Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Freesurfer and FSL
by Ana Arruda 10 Oct '12

10 Oct '12

Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda

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Dimension Issues with mri_surf2surf
by Aimi Watanabe 10 Oct '12

10 Oct '12

Hello, My input to freesurfer is: mri_surf2surf --cortex --fwhm-src 5 --noreshape --hemi rh --tval [$output file] --sval [$input file] --srcsubject [$subject id] --trgsubject fsaverage --tfmt nii When I reopen the resulting image with Nibabel, the dimensions are 27307 x 1 x 6 x 296. While 296 is the time axis, I was hoping to get 27307*6 = 163842 vertices. I have replaced '--noreshape' with '--reshape', '--reshape_factor=6' and the bash output looks proper: 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Saving target data 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Reshaping 6 (nvertices = 163842) 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Saving to [$output file] However, it does not change the resulting image. I have also tried other file types that are not 'nii', like 'mgh', but this does not help either. Please advise? Also, I could easily make a work-around, and reshape the image from a(27307, 1, 6, 296) to b(163842, 1, 296) in FORTRAN (column-major) order. I.E.: 0~27306 then add the next set 27307~54613. If I do this, would the original vertex map be preserved? Thank you!

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hippocampal segmentation
by Hugh Pemberton 10 Oct '12

10 Oct '12

Dear freesurfer crew, I'm having a few issues with segmentation around the hippocampus, I have included a few screenshots of main and aux vol where the hippocampus has been excluded even with the addition of control points. Have you got any tips for rectifying this? It's happened a fair few times with my subjects. Thanks very much in advance and all the best, Hugh

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PhD position available – Cognitive Neuroimaging of Language and Audition
by Narly GOLESTANI 10 Oct '12

10 Oct '12

Dear all, Applications are invited for a PhD in the newly established ‘Brain and Language Lab’ at the University of Geneva in Switzerland, under the supervision of Narly Golestani. Projects will include using functional MRI (fMRI), structural MRI (sMRI), diffusion tensor imaging (DTI) and electroencephalography (EEG) to better understand brain functional and structural plasticity arising from auditory training. The laboratory is affiliated with the Department of Clinical Neuroscience of the Faculty of Medicine at the University of Geneva, and is a member of the Geneva University Neuroscience Center (http://neurocenter.unige.ch/) Geneva offers a thriving international environment, with extensive cultural and outdoor activities, and a high quality of living. Applicants should have strong interest and a background in neuroscience and ideally also in language and/or auditory research. Prior experience with fMRI, sMRI, DTI and/or EEG is required. Salary will start at 45,540 CHF per year and will increase by about 2,200 CHF annually. Applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV including list of publications, a statement of research interests, and the names and full contact details of two referees should be sent to: Narly.Golestani(a)unige.ch.

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motion cut off
by Mürner-Lavanchy, Ines 10 Oct '12

10 Oct '12

Dear FreeSurfers, Due to motion I have to exclude participants from my analysis. Is there an objective measure which could serve as a cut off value concerning motion in the scanner? Can I find it in one of the FreeSurfer files generated through the recon-all process? Subjectively, one can see which images are good or good enough for segmentation. But I'd rather like to include or exclude participants based on an objective threshold. Thank you very much in advance, Best regards, Ines

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Error with updated freeview.bin
by Irwin, William 09 Oct '12

09 Oct '12

Hello- I just downloaded the updated freeview.bin (8/23/2012) file (from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86…) I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux). When I tried to execute freeview, I got the following error: freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN9QListData11detach_growEPii I'm assuming there are updates, improvements to the newer version, which I what motivated me to update. Please advise. Thanks, Wil

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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"). Part A of this Agreement > applies to > > contributions of software and/or data to FreeSurfer (including > making > > revisions of or additions to code and/or data already in > FreeSurfer). Part > > B of this Agreement applies to downloads of software and/or data > from > > FreeSurfer. Part C of this Agreement applies to all transactions > with > > FreeSurfer. If you distribute Software (as defined below) > downloaded from > > FreeSurfer, all of the paragraphs of Part B of this Agreement > must be > > included with and apply to such Software. > > > > Your contribution of software and/or data to FreeSurfer > (including prior > > to the date of the first publication of this Agreement, each a > > "Contribution") and/or downloading, copying, modifying, displaying, > > distributing or use of any software and/or data from FreeSurfer > > (collectively, the "Software") constitutes acceptance of all of the > > terms and conditions of this Agreement. 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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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