Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Install FS on new workstation issues
by Nucleos P 09 Oct '12

09 Oct '12

Hi, Is anyone familiar with Redhat Linux workstation commands? I think the problem here was with the "setenv" command and I looked in root's bin and there is an "env" command? Just need help getting freesurfer to work. Am a total newbe. Thanks, Catherine

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Transform surface to a native volume (different than orig)
by Arnaud Guidon 09 Oct '12

09 Oct '12

Dear Freesurfer experts, I'd like to transform a surface S to a native volume V which is not the original T1. I first computed the transform V_to_orig.mat using flirt. Loading the resulting volume and the lh.pial showed satisfactory results in freeview. Now I'd like to obtain the surface in the native volume. For this I tried applying the inverse of the flirt xform using mri_surf2surf: tkregister2 --fsl orig_to_V.mat --mov orig.nii --targ V.nii.gz --reg orig_to_V.dat --noedit mri_surf2surf --sval-xyz pial --reg orig_to_V.dat --tval pial.native --tval-xyz --hemi lh --s subject However the resulting surface is offset and orthogonal to the native volume. Am I missing anything in the tkregister2 command? Thanks for your help, Arnaud

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accuracy of cerebellar segmenation
by Inês Violante 09 Oct '12

09 Oct '12

Dear all, Does anyone have information on the accuracy of cerebellar segmenation into GM and WM? Thank you very much. ines

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Re: [Freesurfer] freesurfer problems
by Douglas N Greve 09 Oct '12

