[Freesurfer] standardized community affiliation vector

*Dear Colleagues,* I am sorry if my question is a bit out-of-topic... I wonder if there is a an opportunity to find a community affiliation vector estimated using any of the large-scale datasets (like the Human Connectome Project, for example).. I was just thinking that having independently

[Freesurfer] data qcached in different FS versions

(REF: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19370.html)? Of note, I am going to use unsmoothed output. *===* *Best Regards,* *Alexander Lebedev* Stavanger University Hospital, Norway ___ Freesurfer mailing list Freesurfer

[Freesurfer] Extracting SUV values from Freesurfer ROIs

to extract standardized uptake values from the Freesurfer's ROIs (aparc.a2009s+aseg.mgz) in native space. Is there a straightforward way to do this? (preferably, in one command without creating multiple labels from the parcellation) Thank you very much in advance. *===* *Best Regards,* *Alexander Lebedev

Re: [Freesurfer] vertex extraction

* Alexander Lebedev awl...@rambler.ru [Tue, 31 Jan 2012 01:50:03 +0400]: Hello Doug! Thank you so much! Sorry, I've just noticed a mistake... My matrix is 327684x2: the 1st column denotes vertex numbers and the 2nd one contains corresponding regression coefficients... I will try to display

Re: [Freesurfer] persistent bvecs error

I apologize for being late (I just want to finalize this thread). The error was produced even after resaving the bvecs spreadsheet in openoffice. The issue was solved after setting both bvals and bvecs manually using nano. --- Regards, Alex * Alexander Lebedev awl...@rambler.ru [Fri, 02 Dec

Re: [Freesurfer] vertex extraction

-by-327684 matrix (I assume that this is left and right hemis), then a.vol = permute(D(:,1:163842),[2 3 4 1]); MRIwrite(a,'lh.yourdata.mgh'); b.vol = permute(D(:,163843:end),[2 3 4 1]); MRIwrite(b,'rh.yourdata.mgh'); doug Alexander Lebedev wrote: Excuse me for disturbing Douglas

[Freesurfer] vertex extraction

lh.$i.asc done It works fine, but I'm just wondering if there is an easy opportunity to combine the vertices from each subject into one big N-by-V matrix (N - subject № , V- vertex №). Thank you very much for your time! -- Regards, Alexander Lebedev Stavanger University Hospital, Norway

Re: [Freesurfer] vertex extraction

(); for (x in a) { u- t(read.table(x, sep = , header=F, quote=)[, 5]); result - rbind (result, u) }; *** [do the same for the Left H/S and afterwards just concatenate them via 'cbind'] --- Alex * Alexander Lebedev awl...@rambler.ru [Wed, 25 Jan 2012 13:01:32 +0400]: Dear Freesurfer users

Re: [Freesurfer] persistent bvecs error

Hello Anastasia! Thank you very much for your response! My bvecs and bvals were created by saving excel spreadsheet as a tab delimited file on mac. I reformated my bvecs manually using nano and reran the preprocessing. Unfortunately, it exited with the same error. I'm providing you my reformated

[Freesurfer] Interpretation of the curvature analysis

Dear Freesurfer Users! Is it wise to interpret the increased curvature index in neurodegenerative disorders as a more expressed atrophy (which manifests as a flattening)... I am just doubting because I have never worked with curvature analysis previously and its interpretations in different

[Freesurfer] Cluster-wise simulation in small samples

Dear Freesurfers, Could you please tell me about your experience with cluster-wise correction for multiple comparisons in relatively small samples. For instance, is it wise to use CWS for regression with one continuos variable in n=30 sample? --- Regards, Alex

Re: [Freesurfer] Using different versions of FS for the same dataset (5.0 and 5.1)

Thank you very much for your response! May I also ask how about running CUDA and non-CUDA analyses for the same dataset? I am asking because I don't have CUDA support on one of my machines as well (It has ATI videocard). I have found a thread on that topic

[Freesurfer] Using different versions of FS for the same dataset (5.0 and 5.1)

Dear Freesurfer users and developers, I apologize if this question sounds rhetorically or maybe it has been asked previously (I didn't find the answers in the archives). But here it is... I have a big dataset of images and several workstations. I started the analysis on the first one and

[Freesurfer] extracting segmented images with exact values for GM-WM-VL-CSF

Dear FSL users and developers, Please, forgive me for such questions - I am asking because I'm really stuck with it... Would you be so kind to explain me how can I extract segmented image with values for GM-WM-VL(ventricular)-CSF of 150-250-50-10? Purpose: preparation for the high-dimensional

[Freesurfer] extracting segmented images with exact values for GM-WM-VL-CSF

Sorry, that's of course directed to FREESURFER users and developers, and maybe there is a possibility to extract such images cerebellum-stripped? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] tksurfer display problem

, Alexander Lebedev I.P. Pavlov State Medical University 197022, Lev Tolstoy str. 6/8 Saint Petersburg, Russian Federation tel.:+7-921-441-79-42 e-mail: awl...@rambler.ru Skype ID: alexander.vl.lebedev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Continuation of my futile attempts at configuring ATI videocard driver for Freesurfer=)

DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 EndSubSection EndSection = Thank you beforehand. -- Best Regards, Alexander Lebedev

[Freesurfer] segfault error after reinstallation of ati videocard driver

you by trifles. But honestly I tried my best to find a solution (as well as .xdebug_tkmedit) and I keep being stuck at running tkmedit. I am providing a bug report. Would you be so kind to help me in solving this problem? -- Best Regards, Alexander Lebedev. I.P. Pavlov State Medical

[Freesurfer] unable to download data from wiki page

freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz]. Would you be so kind to provide me any other links to this archive? Thank you beforehand. -- Best Regards, Alexander Lebedev