Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

mritotal not found
by Eswar Damaraju 16 Aug '04

16 Aug '04

Hi, I'm experiencing the following problem when I try to talairach a subjects anatomical data. I get the same message below when I run both $ talairach sid (or) $ recon-all -stage1 -sid sid ---------------------------------------------------------- registering bert mri_convert orig orig/orig.mnc reading from orig... TR=0.00, te=0.00, flip angle=0.00 i_ras = (-1, -0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) writing to orig/orig.mnc... /home/edamaraju/Version03/freesurfer/bin/noarch/talairach: /usr/pubsw/packages/mni/current/bin/mritotal: /usr/pubsw/bin/perl: bad interpreter: No such file or directory ------------------------------------------------------------ All other commands that I tried have worked well. My path includes the mni directory required. -------------------------------------------------------- $ echo $path /bin /usr/bin /usr/X11R6/bin /usr/local/bin /usr/X11R6/bin /home/edamaraju/abin /home/edamaraju/abin /home/edamaraju/Version03/freesurfer/fsfast/bin /home/edamaraju/Version03/freesurfer/fsfast/bin/Linux /home/edamaraju/Version03/freesurfer/local/bin/Linux /home/edamaraju/Version03/freesurfer/bin/noarch /home/edamaraju/Version03/freesurfer/bin/Linux /home/edamaraju/Version03/freesurfer/fsl/bin /home/edamaraju/Version03/freesurfer/afni/Linux /usr/pubsw/packages/mni/current/bin ----------------------------------------------------------- It does not recognize the file mritotal even when I cd into the /usr/pubsw/packages/mni/current/bin directory. what could be the problem? I use RedHat linux 9 OS. Thanks, Eswar.

2 1

RAS coordinates, subject A to subject B, C, D etc.
by Darren Weber 16 Aug '04

16 Aug '04

Dear Doug et al., We have selected a few vertex coordinates in subject-A and noted down the RAS coordinates into a file. We want to get the closest vertices in a group of subjects to these vertices from subject-A, using the freesurfer spherical registration transforms. Looking at mri_surf2surf, it seems that it might do the job. However, the vertex RAS coodinates for subject-A are just recorded in an ascii text file with rows of XYZ values. Should we create a dummy .w or .paint file format or is there another function that will work with an ascii file of vertex XYZ values in the RAS coordinate space? We have selected only a small set of vertices (about 25 vertices). Take care, Darren -- Darren L. Weber Postdoctoral Fellow, Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94143-0946, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber Address for express mail/deliveries: 185 Berry Street, Suite 350, San Francisco, CA 94107 "People travel to wonder at the height of the mountains, at the huge waves of the seas, at the long courses of the rivers, at the vast compass of the ocean, at the circular motion of the stars; and they pass by themselves without wondering." --St. Augustine (b. 354, d. 430) "A good traveler has no fixed plan and is not intent on arriving." --Lao Tzu

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decimation of a scalp surface with tksurfer
by Stefan Tomic 16 Aug '04

16 Aug '04

Dear list, Does anyone know where I might find a description of the decimation algorithm used in tksurfer? I am decimating a scalp surface in tksurfer with some success. I am using the tool because it produces a relatively homogenous subsampling. However, it produces exactly the same subsampling on a given scalp surface for any value that I enter for the "spacing" setting. I would like to be able to control the degree of subsampling. I realize that I'm using the tool in a non-conventional way. It seems to me that the decimation algorithm is using surface curvature in some way, which is likely why I am not able to control the degree of decimation on a scalp surface. If anyone has any thoughts on this, or could point me to any documentation, I'd be really grateful. Best regards, Stefan Tomic

3 3

title of the grant
by Bruce Fischl 12 Aug '04

12 Aug '04

for anyone willing to write letters, I think we will call it: Software tools for analyzing cortical structure and connectivity I didn't make this clear before, but we'll need letters mailed to us on letterhead stationary with signatures. thanks, Bruce -------------------------------------------------------- Bruce Fischl email: fischl(a)nmr.mgh.harvard.edu Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2301, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA

3 2

How to display lh.average.tif
by XJ Kang 12 Aug '04

12 Aug '04

Hi, I am trying to convert and display the average template ?h.average.tif. I already used "mrisp_paint" to get the average curve file "lh.avg_curv". How to display the file? Or convert it to an ascii file? Thanks in advance. XJ Kang

3 2

preventative maintenance
by Mark A. Pinsk 12 Aug '04

12 Aug '04

We've noticed that when Siemens performs their quarterly preventative maintenance (PM) on our Allegra scanner that the shape/size of our mprages changes after the system is brought to spec. This may pose a problem if we scan a subject before a PM to create a surface reconstruction, and then scan the same subject again after a PM and want to align the data to the surface volume. Has anyone encountered this problem at their site, and if so, how have they dealt with it? One option we considered is just stopping the PMs, but that wasn't advised by Siemens. Another option is to use some non-linear transformation tool on the software end. Any advice, especially from other Siemens Allegra sites, would be greatly appreciated. Thanks Mark Pinsk _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

1 0

QA and documentation
by Bruce Fischl 12 Aug '04

12 Aug '04

Hi All, I have a favor to ask. We are trying to generate funding to hire a person to do quality assurance, and another to generate documentation, but it has been difficult. We are currently writing a grant explicitly for these positions, and one of the requirements of the funding mechanism is to show that there is a community that would benefit from the proposed resource. That said, it would be a huge help if as many people who use freesurfer as possible would send me letters of support indicating how having such people to work on these things would help their research. Even better, if the research is NIH funded and you could indicate tthe grant that would benefit. I'll append my mailing address. I you are interested, send me email, and I'll send you the offical title of the grant when we finalize it. This will probably be the most boring grant ever written, and I think the only possibility we have for getting it funded is to really document the extensive need for such positions, which I think are absolutely critical as the software has increased in complexity. We know there are bugs in it, it's just a question of putting the effort into finding them :). thanks, Bruce -------------------------------------------------------- Bruce Fischl email: fischl(a)nmr.mgh.harvard.edu Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2301, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA

1 0

overview of motion correction
by Chekema Nayasha Prince 12 Aug '04

12 Aug '04

I would like to take 3 different scan volumes of the same subject and compare their parcellation values. I want to make sure that motion between the scans will not change the parcellation values. Is mri_motion_correct the proper tool to use for aligning the scans before proceeding with the processing stream? -Keyma

2 5

mri_motion_correct
by Chekema Nayasha Prince 11 Aug '04

11 Aug '04

Can you use mri_motion_correct to align orig volumes from 2 different scans without averaging the volumes in the output? -Keyma

1 0

Viewing FEAT statistics on Freesurfer surface
by Yung Lyou 06 Aug '04

06 Aug '04

hi, I have been using the FSL&Freesurfer interoperation webpage http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html as a guide to overlay the functional data processed using FSL. When I try to view the FEAT statistics on the surfrace using tksurfer by calling the script "qsurfer" i run into a command not identified error. All my efforts to find this command has proven fruitless and I'm starting to think that i must have somehow erased the script or not installed it when I downloaded the Freesurfer package. I was wondering if someone could tell me where this script lives in the Freesurfer package and what it does. thanks, Yung

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Freesurfer