Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

problem saving in tkmedit
by Stacey M Schaefer 23 Sep '09

23 Sep '09

Hello freesurfer gurus, We are running into the following error when trying to save edits to the brainmask volume in tkmedit: % ERROR: opening pipe gzip -f -c > /study/midus/data/mri/processed/freesurfer/subject006/mri/brainmask.mgz, errno = 12 Cannot allocate memory mghWrite(/study/midus/data/mri/processed/freesurfer/subject006/mri/brainmask.mgz, -1): could not open file There is also a popup error window that reads; Error: Saving Volume Couldn't save volume The files could not be written. Check to make sure the destination directory exists, that you have permission to write to it, and that there is sufficient disk space. ***However, please note that sometimes it DOES save. When only a few changes are made, it seems to save, but once we start getting about 1/5 to 1/4 of the way through an image, the above errors occur.**** Any suggestions? Thanks very much, Stacey --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm A127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937

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GLOBAL region of the brain empty! error due to error in intensity normalization?
by Ana Catarino 23 Sep '09

23 Sep '09

Hello, I was just running autorecon1 on a subject and I got the mri_watershed Error: GLOBAL region of the brain empty! I am aware that there was a bug in previous versions but I'm using v4.3.1, which I think it's not supposed to have that bug any longer. I tried running -skullstrip with the -no-wsgcaatlas flag, which caused the whole brain and part of the head to be striped out instead of just the skull. Next I tried to compare the output images step by step with images at the same stage for another subject with no error. Regarding the 001.mgz, rawavg.mgz and orig.mgz there were no obvious differences between both subjects, except that the images looked a little darker for the subject that got the error later. However, the nu.mgz image was quite different. The subject with error presented a very dark image, with signal intensities around 40, whereas the subject without error presented normal intensities around 110. The quality of the original images was the same, same sequence, everything. I already ran 20 subjects and this was the first one to show this error. Any help provided with be very much appreciated! Thank you, Ana Catarino

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how to use mri_compute_seg_overlap
by Guang Zeng 23 Sep '09

23 Sep '09

Hi, there, I have two subjects from two time points, I'd like to compare their overlap ratio of FreeSurfer segmented hippocampus. I try to use the command mri_compute_seg_overlap to do it, My command line is: mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz Is it correct? I ran it, but nothing happen. Thanks! Guang _________________________________________________________________ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutor…

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FSL to FreeSurfer registration
by Estephan Moana 23 Sep '09

23 Sep '09

Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 moana(a)email.unc.edu

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Re: [Freesurfer] how to extract segmented hippocampus
by Gonzalo Rojas Costa 23 Sep '09

23 Sep '09

Dear Douglas: And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz with the mri_binarize command ?... Sincerely, Gonzalo Rojas Costa > mri_binarize with --match 17 or --match 53 will do it > > doug > > Guang Zeng wrote: >> Hi, there, >> >> I'd like to extract the left and right hippocampus from aseg.mgz, so >> basically what I want is a volume where left hippocampus have value >> (or label) 17 and right hippocampus have value (or label) 53, all the >> other place are zero. >> >> How can I do it? Using mri_threshold or mri_label2vol? >> >> Thanks a lot! >> >> Guang >> >> >> >> ------------------------------------------------------------------------ >> Hotmail: Free, trusted and rich email service. Get it now. >> <http://clk.atdmt.com/GBL/go/171222984/direct/01/> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Using mris_preproc
by Holly Bridge 23 Sep '09

23 Sep '09

I am trying to register an anatomical ROI (V1Left.nii.gz) in the same volume space as brain.mgz for SubjectX using spherical registration to the average subject brain. I have used the following command mris_preproc --s SubjectX --out ~/SubjectX/lh.ave.v1.mgz --target average --hemi lh --ivp ~/SubjectX/V1Left.nii.gz ~/SubjectX/mri/ transforms/identity.xfm and received this output: nsubjects = 4 ERROR: number of input volumes (1) does not equal number of subjects From where does the code read nsubjects = 4? Thanks for the help, Holly Bridge If required, identity.xfm contains the following MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 ; ------------------------------------------------------------------------ --------------------------- Dr Holly Bridge Royal Society University Research Fellow FMRIB Centre Tel: +44-1865-222582 John Radcliffe Hospital Headington Oxford OX3 9DU Email: hb(a)fmrib.ox.ac.uk Lecturer and JRF, New College ------------------------------------------------------------------------ ---------------------------

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Re: [Freesurfer] Using tksurfer to dispaly the surface
by Nick Schmansky 22 Sep '09

