Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

combining epi dewarping and motion correction w/ mri_vol2vol
by Nathan Tardiff 21 Sep '16

21 Sep '16

Hello, I am attempting to combine my motion correction and b0 unwarping steps. I have .lta files produced by registering every volume of a BOLD run to the first volume using mri_robust_register and a vsmap for dewarping produced by epidewarp.fsl. Is it sufficient to input them both into mri_vol2vol to combine these steps? Something like: The command I was thinking of trying was: mri_vol2vol --mov inFile --targ dstFile --o outFile --lta ltafile --vsm vsmap --cubic Or would something about the creation of the .lta files also need to be changed? Thanks, Nathan

1 0

Failure in testing newly installed FreeSurfer
by Saeed mahdizadeh bakhshmand 21 Sep '16

21 Sep '16

Hello FreeSurfer Developers, I'm trying to test a very basic command (recon-all) according to this page(https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer) after installing FreeSurfer and I receive following error after a few seconds: ERROR:recon-all -s bert exited with ERRORS at Sun Sep 4 17:18:51 EDT 2016 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: x86_64 3) uname -a: Linux saeed-CDS-Custom-Configuration 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Saeed

4 5

Research Fellow or Research Associate Position
by Lili He 21 Sep '16

21 Sep '16

Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier pediatric research institution. We are driven by our mission to improve child health and transform the delivery of care through fully integrated, globally recognized research, education and innovation. Post-doctoral research fellows at Cincinnati Children’s are valued for their unique interests and strengths, and are supported by our institution’s strong programming for post-docs through the Office of Postdoctoral Affairs and the Office of Academic Affairs and Career Development. Mentoring, support for international students and an emphasis on crafting high-quality grant proposals are only a few of the features that set our program apart. Dr. Lili He’s research focuses on developing objective MRI methods for neonates; developing multimodal MRI neuroimaging biomarkers to predict long-term cognitive, behavioral and sensorimotor deficits. We are now seeking a creative and highly motivated individual with good writing skills and training in MRI image processing data analysis. Previous experience on machine learning will be plus. The major duties of this opening are: to develop quantitative method for use in advanced neuroimaging and brain mapping involving structure MRI, functional MRI and DTI; to analyze brain image data using existing commercial and publicly available image analysis programs (such as SPM, FSL, CONN, Freesurfer). Candidates for either Postdoctoral Research Fellow or Research Associate (commensurate with previous experiences) must hold a PhD with a background in any of the following disciplines: computer science, biomedical engineering, bioinformatics, electrical engineering and neuroscience. Emphasis on programming expertise in Matlab, C/C++ and in UNIX environment. The work promises to be challenging and presents a highly exciting opportunity to utilize resources available at Cincinnati Children's Hospital Medical Center (CCHMC) and collaborations from the Department of Pediatrics, Division of Neonatology and with the Pediatric Neuroimaging Research Consortium (PNRC) faculty. Contact: Lili He, PhD Address: Lili.He(a)cchmc.org

1 0

Configuration question for unbuntu
by Thomas Beaudry 21 Sep '16

21 Sep '16

Hi, I installed freesurfer and followed all of the configuration steps. I am now doing the sample tests, and noticed that it can't find libjpeg.so.62. According to this resource: https://surfer.nmr.mgh.harvard.edu/fswiki/Download I should do the following: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3? After doing this is, it works, and I no longer get any errors. However, I am maintaining a cluster, and would prefer not doing this for every machine. Is there a place in the install directory or a parth/variable that I could modify to have it work without having to do the fix mentioned above? Thanks, and have a nice day, Thomas Beaudry

2 2

Recon hires 7T {Disarmed}
by Köbe, Theresa 21 Sep '16

21 Sep '16

Dear FreeSurfer Developers, I am attempting to run recon-all on 7T MP2RAGE images (resolution 0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³. I used the data directly from the scanner (without reorientation to standard etc.) and used the following command: recon-all -s $subject.freesurfer -hires -i $subject.mp2rage.nii -expert /media/NeuroMet_Project/scripts/expert.opts -all -hippo-subfields" As expert option I used only: mris_inflate -n 15 The processing starts fine but ends with the following error: ERROR: dimension mismatch between input volume and seg input 321 321 321 seg 322 322 322 Could you please help me dealing with this problem? I attached also the log-file Thank you so much. Best Theresa ------------------------------------------------------------------------- Charité – Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC Dipl.-Biol. Theresa Köbe AG Kognitive Neurologie Wiss. Mitarbeiter Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2 http://www.charite.de/service/lageplan/plan/map/ccm_sauerbruchweg_5/<redir.aspx?REF=mc29RH9tIXK9qgoNB0UJ6dmsQ-pCBih_Q7so140WG76sl9oBFOLTCAFodHRwOi8vd3d3LmNoYXJpdGUuZGUvc2VydmljZS9sYWdlcGxhbi9wbGFuL21hcC9jY21fc2F1ZXJicnVjaHdlZ181Lw..>