09 Oct '12

Hi Catherine, there is something wrong with that file or else the error msg would not be generated. Make sure it is world-readable. Make sure you did not download it to a windows machine first and then copy it (if so run dos2unix on it). Look inside it and make sure you can see plain text characters. doug On 10/05/2012 10:04 AM, Nucleos P wrote: > Hi doug! > There is a license file and the script is set up to create the 001.mgz > files using mri_convert. So, I am confused as to why I am getting > these errors to begin with? > > Thanks for getting back to me, > Catherine > On Thu, Oct 4, 2012 at 4:51 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Did you follow the instructions in the error message? > doug > > On 10/04/2012 04:46 PM, Nucleos P wrote: > > I am currently using a Linux Workstation with Redhat. I recently > > installed Freesurfer on this computer. It works fine on the other > > computers... These are the errors I am getting: (The important > points > > are in Bold) > > > > proc_fs test_mgi MGI2 > > #############start: /usr/local/freesurfer/bin/proc_fs Thu Oct 4 > > 16:31:57 EDT 2012 ################# > > #############start: recon-all Thu Oct 4 16:31:57 EDT 2012 > > ################ > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/MGI2 > > Actual FREESURFER_HOME /usr/local/freesurfer > > Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 > EST 2011 > > x86_64 x86_64 x86_64 GNU/Linux > > /usr/local/freesurfer/subjects/MGI2/test_mgi > > > > * mri_convert > > > /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 > > /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz > > > > mri_convert > > > /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 > > /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz * > > > -------------------------------------------------------------------------- > > ERROR: Invalid FreeSurfer license key found in license file > > /usr/local/freesurfer/.license > > If you are outside the NMR-Martinos Center, > > go to http://surfer.nmr.mgh.harvard.edu > <http://surfer.nmr.mgh.harvard.edu/> to > > get a valid license file (it's free). > > If you are inside the NMR-Martinos Center, > > make sure to source the standard environment. > > > -------------------------------------------------------------------------- > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from > > > /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562... > > #-------------------------------------------- > > #@# MotionCor Thu Oct 4 16:32:16 EDT 2012 > > *ERROR: no run data found in > > /usr/local/freesurfer/subjects/MGI2/test_mgi/mri. Make sure to > > have a volume called 001.mgz in > > /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig. > > If you have a second run of data call it 002.mgz, etc.* > > See also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > > Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 > EST 2011 > > x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s test_mgi exited with ERRORS at Thu Oct 4 16:32:16 > EDT 2012 > > > > For more details, see the log file > > /usr/local/freesurfer/subjects/MGI2/test_mgi/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > #############end: Thu Oct 4 16:32:16 EDT 2012 ################# > > [prasad@goodman scan_todo]$ > > > > *The mri_convert is supposed to create the mri/orig/001.mgz file and > > works on the other workstations... > > > > Here is the script in detail: > > * > > #!/bin/tcsh > > ####################################################### > > # Program: proc_fs # > > # Author: Dhruman Goradia # > > # Date: 09/19/2010 # > > # Description: Runs freesurfer preprocessing # > > ####################################################### > > set program = $0 > > echo "#############start: $program `date` #################" > > if ( $#argv != 2 ) then > > echo "${program}: Wrong no of arguments" > > echo "Usage: ${program} dicomdir fs_subdir" > > exit > > endif > > set dirdcm = "/usr/local/freesurfer/subjects/scan_todo" > > set fs_subid = $1 > > set study_id = $2 > > set file1 = `ls ${dirdcm}/${fs_subid}/raw | head -n 1` > > setenv SUBJECTS_DIR "/usr/local/freesurfer/subjects/${study_id}" > > echo "#############start: recon-all `date` ################" > > if ( -f ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz) then > > recon-all -s $fs_subid -all > > else > > *#mkdir -p ${SUBJECTS_DIR}/${fs_subid}/mri/orig > > #mri_convert ${dirdcm}/${fs_subid}/raw/${file1} > > ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz > > recon-all -i ${dirdcm}/${fs_subid}/raw/${file1} -s $fs_subid -all* > > endif > > echo "#############end: `date` #################" > > exit > > * > > Here is the LICENSE file: > > FreeSurfer Software License Agreement ("Agreement") > > Version 1.0 (February 2011) > > > > This Agreement covers contributions to and downloads from the > > FreeSurfer project ("FreeSurfer") maintained by The General Hospital > > Corporation, Boston MA, USA ("MGH"). 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None of the names, logos or trademarks of MGH or any of > > MGH's affiliates or any of the Contributors, or any funding > > agency, may be used to endorse or promote products produced in > > whole or in part by operation of the Software or derived from or > > based on the Software without specific prior written permission > > from the applicable party. > > > > 7. Any use, reproduction or distribution of the Software which > is not > > in accordance with this Software License shall automatically > revoke > > all rights granted to you under this Software License and render > > Paragraphs 1 and 2 of this Software License null and void. > > > > 8. This Software License does not grant any rights in or to any > > intellectual property owned by MGH or any Contributor except > > those rights expressly granted hereunder. > > > > PART C. MISCELLANEOUS > > > > This Agreement shall be governed by and construed in accordance with > > the laws of The Commonwealth of Massachusetts without regard to > > principles of conflicts of law. This Agreement shall supercede and > > replace any license terms that you may have agreed to previously > with > > respect to FreeSurfer. > > > > * > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Controlling for age and sex in Qdec?
by Yang, Daniel 09 Oct '12

09 Oct '12

Dear freesurfer experts, I'm using Qdec and I want to control for age (a continuous variable) and sex (f,m or 1,0). Do I need to center age (i.e., subtract the score from its mean) before I select it as a nuisance factor? Do I need to center sex? I found that selecting age_centered as a nuisance factor vs. selecting age_uncentered as a nuisance factor led to very different results… not sure what is the correct way to go. In brief, if I want to control for age and sex, which of the following is the correct way to go? 1. Center neither age nor sex (f,m). Then choose age_uncentered as a nuisance factor, but sex_uncentered as a discrete/fixed factor. 2. Center age but not sex (f,m). Then choose age_centered as a nuisance factor, but sex_uncentered as a discrete/fixed factor. 3. Center age but not sex (1,0). Then choose both age_centered and sex_uncentered as nuisance factors. 4. Center age and sex (1,0). Then choose both age_centered and sex_centered as nuisance factors. Thanks in advance! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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CT transform to MNI152 2mm
by octavian lie 09 Oct '12

09 Oct '12

Dear all, I need to coregister a set of volumes/patient (brain.mgz, ?dpial.ribbon.mgz, and rCT head (CT head already coregistered with the T1.mgz in SPM and imported in FS) to MNI152 2mm space. After I coregister the brain.mgz to MNI152, how do I apply the generated register.dat matix to the ?dpial.ribbon.mgz and rCT head volumes for normalization? Also, that all patient volumes are 1mm and MNI template is 2 mm (I need this specific one) is an issue during normalization? Thank you, Octavian Lie.

