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
Dear Qi, The correct syntax is that of your First try, but I’m very surprised you got that error, as we fixed this a while ago… Can you please send me the complete output? Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" qi.zeng@icahn.mssm.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, April 29, 2020 at 04:44 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
External Email - Use Caution
Hi,
I am trying to use the longitudinal pipeline of the “hippocampal subfields and nuclei of amygdala”. Keep getting error messages when running it longitudinal but with no error message running it cross-sectional. I want to know if there is any way to fix the error and to run a longitudinal pipeline successfully.
I am using Freesurfer/dev and matlab_runtime/2014b.
I got two timepoints for each subject and finished recon-all longitudinal with no errors.
1) First Try
segmentHA_T1_long.sh SUBJ_base
run for about 15 mins and exited with error message:
“Error using kvlGEMSMatlab
/autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327:
itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search direction is not a descent direction!
Error in kvlStepOptimizer (line 11)
Error in SegmentSubfieldsT1Longitudinal”
no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated.
2) Second Try
segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base
segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base
run for about 16 mins, most successful but a few with errors:
“Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)”
Or
“Open file failed because file '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' has invalid content. Details: 'file is closed.failbit is set.'
The file
"/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m"
cannot be executed.
Error in segmentSubjectT1_autoEstimateAlveusML (line 538)”
successful done subject or hemisphere generated mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21.
3) Third Try cross-sectional
segmentHA_T1.sh SUBJ1_timepoint1
segmentHA_T1.sh SUBJ1_timepoint2
run for about 15 mins, all successful with no errors:
all subjects have mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated.
Manual inspection with freeview, it seems fine with all successful longitudinal and cross sectional subfield segmentation outputs mgz.
I wonder if I can fix first try and second try errors so that longitudinal output can be generated.
Thank you for your help!
Best,
Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Zeng, Qi