Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Overlay significant regions
by Dr. Claudia Wheeler-Kingshott 01 May '09

01 May '09

Hi, We have done our region of interest statistical analysis in Stata and we now would like to display the significant regions over the brain template. I guess we need to have images of each individual region in order to do so. Does Freesurfer provide an individual image per each anatomical ROI defined in the atlas, so that we can overlay only some of the regions? best wishes Claudia -- ------------------------------------- Claudia Wheeler-Kingshott, PhD Senior Lecturer in Magnetic Resonance Physics Department of Neuroinflammation Institute of Neurology, UCL Queen Square London WC1N 3BG tel. 0207 8373611 x4301 email: c.wheeler-kingshott(a)ion.ucl.ac.uk

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Bus error testing tksurfer on OSX leopard
by Marco Castellaro 01 May '09

01 May '09

Hi Guys, I have a problem testing the installation of freesurfer on my new macbook pro, my configuration is: OSX Leopard v. 10.5.6 freesurfer-Darwin-leopard-i686-stable-pub-v4.3.0 when I try: tksurfer bert rh pial (suggested in testing page on the wiki) I receive Bus error message. tkmedit and qdec work!!!! Any ideas?? Marco Castellaro Department of Information Engineering (DEI) University of Padova marco(a)castellaro.net

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NIfTI / Analyze Quick Look Plugin
by hui Zhang 01 May '09

01 May '09

This tool could be of general interest to the freesurfer users. The description of the tool and its usage example are included below. Check it out. Best regards, Gary Hui Zhang ================================================== About DTI-TK NIfTI Quick Look Plugin for Mac OS X Leopard This plugin uses the Mac OS X Leopard's built-in innovative Quick Look framework to enable a quick assessment of any 3-dimensional image volume in the supported medical image formats (NIfTI and Analyze) directly from the Finder. Using the Finder?s Cover Flow mode, a large collection of medical images can be browsed through and quickly inspected just as easy as flipping through your photos. Furthermore, a large number of images can be compared side-by-side by selecting them together in the Finder, then pressing the space bar to bring up the Quick Look preview mode. Screenshot showing the cover flow mode: http://www.nitrc.org/project/list_screenshots.php?group_id=207&screenshot_i… Screenshot showing the full screen multi-volume side-by-side preview http://www.nitrc.org/project/list_screenshots.php?group_id=207&screenshot_i… Homepage: http://www.nitrc.org/projects/dtitk Download link: http://www.nitrc.org/frs/?group_id=207

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unsubscribe
by Bird, Anne 30 Apr '09

30 Apr '09

Please unsubscribe me from the list. Thanks! ______________________________________________ Anne C. Bird, M.S. Clinical Research Coordinator Memory and Aging Center 350 Parnassus Avenue Suite 905 University of California-San Francisco San Francisco, California 94143 Telephone: 415-476-2918 Email: abird(a)memory.ucsf.edu Website: http://memory.ucsf.edu On YouTube: www.youtube.com/ucsfmemoryandaging

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selxavg3-sess failure on analysis created with -fsv3 flag
by Jesse Friedman 30 Apr '09

30 Apr '09

Hi, I created an analysis using the -fsv3 flag and created a contrast: <mkanalysis-sess -analysis newEMerror_fsv3_std -TR 2 -paradigm error.par -designtype event-related -funcstem f0mcsm8 -tpef tpx.skip8.dat -nconditions 4 -timewindow 24 -prestim 4 -noautostimdur -fsv3> <mkcontrast-sess -contrast AScvfix -analysis newEMerror_fsv3_std -ncond 4 -wcond 0 1 0 0> and then ran selxavg3-sess: <selxavg3-sess -analysis newEMerror_fsv3_std -sf Subject_files/controlsVasd_jf.txt> which failed and gave me this error: <Computing ErrCovMtx ??? Undefined function or method 'fast_ecvm2wmtx' for input arguments of type 'double'. Error in ==> fast_selxavg3 at 492 [fsv3W fsv3AutoCor] = fast_ecvm2wmtx(ErrCovMtx);> Is this a bug, or is it that I shouldn't expect selxavg3 to work with an -fsv3 analysis in stable4? The -fsv3 flag was available in stabl4, so I gathered this meant I would be able to run selxavg3-sess in stable4. My bugr information is below. Thanks, Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.0-20090430 RedHat release: CentOS release 4.7 (Final) Kernel info: Linux 2.6.9-78.0.13.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/16/users PWD: /space/ventzl/16/users ssh vantz setenv SUBJECTS_DIR /space/ventzl/16/users cd /space/ventzl/16/users

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hardware recommendations
by Elina Pitri 30 Apr '09

