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<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Zeng, Qi" <qi.z...@icahn.mssm.edu<mailto:qi.z...@icahn.mssm.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, April 30, 2020 at 12:48 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Zeng, Qi" <qi.z...@icahn.mssm.edu<mailto:qi.z...@icahn.mssm.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, April 30, 2020 at 09:55 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Zeng, Qi" <qi.z...@icahn.mssm.edu<mailto:qi.z...@icahn.mssm.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, April 29, 2020 at 17:28 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Zeng, Qi" <qi.z...@icahn.mssm.edu<mailto:qi.z...@icahn.mssm.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, April 29, 2020 at 04:44 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
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