Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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

Re: [Freesurfer] convert MNI152 coordinates into vertex index
by Marina Fernández 02 May '20

02 May '20

External Email - Use Caution Thank you for the information, Bruce and Thomas! Thomas, I think this utility is perfect! I tried it with fsaverage subject without problems. Do you think I can use this function to calculate the vertex of the fsaverage5 (instead of the fsaverage)? Really, thank you very much, this help is very useful for us! Best regards, Marina

2 1

mri_glmfit
by jiahui 02 May '20

02 May '20

1 0

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