30 Apr '09

Hello, Can you please recommend me hardware appropriate for Freesurfer? What are the programme's requirements? Thanks, Elina

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RE: [Freesurfer] Measuring cortical thickness with high resolution data
by Nick Schmansky 30 Apr '09

30 Apr '09

Falk, Because the -hires switch disables the use the atlas during the skull- strip step, skull-stripping is more subject to stripping too much or too little brain (which is why use of the atlas was introduced). See this tutorial for ways to correct badly stripped skull: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix I had to add the switch -wsthresh 30 to get your sample subject to skull-strip (although it still left bits and pieces which affected the white matter tesselation step). Nick On Wed, 2009-04-08 at 15:07 +0200, Falk Lüsebrink wrote: > Hi Nick, > > First I wanted to give you a little bit of feedback. I'm still processing > one volume with .6mm which is working perfectly fine until now. The skull > stripping was done really well and no manual intervention was needed. I'm > currently running autorecon3 and will have a look at the final results > pretty soon. Thanks again for your modification and the help you offered. > > But I recently tried to process the data I send to you simultaneously to see > the results of the erroneous segmentation for myself. I just ran autorecon1 > to view the brainmask.mgz and the result isn't as bad as the one you send to > me in terms of remaining dura and skull, but only the right hemisphere is > being shown and a small piece on the anterior is missing. > > I also created a new subject so no older files could somehow influence the > new process. The result is the same. The flags I used were simply -hires and > -autorecon1 (and -clean in case for the older subject), so I don't know what > might have caused this issue. > > Regards, > Falk > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: Monday, April 06, 2009 6:25 PM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Nick Schmansky' > Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution > data > > > Falk, it looks like that file was somehow converted to DOS. try: > > dos2unix recon-all > chmod a+x recon-all > > then re-run > > doug > > > On Mon, 6 Apr 2009, Falk Lüsebrink wrote: > > > Hi Nick, > > > > I tried using your modified recon-all today but as soon as I try to > process any data I receive following error message: > > > > 'nknown option: `- > > Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...]. > > > > Also it doesn't matter at all which flags I add to recon-all or if I don't > use any flags at all, the error is the same. The unmodified recon-all > performs well. > > > > Regards, > > Falk > > > > -----Original Message----- > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick > > Schmansky > > Sent: Thursday, April 02, 2009 3:28 PM > > To: Falk Lüsebrink > > Cc: Freesurfer Mailing List > > Subject: RE: [Freesurfer] Measuring cortical thickness with high > > resolution data > > > > Falk, > > > > There are no plans in the near future, but in the long term we'd like to > remove the dependence on conforming the data. > > > > It just occurred to me that you could have the best of both worlds: > > first run your data through the normal stream (conforming) up through > autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same > resolution as that created using the -hires stream, and copy it over. > > At least that would eliminate having to edit the original hires brainmask, > which would save hours of work. If i get few minutes i will try this. > > > > You can copy that recon-all over top your existing v4.x freesurfer > installation (attached again for the list). > > > > Nick > > > > > > On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote: > >> Hi Nick, > >> > >> Thank you very much. I'll have to look into that and try to process some > other volumes which might work a bit better, with less manual intervention. > >> > >> Are there any plans to improve Freesurfer in the (near) future so that > hires data can be processed within the currently available stream? > >> > >> Regards, > >> Falk > >> > >> -----Original Message----- > >> From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > >> Sent: Wednesday, April 01, 2009 7:53 PM > >> To: Falk Lüsebrink > >> Cc: Freesurfer Mailing List > >> Subject: Re: [Freesurfer] Measuring cortical thickness with high > >> resolution data > >> > >> Falk, > >> > >> Attached is a modified recon-all script where I've added a -hires switch > to force the stream to not conform the data to 1mm^3, and to not use the > atlases. > >> > >> Note that you should add the -clean flag to delete any work that had been > done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz). > >> > >> However, in working with the .8mm data that you sent me, working with > hires data will require quite a bit of manual intervention due to the fact > that the atlases normally used cannot be used. The first problem occurs in > skull-stripping, where quite a bit of dura and skull remains, and seems to > have intensity values close to gray matter. This would have to be manually > erased on each of the slices. If it is not erased (I did not do this > because of the amount of time required), then the wm.mgz file, which is what > is tessellated to create the initial surface, will be very wrong (it > tessellates the garbage surrounding the gray matter). > >> > >> See also Bruce's prior posting on the problems of working with hires data > in freesurfer. > >> > >> Nick > >> > >> > >> On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: > >>> Hi Freesurfers, > >>> > >>> > >>> > >>> Iÿÿm trying to evaluate the usefulness of high resolution scans > >>> acquired at 7T with an isometric voxel size of .6mm for the > >>> measurement of cortical thickness. The inhomogeneities are taken > >>> care of by dividing the scans with another scan of another sequence, > >>> so they are not an issue anymore. > >>> > >>> > >>> > >>> My problem is that Freesurfer usually conforms the voxel size to 1mm > >>> which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags > >>> for the recon-all process to avoid the conformation and to skip the > >>> subcortical segmentation, but another problem arises while using > >>> these flags. > >>> > >>> > >>> > >>> The error I receive is occurring after the WM Segmentation and > >>> states as follows: > >>> > >>> > >>> > >>> #-------------------------------------------- > >>> > >>> #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 > >>> > >>> > >>> > >>> cp wm.mgz wm.seg.mgz > >>> > >>> > >>> > >>> > >>> > >>> mri_segment -keep brain.mgz wm.seg.mgz > >>> > >>> > >>> > >>> preserving editing changes in output volume... > >>> > >>> doing initial intensity segmentation... > >>> > >>> using local statistics to label ambiguous voxels... > >>> > >>> computing class statistics for intensity windows... > >>> > >>> WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] > >>> > >>> GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] > >>> > >>> setting bottom of white matter range to 77.9 > >>> > >>> setting top of gray matter range to 89.4 > >>> > >>> doing initial intensity segmentation... > >>> > >>> using local statistics to label ambiguous voxels... > >>> > >>> using local geometry to label remaining ambiguous voxels... > >>> > >>> > >>> > >>> reclassifying voxels using Gaussian border classifier... > >>> > >>> > >>> > >>> removing voxels with positive offset direction... > >>> > >>> smoothing T1 volume with sigma = 0.250 > >>> > >>> removing 1-dimensional structures... > >>> > >>> thickening thin strands.... > >>> > >>> 20 segments, 4813 filled > >>> > >>> 10270 bright non-wm voxels segmented. > >>> > >>> 5589 diagonally connected voxels added... > >>> > >>> white matter segmentation took 2.4 minutes > >>> > >>> writing output to wm.seg.mgz... > >>> > >>> ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 > >>> height=320. > >>> > >>> > >>> > >>> The dimensions of the data Iÿÿm trying to process is 320 x 320 x 224 > >>> and is changed to 320 x 320 x 320 while using the ÿÿcm flag. It > >>> seems the mri_segment process canÿÿt handle any dimensions above 256 > >>> or Iÿÿm missing another flag. > >>> > >>> > >>> > >>> Does someone has any ideas about that issue? > >>> > >>> > >>> > >>> Regards, > >>> > >>> Falk > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > _______________________________________________ > > 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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Getting standard space coordinates for anatomical parcellations
by David Hawellek 30 Apr '09

