Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30051 discussions

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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overlay problems
by Nguyen, Thang Q 19 Jul '04

19 Jul '04

Hello all, I have been trying to overlay PET data. When I open tkregister2, it shows the data as a gigantic white block. However, when I open my PET images in SPM, they look fine. I have tried searching the email archives and have not found an answer. What could this possibly be? Thanks, Thang ------------------------ Thang Nguyen Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine Email: thangqn(a)uci.edu This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

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moving a label in tkmedit
by Chekema Nayasha Prince 14 Jul '04

14 Jul '04

Can you move a label to a new location that has already been drawn in tkmedit without redrawing the label ? -Keyma

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new segmentation error
by Chekema Nayasha Prince 14 Jul '04

14 Jul '04

I used the new segmentation in tkmedit to draw labels in the orig volume. When I went to "File-> Save segmentation As" and tried to same it in a new directory I got the following error: "Error:Invalid Command Name "Save Segmentation"" Is there another way to save the segmentation volume? -Keyma

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