Uuummm interesting… thanks a lot! I’m still investigating this
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 "Zeng, Qi" qi.zeng@icahn.mssm.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 4, 2020 at 14:51 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio,
Another information: though script exited with errors, all the left hemispheres generated hippoSFVolums and amydNucVolumes as outputs. Missing right hemispheres for all.
Best, Qi
On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Qi, I’m really sorry you’re running into all these problem. We’ll look into it and get back to you asap Cheers, /Eugenio
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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, May 4, 2020 at 12:37 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio,
I installed freesurfer/7.0.0 and ran longitudinal hippocampal & amygdala subfields again. Error message indicates: "Error in SegmentSubfieldsT1Longitudinal (line 1795)". I have attached the log file. Can you help figure this out?
Thank you so much ! Best, Qi
On Fri, May 1, 2020 at 1:35 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: That’s easy ;-) https://surfer.nmr.mgh.harvard.edu/fswiki/License
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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, May 1, 2020 at 12:28 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio,
I installed the FS7.0.0 and matlab_runtime/R2014b and ran a longitudinal hippocampal subfield again. Get following errors: "ERROR: FreeSurfer license file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not found" and same error "Error in kvlReadCroppedImage (line 11) Error in SegmentSubfieldsT1Longitudinal (line 403)" Where do I find the Freesurfer license? Here attached the log file.
Thank you so much! Best, Qi
On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> wrote: Thank you so much. I will upgrade the dev and run it again, fingers crossed.
Best, Qi
On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Ah! I think you were unlucky enough to download the dev version literally days before we fixed these issues ;-) If you upgrade to the latest dev, it should be fixed! Or, wait a bit until FS7 comes out, there’s rumors that it may be pretty soon. 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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 30, 2020 at 12:48 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio: recon -all --version freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28 operating system: Linux
Best, Qi
On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: This was very helpful, thanks. Can you please send me the output of the following command? recon-all --version as well as your operating system? Cheers, /Eugenio
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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 30, 2020 at 09:55 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio,
Sorry, this one is from another individual from the control group. Here attached the error script I described. Sorry for the confusion.
Best, Qi
On Wed, Apr 29, 2020 at 5:47 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Wait but this isn’t the error your first described…?
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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, April 29, 2020 at 17:28 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution Hi Eugenio,
Thank you so much for the prompt reply ! Here attached the log file. The files generated: SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
Best, Qi
On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> wrote: Hi Eugenio,
Thank you so much for the prompt reply ! Here attached the output error and log file. The files generated: SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
Best, Qi
On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Qi, The correct syntax is that of your First try, but I’m very surprised you got that error, as we fixed this a while ago… Can you please send me the complete output? Cheers, /Eugenio
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 "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, April 29, 2020 at 04:44 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution
Hi,
I am trying to use the longitudinal pipeline of the “hippocampal subfields and nuclei of amygdala”. Keep getting error messages when running it longitudinal but with no error message running it cross-sectional. I want to know if there is any way to fix the error and to run a longitudinal pipeline successfully.
I am using Freesurfer/dev and matlab_runtime/2014b.
I got two timepoints for each subject and finished recon-all longitudinal with no errors.
1) First Try
segmentHA_T1_long.sh SUBJ_base
run for about 15 mins and exited with error message:
“Error using kvlGEMSMatlab
/autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327:
itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search direction is not a descent direction!
Error in kvlStepOptimizer (line 11)
Error in SegmentSubfieldsT1Longitudinal”
no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated.
2) Second Try
segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base
segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base
run for about 16 mins, most successful but a few with errors:
“Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)”
Or
“Open file failed because file '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' has invalid content. Details: 'file is closed.failbit is set.'
The file
"/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m"
cannot be executed.
Error in segmentSubjectT1_autoEstimateAlveusML (line 538)”
successful done subject or hemisphere generated mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21.
3) Third Try cross-sectional
segmentHA_T1.sh SUBJ1_timepoint1
segmentHA_T1.sh SUBJ1_timepoint2
run for about 15 mins, all successful with no errors:
all subjects have mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated.
Manual inspection with freeview, it seems fine with all successful longitudinal and cross sectional subfield segmentation outputs mgz.
I wonder if I can fix first try and second try errors so that longitudinal output can be generated.
Thank you for your help!
Best,
Qi
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ph.D. candidate Icahn School of Medicine at Mount Sinai