Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

Re: [Freesurfer] Registering set of extracted hippocampus
by Chester Dolph 01 Oct '15

01 Oct '15

Hello, Rewording to clarify in case the wording was confusing. What I would like to do is to use each registered ROI for intensity based analysis. I am confused how to use Freesurfer to register and align about three axis. I understand there is variability with positioning the head within the scanner of MRI. I am guessing one solution might be to align each ROI centroid to the same location. This seems to be a trivial concept, but I was hoping there was a simple way of doing this using Freesurfer tools. I appreciate your time and help. Thanks, Chester > On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH <cdolp001(a)odu.edu> wrote: > > Dear experts, > > I look like to register a set of extracted hippocampus to a common atlas. Here is my workflow: > > I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the axial axis. > > I have been looking at the registration tools at: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration> > > Would someone please make a recommendation of a freesurfer tool well suited to registering a set of extracted left or right hippocampus to a common atlas? Also is there a flag to indicate the region, for instance from the look up table: $FREESURFER_HOME/FreeSurferColorLUT.txt > > Thanks, > Chester

2 1

Re: [Freesurfer] Error Messages for Accessing Bin
by Bruce Fischl 01 Oct '15

01 Oct '15

can you try chmod a+x on one of them and see if it can then be executed? e.g.: chmod a+x /home/tle7/freesurfer/bin/mri_convert /home/tle7/freesurfer/bin/mri_convert and see if you get an error. If not, you probably downloaded the wrong hardware version cheers Bruce On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote: > > Hello, > When I run the command "sFSstart" on version 5.0.0, I am receiving the > messages below. Would you please explain to me what the problem is? It > seems like there is trouble accessing the bin. > Thank you > > -------- freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/tle7/freesurfer > FSFAST_HOME /home/tle7/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /home/tle7/freesurfer/subjects > MNI_DIR /home/tle7/freesurfer/mni > tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2 > studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter > H 0 > checking sid number 00152-DT2 > 1 > 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects > Actual FREESURFER_HOME /home/tle7/freesurfer > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file > not executable. > -cw256 option is now persistent (remove with -clean-cw256) > /home/tle7/freesurfer/subjects/00152-DT2_v5 > > mri_convert/home/tle7/freesurfer/subjects/practicemotherdaughter/rawdata/00152-DT2/MR. > 1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > /home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz > > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 00152-DT2_v5 exited with ERRORS at Mon Sep 28 10:43:57 > PDT 2015 > > tle7@sni-vcs-gotlib:~$ > > > >

2 1

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
by Anastasia Yendiki 01 Oct '15

01 Oct '15

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep 2015, andrea cristina Lima wrote: > I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c > /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt > > INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer > > INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... > > Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; > root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 > > > -- > Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573 > >

1 0

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
by Bruce Fischl 01 Oct '15

01 Oct '15

Hi Kie Woo can you run mris_euler_number on those surfaces to see if they are topologically correct? cheers Bruce On Thu, 1 Oct 2015, Nam, Kie Woo wrote: > > Dear experts, > > > > I’m trying to calculate local gyrifcation index using CIVET’s surface file > (‘.obj’). > > > > > > > > > > First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created > a ‘.pial’ file - below are the commands that worked for ‘CIVET --> > FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. > > CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big > Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj > -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” > > FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface > -i_fs lh.pial -o_mni lh.pial” > > > > > > > > > > Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the > following message. > > ************************************************************************ > > lGI for vertex number 5501 of the outer mesh is 4.1122 > > lGI for vertex number 5601 of the outer mesh is 0.86156 > > lGI for vertex number 5701 of the outer mesh is 3.8343 > > ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. > > WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high > (lGI=62.3205)... > > ...lGI computation will be stopped. This may be caused by topological > defects, check mris_euler_number on the pial surface. > > ************************************************************************ > > > > The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, > but it’s not an option for me because I have no other FreeSurfer compatible > files except “.pial”. > > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html > > > > > > > > So, could there be any solution for this? > > > > > > > > Best wishes, > > > > Kie Woo > > >

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 October 2015