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)
*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.
- 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.
- 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.
- 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
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
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.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
--
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
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
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)
*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)
*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.
- 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.
- 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.
- 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
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
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.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
--
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
--
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
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.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
--
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
--
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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
External Email - Use Caution
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)
*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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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)
*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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
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
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.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
--
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
--
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.edumailto: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.edumailto: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.edumailto: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
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)
*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)
*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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
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
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.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
--
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
--
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.edumailto: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.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
External Email - Use Caution
Thank you so much !
Best, Qi
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)
*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)
*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)
*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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
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
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.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)
*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)
*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)
*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)
*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)
*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)
*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.
- 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.
- 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.
- 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
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
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
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
--
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
--
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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.edumailto: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@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Zeng, Qi