30 Apr '09

Hello there, I'd like to extract standard space coordinates (in the end I would like to use MNI coods) for each vertex of a structure of an anatomical parcellation. This so far seems pretty straight forward from what I read, but I somehow got lost between coordinate systems while doing the following: - Having an aparc.annot file I created a .label file for each structure using mri_annotation2label (with the pial surface). - After reading the comments by Darren Weber, I used mris_info to get the transformation from the surfaceRAS to talairached surface RAS coordinates and applied it to the data in the label files in Matlab (Using read_label.m and Darren's freesurfer_label2tal.m instructions). - In order to get the information to MNI space then, I simply used tal2mni.m. What I see is not totally absurd, but I noticed a slight backward shift. Is it that I'm lacking a further transformation for the surface coordinates? Or do you perhaps even know a more elegant way of doing this? Thanks for the support! David ---------------------------------------------------------------- David Hawellek Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg, Germany +4940 7410 55132 d.hawellek(a)uke.uni-hamburg.de ---------------------------------------------------------------- -- Pflichtangaben gem�� Gesetz �ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit�tsklinikum Hamburg-Eppendorf K�rperschaft des �ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J�rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

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Surface area and curvature
by Richard Frye 30 Apr '09

30 Apr '09

What is the best reference regarding the calculation of surface area and surface curvature and are there any studies looking at the reliability of these measures? Thanks Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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tksurfer question
by Sebastian Moeller 29 Apr '09

29 Apr '09

Hi fellow Surfers, in 3.0.5 (Linux centos4_x86_64) I used to be able to the following from a subdirectory myscripts-anat in the subjects directory: tksurfer subjects_name lh inflated -overlay lh.sulc Now, on macosx 4.3.0 this does not work anymore. I get: ERROR: cannot find lh.sulc using: tksurfer subjects_name lh inflated -overlay ../surf/lh.sulc does work. Now, is this a difference related to the switch linux to macosx or to the switch 3.0.5 to 4.3.0? And more importantly do you consider this something you will fix, or is this something I will have to change in all my scripts? Please let me know... ahoi Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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