Freesurfer

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30132 discussions

qdec question
by Maria Jalbrzikowski 04 Jan '13

04 Jan '13

Dear Freesurfer users, I have a question regarding qdec and I would like your help. When conducting qdec analyses, is it possible to restrict the analyses to specific brain regions? I would like to limit my qdec analyses to brain regions typically associated with social cognition and have chosen these regions based on the existing literature. If so, could you tell me how this is done? Thank you so much for your help! Best, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles

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ghosting problem in raw anatomical images
by Skyler Gabriel Shollenbarger 04 Jan '13

04 Jan '13

Hello, We want to create a surface model in freesurfer. Our raw spgr T1-anatomical images have a bad ghosting problem. We have attached a pic to show the prob. Is there any corrections that we can do to fix this? Thanks in advance! Skyler and Jon -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee CONFIDENTIALITY NOTICE! This email transmission may contain confidential and privileged client health information that may not be re-disclosed without further written authorization by the client. The information contained in this transmission is intended for the addressee only. If the receiver of this information is not the intended recipient or an agent responsible for delivering the information to the intended recipient, you are hereby notified that you have received this document in error. Review, copying, modification, or dissemination of this information under these circumstances is strictly prohibited. IF YOU HAVE RECEIVED THIS COMMUNICATION IN ERROR, PLEASE TELEPHONE US IMMEDIATELY. Thank You.

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trac-all bval bvecs bedpostx not running
by Gerit Pfuhl 04 Jan '13

04 Jan '13

Dear all, despite reading the list and having tried various versions of the bvals and bvecs files, I still get the message in dtifit: Error: bvecs and bvals don't have the same number of entries. but it also says "trac-preproc finished without error" and the generated bvals and bvecs in folder dmri look similar to the ones from the tutorial (tab stop checked, everything done in Ubuntu, no OS Windows anywhere) but when I then try to run trac-all -bedp -c owndata the process finished after 1 min with 0 slices processes. I attach the bval and bvec files as they are from the scanner, as they are modified by me according to the tutorial instructions (1 column and 3 columns) and how they look after the cp command in the folder dmri (there is no error message during this step) Attached also the log file (error message on line 357). Regards Gerit Pfuhl

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fscalc / mris_calc problem
by Fred Lado 03 Jan '13

03 Jan '13

Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... ---------------------- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses & North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladofred(a)gmail.com

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Brain imaging PhD trainee project available at the Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
by Diederick Stoffers 03 Jan '13

03 Jan '13

Dear all, Please find attached a description of PhD trainee project available at the Netherlands Institute for Neuroscience, Amsterdam, The Netherlands, that I am posting on behalf of my group leader. Relevant keywords for this project are sleep, emotion, arousal, high-density EEG, fMRI, insomnia and internet. Cheers, Diederick

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FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 02 Jan '13

02 Jan '13

HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff

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gca atlas creation
by Gabriel Gonzalez Escamilla 02 Jan '13

02 Jan '13

2 1

about ROI to SPSS
by xiangbo_2010 02 Jan '13

02 Jan '13

Dear experts I has obtained a ROI with attachment, and extract it to analysis using SPSS, but find that there no significant in these ROI, theother conditionsare consistent, I hope that have experts to help me, thanks! Bo Xiang

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about ROI
by xiangbo_2010 02 Jan '13

02 Jan '13

Dear experts I has obtained the ROI by analysis, I want to obtain the label of this ROI, whether has the command to direct keep label, not drawing this ROI? thanks! Bo Xiang

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white/gray surface and volumetric segmentation (aseg) difference...
by Gonzalo Rojas Costa 31 Dec '12

31 Dec '12

Hi: With some mprage images, I got differences in the volumetric segmentation (aseg) of the cortex and the white/gray surface... Why ?... I know that both methods are totally different... In the aseg I got some bad segmentation of the cortex, but it in the white/gray surface I got very better results... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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