Freesurfer July 2004

freesurfer@nmr.mgh.harvard.edu

16 participants
23 discussions

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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mri_normalize error
by Chekema Nayasha Prince 04 Aug '04

04 Aug '04

Hello, I'm trying to normalize an MPRAGE dataset and I received the following message from the mri_normalize: MRInormalize:could not find any valid peaks no such file or directory mri_normalize: normalization failed no such file or directory I tried to set control points ( 4 of them specifically) in the wm and tried to rerun the mri_normalize but I received the same error. my orig volume looks just like my other datasets that worked properly. Can you let me know what could be causing the error? -Keyma

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SaveSegmentation problem fixed in tkmedit
by Kevin Teich 02 Aug '04

02 Aug '04

I finally found the source of the SaveSegmentation error many of you have been getting. Download this file: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit.tcl Move it to this location: $FREESURFER_HOME/lib/tcl/tkmedit.tcl You can overwrite the existing file. -- Kevin Teich

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Re: registering functional to anatomical
by Bruce Fischl 30 Jul '04

30 Jul '04

not sure, but this is probably part of your problem (Doug?): gate [bold] tail -20 001/inorm.log > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_inorm.m at line 183 Warning: Divide by zero. > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_inorm.m at line 184 Warning: Divide by zero. > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_inorm.m at line 185 Warning: Divide by zero. > In /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_inorm.m at line 192 ??? Error using ==> betainc X must be in the interval [0,1]. Error in ==> /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/tTest.m On line 37 ==> p = betainc(z,dof/2,0.5); Error in ==> /space/lyon/1/home/inverse/freesurfer_alpha/fsfast/toolbox/fast_inorm.m On line 223 ==> tSigCor = tTest(s.ntp-2,tCor); >> Fri Jul 2 13:46:44 EDT 2004 inorm: finished On Fri, 30 Jul 2004, Tamara Knutsen wrote: > so in /space/meso/26/users/040630Edgar > i ran: > tkregister-sess -sf sf -df df -nosurf -rsd bold -fsd bold -surf white > > first setting my SUBJECTS_DIR to /space/orsay/2/knutsen > and subjectname file to edgar > > and this is what i get in the horizontal view. > > the functional data is completely unreadable, yet, when viewed in > sliceview-sess or xds, it looks fine. > > so in addition to massive orientation and scaling problems upon trying to > begin registration, now i have some weird saturation of my functional volume. > > do any of you have any ideas on how i might fix this? or can you point me in > the direction of whomever may? > > thanks, > tamara

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question
by Wan Park 30 Jul '04

30 Jul '04

Hello, I used mri_convert to transform DIACOM files to COR files. I want now to do the structural scan but I guess I need to obtain I files (eg. I.001). How can I do that? Thanks, Wan Park

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Re: [Freesurfer] problems with mris_glm
by L.Scheef＠uni-bonn.de 29 Jul '04

29 Jul '04

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problems with mris_glm
by L.Scheef＠uni-bonn.de 29 Jul '04

29 Jul '04

Hi freesurfer folks, I try to run some example cortical thickness calculations as outlined in mris_glm --help. The first step (read thickness maps, smoothing and resampling to average7 as well as saving the regression coefficient works fine, however it crashes with the complain that it does not find: /data/FreeSurf_Subjects/average7/surf/lh.white when testing the data for any effect. I wonder, where I could find the surf/lh.white (and surf/rh.white)? It is not in the diectory where it is supposed to be. Many thanks for your help in advance... Lukas PS: we are running freesurfer-20030724-Linux.tar.gzLukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef(a)uni-bonn.de

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selxavg-sess: error message
by Olivier Piguet 27 Jul '04

27 Jul '04

Good morning, I am getting the following error message whilst trying to run the selxavg-sess command: ERROR: paradigm is ill-conditioned (5.37345e+18). Check your paradigm file for file for periodicities or for some event types that all ways follow other event types (or itself). >> >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed ERROR (/autofs/space/engram_010/users/rk_fmri_test/YNS15_060404): selxavg failed What is the meaning of this message? I have checked the mail archives but couldn't find any information. I am analysing data for a retrieval memory task and the para file (number of conditions and response types) is based on the subject responses and therefore some response types may or may not be repeating themselves. Thanks Olivier -- ------------------------------------- Olivier Piguet, Ph.D. Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE 20-392 77 Massachusetts Avenue Cambridge MA 02139 USA For overnight or express deliveries, send to: 3 Cambridge Center Suite 392 Cambridge, MA 02142 USA Voice: (+ 1) 617-253-8976 Fax: (+ 1) 617-253-1504 E-mail: olivier(a)mit.edu

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mris_register: -parea, -dist
by Colleen Tuffy 27 Jul '04

27 Jul '04

Good afternoon, Could anyone out there tell me what exactly the -parea and -dist options to mris_register do? I'm working on a project comparing across a large number of brains and would like to find the optimal registration parameters before running all the morphs. But I wasn't able to get any information about mris_register flag functionality from this list's mail archive, an online search, or --help. Thanks in advance for your assistance, Colleen Tuffy UCSD Human Development Program

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labels to annot files?
by Daniel Goldenholz 22 Jul '04

22 Jul '04

Is there a command out there that converts a set of labels into an annot file automatically? It would be very useful... -- Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/

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Freesurfer July 2004