22 Sep '09

QQ, Does the sample subject 'bert', found in freesurfer/subjects/bert, display overlays correctly? ie. does thickness display normally? I need to disambiguate whether its a system problem or a data problem. If bert doesnt display correctly, then I'd try updating the graphics driver. Also, are you displaying over vnc, or locally? vnc connections can be problematic for display. Nick On Tue, 2009-09-22 at 07:23 -0400, Bruce Fischl wrote: > Hi QQ, > > you should post these to the list so someone else can help. > > Nick: any ideas? > > Bruce > On Tue, 22 Sep > 2009, QQ Liu wrote: > > > Hi Bruce, > > > > Although I chose the auto-redraw in the menu of view, the picture is > > still as before. Then I choose all the options, but it's still discrete, > > which is attached in this mail. > > > > Thanks > > > > QQ > > 2009/9/21 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > >> can you try clicking redraw? > >> > >> On Mon, 21 Sep 2009, QQ Liu wrote: > >> > >> Hi Bruce, > >>> I did not click the redraw button. tksurfer cannot show the image > >>> staidly and there isn't the smooth surface. I have to put the mouse on it > >>> and click the image then I can capture the picture attached in the last > >>> mail. > >>> Not only tksurfer but also tkmedit cannot give the steady picture in the > >>> window. > >>> > >>> I only used this command: > >>> > >>> tksurfer fsaverage lh inflated -annot > >>> lh.g1v0.glmdir/onegroup/mc-z.negative.sig.ocn.annot -fthresh 2 -curv > >>> -gray > >>> > >>> Thanks. > >>> > >>> QQ > >>> > >>> 2009/9/21 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >>> > >>> it looks cool. I assume you tried clicking the redraw button? > >>>> > >>>> On Mon, 21 Sep 2009, QQ Liu wrote: > >>>> > >>>> Hi all, > >>>> > >>>>> > >>>>> When I use tksurfer to display the results of group analysis, there is > >>>>> a problem. I have to put the mouse on the image then it can be in the > >>>>> front. > >>>>> However, there is not the smooth surface as that in the tutorial of > >>>>> group > >>>>> analysis in wiki. The image showed up is just some dots in the black > >>>>> ground. > >>>>> > >>>>> > >>>>> What's wrong about this? and how to solve this problem? The image > >>>>> captured is attached in this mail. > >>>>> > >>>>> Thanks a lot. > >>>>> > >>>>> QQ > >>>>> > >>>>> > >>>>> > >>>>> > >>> > >>> > >>> > > > > > > > >

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How do Control Points and Pial Surfaces Interact?
by Sherri Novis 22 Sep '09

22 Sep '09

Hello - I am trying to compare normalized segmentation stats across groups. We are adding control points to the white matter in an attempt to push out the pial surfaces when it appears grey matter has been clipped or cut short. I am loading the following: tkmedit [SubjectID] brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white. The CPs are being saved, and after running autorecon-all the CPs are referenced in the recon-all.log file - however the pial surfaces are not redrawn around the control points. Should the white matter CPs force new pial surfaces? Am I missing a step in here? I checked the archive for the last year without luck - so I apologize if this is a repeat question. Thanks much for your help - Sherri

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Bvecs and image orientation
by Satrajit Ghosh 22 Sep '09

22 Sep '09

This question was asked on the FSL list and I thought it would be pertinent on this list as well in relation to mri_convert. ---------- Forwarded message ---------- From: Saad Jbabdi <saad(a)fmrib.ox.ac.uk> The bvecs are supposed to be relative to the image grid. On 22 Sep 2009, at 13:34, Laura Mancini wrote: Dear all, > > In FSL, do the x, y, z components of the bvecs correspond to the image > axes (i.e. along the directions of the data matrix indices), or to the > patient axes as defined in the nifti header, or something else? > > Many thanks, > Laura > ------------------------------------------------------------ when one converts a dicom data set containing diffusion data with mri_convert it generates bvecs and bvals. the bvecs are unit vectors relative to some coordinate system. is this the coordinate system of the scanner or the coordinate system of the image volume? cheers, satra

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Getting Started
by Weisinger, Brian (NIH/OD) [E] 22 Sep '09

22 Sep '09

I must be really cpu challenged because I can't even seem to get this thing started. I am trying to perform basic set up right now. I have downloaded freesurfer so far and in the freesurfer setup and configuration section of the wiki I have been able to If using bash or sh, type: export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh And I do have this come up in the window. Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Now this is where my problems start I would like to do this but I do not see any of these files anywhere. I am using bash but I do not see the corresponding .bashrc file anywhere to include the export and source commands. Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). Also I am having trouble with the license step.I tried making the .license file and pasting my information in as well as trying the ways suggested in previous peoples problems (using pico). I guess I am having a problem understanding where my $FREESURFER_HOME is located to put my .lisence file. I am still fresh to using the unix terminal so I apologize if my problem is due to my inexperience but if you could help me out I would really appreciate it. Thank you

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Freesurfer September 2009