Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

Re: [Freesurfer] mri_cvs_register can not find
by lzollei＠nmr.mgh.harvard.edu 06 Nov '11

06 Nov '11

Hi Martin, Could you give more details? Which version of mri-cvs-register are you using? Was there a log file that you could share also? Thanks, Lilla ------Original Message------ From: Martin Kavec To: Freesurfer mailing list To: Lilla Zollei Subject: mri_cvs_register can not find Sent: Nov 4, 2011 03:44 Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one with the exactly the same name, but different suffix .tm3d is there. Anybody encountered similar problem? Any idea what can be wrong? Thanks in advance, Martin Sent via BlackBerry by AT&T

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Visulaization of FreeSurfer-defined ROI
by Jade 04 Nov '11

04 Nov '11

Hello Freesurfer experts, I am a beginner in using Freesurfer. I want to make a figure illustrates a specific area of ROIs (e.g., lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? Thanks in advance!

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func2roi-sess question
by Khena Swallow 04 Nov '11

04 Nov '11

Hi, I've been using func2roi-sess for region of interest analyses and was hoping that someone here could answer what might be a pretty basic question. Does anyone know when in the analysis stream the data from voxels in an ROI are averaged? I can think of two possibilities. The first is that the BOLD data are first averaged and then the response of the ROI to different types of events is estimated. The other possibility is that the model estimates are first calculated for each voxel, and these are averaged to produce a single estimate for the ROI. I've read through the func2roi-sess help page and still have some doubt about what the answer is. Any help on clarifying which of these approaches func2roi-sess uses would be greatly appreciated! Thanks! Khena -- Khena M. Swallow, Ph.D. Research Associate Department of Psychology University of Minnesota

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Error During Talairach Transform
by Joshua Lee 04 Nov '11

04 Nov '11

#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011 For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

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Re: [Freesurfer] .license error
by Bruce Fischl 04 Nov '11

04 Nov '11

Hi Nooshin you should post this type of question to the list so others can answer. Are you sure that the file /Users/nzadeh/freesurfer/.license exists? thanks Bruce On Tue, 1 Nov 2011, Zadeh, Nooshin N. wrote: > > Hi and Good afternoon > > I have downloaded the FS and in next steps to set it up, I got the license and made a file and copied that license and saved on the "/Users/nzadeh/freesurfer" named "license". but when I start reconning one subject I received the following error message. When I changed the name of license file to ".license" it says that file would be hidden. After that, with reconning the subject again, I received same error message. With running other FS commands, I get the same error message. Can you please guide me how can I install FS properly and where is my mistake? I appreciate your time. > > > ERROR: FreeSurfer license file /Users/nzadeh/freesurfer/.license not found. > If you are outside the NMR-Martinos Center, > go to 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. > > Thanks > Nooshin > > >

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Longitudinal pipeline question
by Irene Altarelli 04 Nov '11

04 Nov '11

Dear Fs experts, I am running a longitudinal dataset through the longitudinal pipeline, and noticed that for one subject, although we kept everything the same (sequence, coil etc) the two timepoints' brainmasks look different: timepoint one (in the attached snapshot, gs_tp1) looks as if it has been smoothed, compared to timepoint two (gs_tp2). I have checked some other images from this subject, and the same seems to occur for orig.mgz, but not for rawavg.mgz. Any idea on what could be causing the difference would be greatly appreciated. Thanks in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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[Fwd: [FSL] Announcement: The 2012 FSL & FreeSurfer Course]
by Nick Schmansky 04 Nov '11

04 Nov '11

---------------------------- Original Message ---------------------------- Subject: [FSL] Announcement: The 2012 FSL & FreeSurfer Course From: "Mark Jenkinson" <mark(a)FMRIB.OX.AC.UK> Date: Thu, November 3, 2011 12:54 pm To: FSL(a)JISCMAIL.AC.UK -------------------------------------------------------------------------- We are pleased to announce the 2012 FSL & FreeSurfer Course, to be held in Auckland, New Zealand (May 14-18). It will run immediately after the ISMRM conference, which will be in Melbourne, Australia. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets. The course lasts 5 days, from May 14-18, 2012. Numbers of attendees are strictly limited and are available on a first-come-first-served basis. For full information and to register for the course, please go to: http://www.fmrib.ox.ac.uk/fslcourse/current.html Regards, course organisers. Dr Mark Jenkinson University Research Lecturer Head of Structural Image Analysis FMRIB Centre, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222769 (fax 222717) mark(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~mark

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mri_cvs_register can not find
by Martin Kavec 04 Nov '11

04 Nov '11

Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one with the exactly the same name, but different suffix .tm3d is there. Anybody encountered similar problem? Any idea what can be wrong? Thanks in advance, Martin

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How to specify -gcut for Freesurfer 5.1 release
by Vy Dinh 03 Nov '11

03 Nov '11

Dear Experts, I've read that the latest Freesurfer release, v5.1, allows one to rerun the skullstripping step to remove extra dura. This would be a godsend for us since most pial surface corrections involve removing the dura. However, we have been using v5.0, which does not have this feature. It also appears that mri_gcut, the v5.0 equivalent of -gcut, is run by default in v5.0. Could someone please confirm this? I'd really appreciate it if there is a way to remove the extra dura automatically after running recon-all. Since we preprocessed our subjects using v5.0, we have not used v5.1 at all, unless it is more beneficial to start editing using v5.1. Thanks in advance, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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converting "annotation values" to "label codes"
by David Grayson 03 Nov '11

03 Nov '11

Hi, I have converted a custom-made annotation file to a volume, and now I am trying to find a table with the labels and their corresponding label codes (index values which are created when the annotation file is converted to a volume). I only have the “annotation values” or color codes for each region, which I found with the read_annotation() function in matlab. The online wiki states that this color code then has to be used to look up the label code, but it’s unclear to me how to do this. Is there be a table somewhere so that I can cross-reference the color codes to the label codes? Thank you, David

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Freesurfer November 2011