2 1

fmri pipeline
by A Nunes 20 Sep '16

20 Sep '16

Hi, I am getting a bit confused from the mailing archive on how to properly map volume fmri data into surface fsaverage5. 1. Should I map the volume fmri into individual surface first and then to fsaverage, or I won't loose data if I map it directly to fsaverage5? 2. Should I smooth the data when mapping into the individual surface or from individual surface to fasaverage5? Thanks Adonay

1 0

Freeview error: Surface does not contain valid volume geometry information
by Claudia Dacquino 20 Sep '16

20 Sep '16

Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I get this warning: Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces. What's wrong? I'm using 5.1 version. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

2 1

local intensity inhomogeneity
by Jason Tourville 20 Sep '16

20 Sep '16

Hello freesurfers, We've seen some poor surface reconstructions due to local inhomogeneities that remain in the brainmask volume. We see omission of significant portions of brain tissue due to signal fall off (both gray and white voxels are darker than in surrounding area) that we are unable to current through control points or other manual interventions. Can anyone suggest a tool for correcting latent local inhomogeneities? Is anyone aware of a manual tool that allows one to "brighten" the voxels from some point outward at some falloff rate? Any help would be greatly appreciated. Best, Jason

2 1

LGI and MATLAB
by Alan Francis 20 Sep '16

20 Sep '16

Hi Marie - I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am getting an error. Is there any way to overcome this? Thanks, Alan afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer afrancis-mac:~ afrancis$ source /Applications/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl afrancis-mac:~ afrancis$ export MATLABPATH=/Applications/MATLAB_R2015a.app/bin afrancis-mac:~ afrancis$ export PATH=${MATLABPATH}/bin:${PATH} afrancis-mac:~ afrancis$ recon-all -s DM55 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 948660 Sep 16 09:50 /Applications/freesurfer/subjects/DM55/scripts/recon-all.log Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM55/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Sep 16 09:55:23 EDT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 recon-all -s DM55 exited with ERRORS at Fri Sep 16 09:55:23 EDT 2016 For more details, see the log file /Applications/freesurfer/subjects/DM55/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

2 2

Re: [Freesurfer] White matter surface don't change after editing
by Cong 20 Sep '16

20 Sep '16

> On Sep 10, 2016, at 1:15 AM, 3110103623(a)zju.edu.cn wrote: > > Hi Dear Bruce > Thanks very much for your reply, I improved min_border_white to 100, the lh.white line shrinks but still is far out in some area, and I notice many topological defect appears as a result. > I failed to upload subject through ftp, it's always appear an error called "553 Could not create file", so I send a subject to you through FileDrop. Can you receive a file named Cong2Bruce.zip? > Thanks again for your help. > > Best Wishes > Cong Chen > > Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > Hi Cong > > you could try using expert options to modify the mris_make_surfaces > parameters. It looks like you white surface is too far out. Try > increasing min_border_white and/or increasing max_gray. If you can't get it > working feel free to upload the entire subject dir and we will take a look > > cheers > Bruce > > > On Thu, 8 Sep 2016, Cong wrote: > > Hi dear all > I attach a new picture to illustrate this problem. I erased some voxels in wm.mgz and rerun. The lh.orig(blue line) looks well, but lh.white(yellow line) don?t along the white surface in some area. Could anyone give me some advice? Thanks very much. > > Best wishes > Cong Chen > > > Date: Sun, 4 Sep 2016 15:15:42 +0800 > From: Cong <3110103623(a)zju.edu.cn <mailto:3110103623@zju.edu.cn>> > Subject: [Freesurfer] White matter surface don't change after editing > > Dear freesurfer team? > I have some MRI images from a GE scanner, it seems that images? quality is poor because grey matter is bright in so much area and these grey matter is included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and rerun through command ? recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But ?h.white (yellow line) don?t change after rerunning as you can see in the attached picture. Is this problem caused by deleting too many voxels and how to fix it? Thanks very much. > > Regards > Cong Chen

2 2

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