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,

On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. <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.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 12:37
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,

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.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.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, May 1, 2020 at 12:28
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,

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.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.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.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, April 30, 2020 at 12:48
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:

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.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.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, April 30, 2020 at 09:55
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,

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.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.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 29, 2020 at 17:28
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,

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.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.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.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 29, 2020 at 04:44
To: "freesurfer@nmr.mgh.harvard.edu" <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

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ph.D. candidate

Icahn School of Medicine at Mount Sinai