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