Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

mri_convert documentation error
by Johannes Klein 02 Mar '06

02 Mar '06

Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, Johannes

2 3

two functions location
by Joongnam Yang 01 Mar '06

01 Mar '06

Hi, "mris_preproc" and "mri_glmfit" These two functions are not included in the version of Freesurfer that I have. Does anyone know where I can get them? Nam.

2 1

Help!
by yanxia 01 Mar '06

01 Mar '06

Dear All, I am a new user of FreeSurfer. I have two questions: 1> Is there a way to convert FreeSurfer surface files to Analyze format? I use 'tkmedit bert brain.mgz lh.pial' to view the image with the surface bounday, and hope that I can save the image and the surface boundary with Analyze format. 2> mri_convert can be use to convert *.mgz file to Analyze file. I use "mri_convert brain.mgz brain.img"> It is empty when I try to open "brain.img" with MRICON software. Thank you so sume. Best Regards, Yan

3 2

FreeSurferEnv.sh problems
by Sebastian Moeller 01 Mar '06

01 Mar '06

Dear All, my copy of freesurfer-Linux-centos4_x86_64-dev20060224-full contains a small error in the file FreeSurferEnv.sh. In line 155 "export =$MNI_INSTALL_DIR/data" should read "export MNI_DATAPATH=$MNI_INSTALL_DIR/data". Ahoi Sebastian "friend of bash" Moeller -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

1 0

FS-FAST spatialsmooth-sess error
by raij＠nmr.mgh.harvard.edu 28 Feb '06

28 Feb '06

Hi Doug, spatialsmooth-sess failed on the second run (out of 6 runs) with the output: ... ERROR: failure writing /tmp/ipfsl_19705/fmc.img as volume type 16 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold mri_convert 005/fmc.bhdr /tmp/ipfsl_19705/fmc.img --out_type analyze4d ERROR: mri_convert failed ERROR: ipfsl failed Two explanations come to mind: A. Each number has a different number of TRs. Does the ntrs value in the seq.info (inside bold dir) have to match the actual number of TRs in each run? I here tried to smooth all runs in one step... obviously this is not going to work if the ntrs value has to be correct. Should I process the runs one at a time with -fsd NNN and adjust the seq.info ntrs value between? B. The number of images was big = 666 / 1095 / 1741 per run (2 runs each size). Did the scratch disk or mri_convert run out of memory? *** Detailed problem report: *** on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri cd /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT which mc-sess /usr/local/freesurfer/dev/fsfast/bin/spatialsmooth-sess spatialsmooth-sess -sf sessid -df sesspar -fwhm 6 -i fmc -o ifmcsm6 ------------------------------------------------ ------------------------------------------------ /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT Tue Feb 28 18:50:28 EST 2006 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT RunList 004 005 006 009 010 011 ---------------------------------------------- /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold ... Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0 Thanks, Tommi

2 1

Re: Re: [Freesurfer] activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Thanks for the answer, > If you want to create statistical maps in surface space, then use > mris_preproc to assemble the data. Then use one of the FSL tools to > do stats or use mri_glmfit Where could I get mris_preproc and mri_glmfit? Google displays nothing on those two functions.....^_^ > You cannot do corrections for mult comparisons > on the surface with the fSL tools. I wanted to know if it's possible to pinpoint a data point corresponding to a particular voxel. If I can do that, I want to do statisitcal test of my own. You mean it's not possible? I mean, 'is it not possible to match each voxel with each data point in the data file?' Nam.

1 0

cannot locate talairach.xfm
by Darren Weber 28 Feb '06

28 Feb '06

I have some path problems when using tksurfer, eg dnlweber:/data/freesurfer/subjects> tksurfer -ucsf_cj rh inflated surfer: current subjects dir: /home/dweber/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/freesurfer/subjects can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info INFO: NOT fixing vertex area surfer: vertices=154539, faces=309074 can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: using interface /home/dweber/freesurfer/home/lib/tcl/tksurfer.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_common.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_wrappers.tcl Reading /home/dweber/freesurfer/home/lib/tcl/fsgdfPlot.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl The .xfm file exists, ie dnlweber:/data/freesurfer/subjects> ls ucsf_cj/mri/transforms/ talairach.xfm So the question is, how can I work around this failure to find the talairach.xfm file? Do I need to edit the tksurfer.tcl script? It seems to have a strange way of using relative paths (..) to find the talairach.xfm file. In case it makes any difference, this is my set up: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/dweber/freesurfer/home FSFAST_HOME /home/dweber/freesurfer/home/fsfast SUBJECTS_DIR /home/dweber/freesurfer/subjects FUNCTIONALS_DIR /home/dweber/freesurfer/sessions MINC_BIN_DIR /home/dweber/freesurfer/home/mni/bin MINC_LIB_DIR /home/dweber/freesurfer/home/mni/lib PERL5LIB /home/dweber/freesurfer/home/mni/lib/perl5/5.8.0 GSL_DIR /home/dweber/freesurfer/home/lib/gsl QTDIR /home/dweber/freesurfer/home/lib/qt TCLLIBPATH /home/dweber/freesurfer/home/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl where the /home/dweber/freesurfer contains symlinks (please don't ask me why), eg: dnlweber:/data/freesurfer/subjects> ls -l /home/dweber/freesurfer/ total 0 lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 functionals -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 21 2006-02-24 20:26 home -> /usr/local/freesurfer lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 sessions -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 subjects -> /data/freesurfer/subjects -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

2 8

activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Hi all, When I overlay functional data (e.g. from FSL) onto a Freesurfer-produced inflated brain, I see the activations shown in colors. I want to pick a voxel in Talairach coordinates in those activations and see how the particular voxel's activation level changes throughout different data sets of the same brain. So, my question is how can I get the activation level of a particular voxel consistently throughout different data sets, so that I can do some sort of statistical tests? Thanks in advance. Nam.

2 1

Question: FS-FAST mc-sess -perrun
by raij＠nmr.mgh.harvard.edu 28 Feb '06

28 Feb '06

Hi Doug, The issue is motion correction in FS-FAST. The environment is nmr-dev-env. mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)". 1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run? 2. Does this equal to using the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

2 3

mri_motion_correct2 woes
by Sebastian Moeller 28 Feb '06

28 Feb '06

Dear All, I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

2 5

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