Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
by Zeng, Qi 04 May '20

04 May '20

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(a)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(a)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(a)nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" >> <qi.zeng(a)icahn.mssm.edu> >> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> *Date: *Wednesday, April 29, 2020 at 04:44 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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(a)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

2 13

Recon-all exited WITH errors
by Mason Wells 04 May '20

04 May '20

External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

2 4

Files generate in the process of "recon-all -autorecon3" are all missing
by Frank Chau 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer experts, I ran recon-all on a batch of subjects on the Linux CentOS virtual machine base on Windows 10. I found all files which should be generated in the "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3" are all missing in this batch of subjects. ( "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3"refer to the page of FreeSurfer Tutorial: Process Flow: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1)<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1> However, this problem did not appear on the MAC platform. I wonder that why this problem only appear on Linux platform. I attached the recon-all.log of a subject which the "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3" files were missing. Could you kindly help me to speculate the cause of this problem. Thank you. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

2 1

recon-all
by jiahui 04 May '20

04 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare two groups' cortex, but for some of my subjects I get the following error when I run mri_glmfit \ --y rh.thickness.10.mgz \ --fsgd g3v1.fsgd dods\ --C group.mtx \ --surf fsaverage rh \ --cortex \ --glmdir g3v1.rh ERROR: DOF=0(this is error?) g3v1h.rh only 4 files(should have beta.mgh sig.mgz files...) I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) mri_glmfit.log and figure01 figure02 figure03: see attached

2 3

Question regarding design matrix/fsgd/resulting statistical tests
by s7675854＠stud.uni-frankfurt.de 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer experts, I have a beginner question regarding fsgd and mtx files. For example, if I have one group and am interested in the correlation between some test score and cortical thickness/surface area, controlling for age and intracranial volume. I would have 1 group and 3 covariates, e.g. class 1 score age icv subj1 1 55 20 3333 subj2 1 43 24 3333 Now if I am interested in the correlation between the test score and an anatomical parameter, I would go with the design matrix: 0 1 0 0 (doss). My question is, why does this calculate an F test, if I am only interested in one group? (I would understand a t-test with test-score slope >0, but where does the F come from?) I am drawing a mental blank here and would appreciate your help! Thanks a lot, Dorothee

3 3

segmentHA_T1.sh fails with "Error in myMRIread: temporary directory does not exist"
by Soichi Hayashi 04 May '20

04 May '20

External Email - Use Caution Hello. I am trying to run segmentHA_T1.sh right after successfully completing recon-all -all I have a freesurfer output directory under my currently working directory inside ./output. So I ran this command. $ segmentHA_T1.sh output . When I do I run into the following error message. #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Mon May 4 09:16:43 EDT 2020 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > .:/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/.singularity.d/libs > Registering imageDump.mgz to hippocampal mask from ASEG > Error using myMRIread (line 16) > Error in myMRIread: temporary directory does not exist > Error in segmentSubjectT1_autoEstimateAlveusML (line 157) > > > > Linux elogin2 4.4.180-94.103-default #1 SMP Mon Aug 19 15:06:57 UTC 2019 > (62f4295) x86_64 x86_64 x86_64 GNU/Linux > T1 hippocampal subfields exited with ERRORS at Mon May 4 09:16:58 EDT 2020 > For more details, see the log file > ./output/scripts/hippocampal-subfields-T1.log How can I correct this problem? Soichi

2 1

TRACULA prep roc error
by Batra, Vinita R. 04 May '20

04 May '20

External Email - Use Caution Hello team, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. #@# Image corrections Sat May 2 19:57:18 CDT 2020 mri_convert --bvec-voxel /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/ /Users/sunlab/Documents/FreeSurferDirs/subjects_109//dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/ /Users/sunlab/Documents/FreeSurferDirs/subjects_109//dmri/dwi_orig.nii.gz corRead(): can't open file /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/COR-.info $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/sunlab/Documents/FreeSurferDirs/subjects_109_data/... Darwin Suns-iMac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Oct 10 23:06:14 PDT 2018; root:xnu-4570.71.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat May 2 19:57:18 CDT 2020 Thank you, Vinita Batra

2 1

PhD position at Lund University
by Laura Wisse 04 May '20

04 May '20

External Email - Use Caution Dear all, We have a PhD position available on imaging of the medial temporal lobe in aging and dementia at Lund University, Sweden, with the Biofinder Group. See here for more details and applying: https://lu.varbi.com/en/what:job/jobID:331266 The application deadline is June 7. Best, Laura Wisse

1 0

error while obtaining lGI
by Yana Hoboken 04 May '20

04 May '20

External Email - Use Caution Dear Community, I am new to the software, so please bare with my ignorance! I have a triangular meshes of both hemispheres that were created not in FS but in another mesh generating software. I converted them with nibabel into two .pial files. When I run a 'read' command on them, I see the same structure as I see on native .pial file: [image: image.png] Previously I have already run a recon-all on the MRI data I have and generated lh/rh.pial files. I also run -localGI on them, and also got the results just fine. Every time I work on the same computer. THe meshes that I converted with nibabel look the same (except for transcription) as the one I got from MRI. I cannot distinguish them in Freeview. But when I try to get lGI I got the error message. The command I use : recon-all -s name -localGI THe error I got: I will attached the log file for more information. FS version I am using: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I will be very grateful for any tips what this error is about, as I cannot find any reference about it anywhere. Thank you for you time! Yana

2 2

Re: [Freesurfer] Freesurfer Digest, Vol 194, Issue 45
by atira gan-zvi bick 03 May '20

03 May '20

External Email - Use Caution Hi Bruce > It worked! how simple... Thank you so much. Atira > > > ------------------------------ > > Message: 2 > Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] exporting segmented mgz file > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.2004261203210.6647(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Atira > > what was your mri_convert command line? Make sure to specify no scaling of > the intensity volume. Can you try adding: > > -ns 1 > > to the mri_convert command line, and if that doesn't work send us the full > command line and full screen output from it? This is always a good thing > to > do as it gives us enough information to help > > cheers > Bruce > > > > On Sun, 26 Apr 2020, atira gan-zvi bick wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hi > > I'm new to freesurfer. > > > > I used freesurfer to preform Thalamus segmentation, and can see the > segmented?volume in freeview. > > I would like to export?the segmented volume to nii to continue analysis > in MRvista. > > I was able to do this using?mri_convert - however the values in the > nifti are not those on the label > > list (as seen in ?freeview). The number of different values is similar > but not the same, and the values > > themselves? are totally different?(8103-8233 in freeview, 16384 - > 32767). It is possible to compare > > regions based on visual inspection - however that is tedious?and might > lead to mistakes. > > How can I export the labels of each region in the segmented mgz? > > > > Any suggestions? > > I'd appreciate?to learn fro your experience > > > > Thanks > > Atira > > > > -- > > ?"? ????? ??-??? ??? > > ????? ?????? ???????? > > ???? ???-??? > > ??????????? ?????? > > > > Atira Bick (Phd) > > fMRI unit > > Hadassah medical center, Hebrew University > > Jerusalem > > > > > > ------------------------------ > > > > -- ד"ר עתירה גן-צבי ביק יחידת ההדמיה התפקודית הדסה עין-כרם האוניברסיטה העברית Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer