use Caution

Oh, I'm sorry for the careless mistake. It works!

Thank you for your patience.

Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu 于2020年8月20日周四下午10:44写道：

...

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)

http://www.jeiglesias.com

*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
   External Email - Use Caution        *
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)

http://www.jeiglesias.com

*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

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Iglesias Gonzalez, Juan E.
Yang Molly