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Re: [Freesurfer] integrating FSL and Freesurfer
by noam Schneck 09 Oct '12

09 Oct '12

Hi Doug Here are more detailed versions of my first two questions. 1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain. 2) Originally, I ran BBR on a subject that I had run Recon-all for. I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted. This is viewed in fslview, The corresponding T1 images created by mri_convert are not. What can I do to allow me to use BBR's fsl.mat within ApplyXFM?

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Re: [Freesurfer] FS install ubuntu 11.1
by Knut J Bjuland 09 Oct '12

09 Oct '12

This errer message mean that you are missing /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh in your /usr/share/fsl/5.0/etc/fslconf. You should get a copy of this file and place in /usr/share/fsl/5.0/etc/fslconf/f knut J On 10/09/2012 02:00 PM, David Soto wrote: > hi - so the output to source $FREESURFER_HOME/SetUpFreeSurfer.csh > > was: >> >>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /usr/local/freesurfer >>> FSFAST_HOME /usr/local/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /usr/local/freesurfer/subjects >>> MNI_DIR /usr/local/freesurfer/mni >>> /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found. >>> FSL_DIR /usr/share/fsl/5.0 >> > > On Tue, Oct 9, 2012 at 11:54 AM, Knut J Bjuland <knutjbj(a)hotmail.com > <mailto:knutjbj@hotmail.com>> wrote: > > Can you please send me the output again? The files should not > prevent you from starting since fsl and freesurfer need that file > to be able to set the environment right. > > > On 10/09/2012 10:41 AM, David Soto wrote: >> thanks, I'll try though I have already reinstalled >> FSL now I have FSL 5.0.1- should that fine prevent >> FS from starting up anyway? >> Cheers >> >> On Tue, Oct 9, 2012 at 9:06 AM, Knut J Bjuland >> <knutjbj(a)hotmail.com <mailto:knutjbj@hotmail.com>> wrote: >> >> Hi >> >> You should reinstall FSL 5.0 since it is missing a file. >> >> Knut J >> >> >> >> On 10/08/2012 08:05 PM, David Soto wrote: >>> Hi, just trying to install Fresufer in Ubuntu OneiricOcelot >>> 11.10, >>> >>> I followed the installation steps in your web and seemed fine >>> >>> in one of the last steps I did >>> >>> wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh >>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >>> -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /usr/local/freesurfer >>> FSFAST_HOME /usr/local/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /usr/local/freesurfer/subjects >>> MNI_DIR /usr/local/freesurfer/mni >>> /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not >>> found. >>> FSL_DIR /usr/share/fsl/5.0 >>> >>> >>> the thing is that when I test the install by typing >>> >>> tkmedit >>> >>> it says command not found & cannot get Freesurfer to start >>> >>> can you help please? >>> >>> Thanks! >>> >>> David >>> http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>> contains patient information, please contact the Partners Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and properly >>> dispose of the e-mail. >> >> > >

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import dicom files with # in name and when to run talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
by Knut J Bjuland 09 Oct '12

09 Oct '12

Hi, I have two questions about Freesurfer. How can I import dicom files, which include "#" as part of the files names into freesurfer witouth renaming the files? Recon-all -i seem to cut the files name after "#" so that image#1.dcm becomes image. Would you recommend me to run this command for all my processed subjects? As stated in the relase notes? Can I use QA_tools to measure the quality of the recons? cd subjid/mri talairach_avi --i nu.mgz --xfm transforms/talairach.xfm recon-all -s subjid -segstats

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FS install ubuntu 11.1
by David Soto 09 Oct '12

09 Oct '12

Hi, just trying to install Fresufer in Ubuntu OneiricOcelot 11.10, I followed the installation steps in your web and seemed fine in one of the last steps I did wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni /usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found. FSL_DIR /usr/share/fsl/5.0 the thing is that when I test the install by typing tkmedit it says command not found & cannot get Freesurfer to start can you help please? Thanks! David http://www1.imperial.ac.uk/medicine/people/d.soto/

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Freesurfer October 2012