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. < jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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. < > jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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.z...@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. < > jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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. < > jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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. < > jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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.z...@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. < > jiglesiasgonza...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@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 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 -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
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