Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

ROI illustration
by Liukarl 04 May '11

04 May '11

Hello. Freesurfer experts: After autorecon3, Freesurfer generates the thickness measure of pre-defined ROIs from Desikan’s parcellation. Now I want to make a picture illustration of thickness but only with rostral middle frontal ROI. My questions are: 1 which surface would be fit for the illustration purpose, the pial surface? 2 how can I only color label the rostral middle frontal ROI without any other regions? And any way to export high resolution of picture from Freesurfer? Thanks in advance! Karl

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subcortical volume and qdec
by 汪贵宏 04 May '11

04 May '11

Dear freesurfer experts: I had processed my data with recon-all, and also ,I had compared the cortical thickness difference between the con and pat with qdec .however,when i I try to compare the sub-cortical volume difference between con and pat ,the results were the same as the thickness,even in Analysis Results window,the option is not changed,as the "Does the average thickness differ between con and pat?" So, I have no idea about it,because I chose the ASEG.VOLUME in the "Stats Data Import" window. In addition ,I wander whether the volume differ comparison is processed based on ROI or vertex? Did anyone can help me with any suggestion. thank you wang

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[New release] - iSurf Brainview 2.1.1
by Pedro Paulo de Magalhães Oliveira Junior 04 May '11

04 May '11

Today it was released a new upgrade of iSurf Brainview. (2.1.1) *New features: * Phone / IPod Touch - IPhone now show webpage with structure description when you tap the name of the structure All iOS - More structures with webpage description - Cache webpages for speedup As usual suggestions are welcome. Upcoming features should include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr.

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A problem about mri_glmfit result
by soft.join Huang 04 May '11

04 May '11

Hi all, I'm working on a group analysis using mri_glmfit. In analysis directory, I got a X.mat file which containing the matrix X ( size 50x4 ) used to regress analysis, also the beta value from beta.mgh file. Strangely, I loaded the X.mat in Matlab and recalculated the beta using function regress in matlab, but got a different result from that of mri_glmfit. I don't know where the problem is, is there any difference in algorithm between mri_glmfit and matlab function regress( regress(Y,X) )? or I made some mistakes during the procedure. The X.mat file and the dependent variable Y.mat are in the attachment. Thanks in advance Lijie Huang

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resample data to surface that is already in conformed space
by GREGORY R KIRK 03 May '11

03 May '11

I have probabilistic tractography output that is already in freesurfer conformed space, i need to resample it onto the cortical surface, how can I ? i.e. mri_vol2surf does not have an option for the data already being in registration ( requires transform. i know i can load in freesurfer and save but i have hundrends of subjects and many seed regions thank you greg

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Openmi version of freesurfer
by Knut J Bjuland 03 May '11

03 May '11

HI is ther any plans to produce an version of freesurfer for openmpi and/or cuda 4.0? Do Anders Dale produce an version of freesurfer for openmi interface that enable use of freesurfer on supercomputer? Knut J Bjuland

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How to determine gray matter in the aseg.mgz
by Lucas Eggert 03 May '11

03 May '11

Dear Experts, I would like to generate a gray matter mask using the aparc+aseg.mgz file. Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify). Or is there a easier way to create a gray matter mask? Thank you very much in advance! Best regards, Lucas Eggert -- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany Phone: +49-541-969-44-28 Website: http://www.cogsci.uni-osnabrueck.de/~leggert/

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Neuroimaging position
by Centre Recerca Cognitiva 03 May '11

03 May '11

Applications are invited for a position at a Hospital Research Center in Barcelona, Spain. The position is full-time for 15 months (with a probable extension to 18 months). It entails working mainly on neuroimaging data. The postholder will help in analyzing functional, structural, and diffusion tensor data. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of Freesurfer, SPM and programming skills in MATLAB. The position is available to start 1st of September 2011. Annual salary will be around €26,000 (plus social security, health and unemployment benefits). Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, all in one pdf file) to cenicogni(a)gmail.com, with the subject line "Neuroimaging position".

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question regarding the comparison of two methods
by Jacobs H (NP) 03 May '11

03 May '11

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothed both data sets. Now we are trying to convert the structure from our method to FreeSurfer space (256 x 256). Then, our plan was to put all the data of the structures of both methods all the subjects together (4D) and to run mri_glmfit (comparing method one with method two). Does this seems logically? But, we were wondering how we should deal with the warping towards the fsaverage (which is ofcourse not similar to the subcortical structure) in the mri_glmfit? Do you have any idea? Thank you very much. Best Heidi Jacobs [cid:149263716@29042011-1A80] Heidi Jacobs, MSc. PhD student Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Alzheimer Center Limburg Division Cognitive Neuropsychiatry and Clinical Neurosciences h.jacobs(a)maastrichtuniversity.nl <mailto:h.jacobs@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 Note: the email addresses have changed! [cid:149263716@29042011-1A87] Please consider your environmental responsibility before printing this e-mail.

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Compiling stats file for ROI label in QDec
by Krista Kelly 02 May '11

02 May '11

Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats file (lh.G_cuneus.stats) that corresponds to this ROI for each participant in my group. Is there a quick way to compile cortical thickness data for this ROI from all participants? The manual suggests using aparcstats2table but I'm not sure how to select the stats for just this one ROI. Any help would be appreciated!

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Freesurfer May 2011