Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mri_convert 001.mgz looks bad
by Angela Wang 04 Feb '09

04 Feb '09

I am using mri_convert to convert some MR images in dicom format to 001.mgz. When I view 001.mgz, using tkmedit, each transaxial slice looks like it is pieced together from the wrong slice of the original transaxials. As I progress from one slice to the next, this band moves across the image. It shouldn't look like this, should it?. Is there something I can do to prevent this when converting to mgz format? Angela

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Research Assistant Positions in Structural and Functional Neuroimaging (Boston)
by Stephanie Lee 04 Feb '09

04 Feb '09

Posted on behalf of Dr. H. Diana Rosas: Research Assistant Positions Available in structural and functional neuroimaging. Massachusetts General Hospital-Athinoula A. Martinos Center for Biomedical Imaging, Charlestown MA PLEASE POST FOR ALL INTERESTED PARTIES. START DATE: Immediately Full-time research assistant positions are available in structural and functional magnetic resonance imaging at the Athinoula A. Martinos Center for Biomedical Imaging in the Department of Radiology at Massachusetts General Hospital. The research assistant position will focus on the application of structural and functional image analysis procedures in the study of brain aging and neurological diseases including Alzheimer's and Huntington's disease. Other tasks include participant scanning, data organization, statistical analysis, and additional lab duties. This individual will be working with patients, so excellent interpersonal, organizational and communication skills are required. This position requires a Bachelor of Arts or Bachelor of Science degree, and some prior research experience is preferred. Familiarity with Linux/Unix and Matlab would be extremely useful. A two year commitment is required. This is an excellent position for a recent college graduate who wants to spend two or more years in a research setting before going on to graduate or medical school. Please send a resume and cover letter or questions to: Dr. H. Diana Rosas, MD rosas AT HELIX.MGH.HARVARD.EDU

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questions
by Silvia biopanda 04 Feb '09

04 Feb '09

1) I need to do the manual segmentation of the hippocampus with freesurfer. How can I do that? 2) How can I export the segmentated image to the binary format? Thanks, Silvia

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Qdec version and covariates
by Vina Goghari 03 Feb '09

03 Feb '09

Hello Freesurfer group, I have a couple of questions - I'm using FreeSurfer 4.0.3 to recon-all my data. I've started using Qdec and I realized that it won't accept more that 4 variables to be selected. I would like diagnosis to be my main variable and then age, gender, and scanner version as covariates. Do you know if there is a different version of Qdec that would allow me to do that analysis and if it is a problem to use data processed with a different prior version with it? Thanks, Vina

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Talairach X axis seems to be inverted between tkmedit and tksurfer
by Thomas Wallis 03 Feb '09

03 Feb '09

Hello, I have recently started using freesurfer for reconstruction. If I note the Talairach coordinate of a vertex in the left hemisphere in tksurfer, then enter this coordinate into tkmedit, the point appears on the right of the image (i.e. in the "right" hemisphere). Is this as it should be, or have I made a mistake somewhere? I couldn't seem to find anything documenting this in the wiki. Regards Tom Wallis

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ROI
by Kelly Silva 03 Feb '09

03 Feb '09

Hello, I´ sending an image and I need to create a ROI with this results. How can I do that? Thanks and best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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thresholds for segmentation
by Bai Xue 03 Feb '09

03 Feb '09

Hi, What is the different thresholds set in Freesurfer for segmenting white matter, grey matter and CSF? Thanks a lot! Bai

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read_surf/patch issue
by Keller, Corey J. 02 Feb '09

02 Feb '09

Hi Freesurfers, I am having some issues plotting a reconstructed brain in matlab. I have used the read_surf function to load in the pial surface file lh.pial and save the lh_pial.vert and lh_pial.tri. I get the following output: fv.vertices fv.faces] = read_surf('lh.pial') fv = vertices: [140817x3 double] faces: [281630x3 double] h = patch(fv,'FaceColor',[.5 .5 .5]) ??? Error using ==> patch Faces values must be >= 1.0. My first 10 face values are: fv.faces(1:10,1:3) ans = 0 1 5 6 5 1 0 26 1 27 1 26 0 5 26 39 26 5 1 2 6 7 6 2 1 27 28 1 28 2 This seems to be the issue because every other row the faces values are greater than zero. Do you know why all of my recon output pial files look like this and how I can fix the issue. Thanks. Best, Corey

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lGI value aberrantly too high but no topological defect
by Christian Scheel 02 Feb '09

02 Feb '09

Dear all, I have successfully run 'recon-all -lgi' for all my subjects. However the computation process stopped in one of the brains claiming an lGI vertex value was aberrantly too high and giving me the following error message: ##### ... remeasuring lGI value for vertex iV = 32501. It may take a few minutes. WARNING -- Problem for vertex iV = 32501, lGI value is aberrantly high (lGI=40.5282)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/home/freesurfer/christian/34/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! ##### I have already restarted the computation twice without success. The script always crashes at the same vertex. The error message and the wiki page mention such an error in connection with possible topological defects. However when I check the mris_euler_number for the subject's rh.pial it interestingly does not show me any topological defect. Here is the output: ##### [freesurfer@localhost ~/christian]$ mris_euler_number /home/freesurfer/christian/34/surf/rh.pial euler # = v-e+f = 2g-2: 133775 - 401319 + 267546 = 2 --> 0 holes F =2V-4: 267546 = 267550-4 (0) 2E=3F: 802638 = 802638 (0) total defect index = 0 ##### In all other brains the lGI calculation was successful. Does anyone of you have an idea? Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry

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cortical thickness maps
by Feng-Xian 01 Feb '09

01 Feb '09

Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer to Windows XP? Thanks in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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