Freesurfer August 2004

freesurfer@nmr.mgh.harvard.edu

20 participants
30 discussions

Stripping the skull
by Wan Park 23 Aug '04

23 Aug '04

I am having problems stripping the skull. I am converting DIACOM files into COR. Do you think that it is a problem of convertion? Should I use any extension for mri_convert? I checked the original files and the image seems to be quite Ok (I used MRIConvert and then opened with medx). I will thank you very much any suggestion. Thanks again. I received this message: Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 3D bias adjustment took 3 minutes and 18 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=79 z=128 r=67 first estimation of the main basin volume: 1304691 voxels Error w=White Matter =Intensity too high (>240)...valid input ? Command Finished

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Re: [Freesurfer] Stripping the skull
by evelina＠nmr.mgh.harvard.edu 23 Aug '04

23 Aug '04

Hi Wan Try setting a few control points in the white matter of any dimmer areas of the T1 volume, and save them by selecting File --> Save Control Points. Next, get back to the mri/directory (or if you already there, make sure to move the control.dat file (control points) to SUBJECT_name/tmp/control.dat >From mri/ run your mri_normalize again using: mri_normalize -no1d -f ../tmp/control.dat orig T1 Check the voxel values of the output -- if they are in the normal range (i.e. WM 90-110 or so, then your skull strip should work. All of this is assuming the T1 volume has excessively high voxel valuues. Let me know if this works! > I am having problems stripping the skull. I am converting DIACOM files > into COR. Do you think that it is a problem of convertion? Should I use > any extension for mri_convert? I checked the original files and the > image seems to be quite Ok (I used MRIConvert and then opened with > medx). I will thank you very much any suggestion. Thanks again. > > I received this message: > > Command Finished > /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize > /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig > /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 > reading from /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig... > normalizing image... > 3d normalization pass 1 of 2 > building Voronoi diagram... > performing soap bubble smoothing... > 3d normalization pass 2 of 2 > building Voronoi diagram... > performing soap bubble smoothing... > writing output to /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 > 3D bias adjustment took 3 minutes and 18 seconds. > > Command Finished > /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed > /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 > /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain > > > ************************************************************ > The input file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 > The output file is > /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain > If this is incorrect, please exit quickly the program (Ctl-C) > > > *************************WATERSHED************************** > preflooding height equal to 25 percent > Sorting... > first estimation of the COG coord: x=127 y=79 z=128 r=67 > first estimation of the main basin volume: 1304691 voxels > Error > w=White Matter =Intensity too high (>240)...valid input ? > > Command Finished > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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tksurfer.static
by Maria Virginia Centeno 20 Aug '04

20 Aug '04

Hi ! I have the same problem with tksurfer as they detail in the mail (see link). http://www.mail-archive.com/freesurfer@mail.nmr.mgh.harvard.edu/msg00642.ht… I installed last version of freesurfer (20040218) wich doesn't have tksurfer.static. Perhaps it's in an earlier version... Can somebody send it to me ? Thanks Marivi 100mb gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo ¡Tenelo ya!

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tkmedit (development version)
by George Papadimitriou 19 Aug '04

19 Aug '04

Hi Kevin, Is the development version of tkmedit still available? I need to use it, because I can't load functional overlays using the regular version. Even though I am using the use_dev alias, I can't seem to access it (please look at example below). [hereford:~] (nmr-std-env) use_dev $Id: nmr-std-env,v 1.8 2004/08/18 16:59:33 greve Exp $ Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.2 2003/05/09 16:08:12 kteich Exp $ FREESURFER_HOME /space/lyon/1/home/inverse/freesurfer_alpha FSFAST_HOME /space/lyon/1/home/inverse/freesurfer_alpha/fsfast AFNI_DIR /space/lyon/1/home/inverse/freesurfer_alpha/afni FSL_DIR /space/lyon/1/home/inverse/freesurfer_alpha/fsl SUBJECTS_DIR /space/sake/3/users/inverse/subjects WARNING: directory /usr/bsd does not exist WARNING: directory /usr/ucb does not exist [hereford:~] (nmr-std-env) ls -l `which tkmedit` -rwxrwxr-x 1 kteich fsdev 5232854 Apr 24 2003 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tkmedit* Can you please assist? Please, let me know if you need additional info. George P.

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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.

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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

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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

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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

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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!

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Freesurfer August 2004