Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

question about mris_ca_train
by Guang Zeng 07 Jan '10

07 Jan '10

Hi, there, I have created our own template and am creating our own atlas now. I have annotation files for each subject in my training set, and my mris_ca_train command line is: mris_ca_train -n 2 -t /home/freesurfer-install/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot custom_1 custom_2 custom_3 custom_4 lh_myatlas.gcs my question is here, I should use the lh.sphere.reg file which register the sphere to the FS default template or the registration file which register the sphere to my own template? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390707/direct/01/

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tkmedit : Functional RAS to Functional index
by Oya, Hiroyuki 07 Jan '10

07 Jan '10

Hello Experts, Transformation from Volume RAS to Functional RAS is done with anat2exf.reg.dat. But how does tkmedit calculate Functional index from Functional RAS ? Thank you in advance. Hiroyuki

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Re: [Freesurfer] --bg option for mri_glmfit-sim
by Douglas N Greve 07 Jan '10

07 Jan '10

You can only run it on one node. The problem is going to be that you can't submit it to a scheduler. You'd have to ssh into the node and run it from the cmd line. doug Xiangchuan Chen wrote: > Dear FreeSurfer experts, > > Our cluster has 8 nodes. Each node has 8 cpu cores sharing 8GB ram. So, if I > want to apply --bg option when running mri_glmfit-sim on this cluster, which > value I can set for it: <8 or <64? > > Thanks in advance, > > Xiangchuan Chen > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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--bg option for mri_glmfit-sim
by Xiangchuan Chen 07 Jan '10

07 Jan '10

Dear FreeSurfer experts, Our cluster has 8 nodes. Each node has 8 cpu cores sharing 8GB ram. So, if I want to apply --bg option when running mri_glmfit-sim on this cluster, which value I can set for it: <8 or <64? Thanks in advance, Xiangchuan Chen

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Voxel correspondence from Functional to Structural
by Oya, Hiroyuki 07 Jan '10

07 Jan '10

Dear Experts, I would like to find the voxel correspondence from FSL functional volume (tstat volume) to FSL structural volume (orig.mgz) in a subject explicitly. Is it enough to use anat2exf.reg.dat transformation matrix (I have already processed functional data with reg-feat2anat)? Thank you very much. Hiroyuki

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anat2exf.reg.dat
by Oya, Hiroyuki 06 Jan '10

06 Jan '10

Deal all, A basic question. What is the first 3raws in anat2exf.reg.dat ? Many thanks. Hiroyuki

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w file overlay tkmedit - surface to volume?
by Nela Cicmil 06 Jan '10

06 Jan '10

Dear all, I'm at a dead end and would be really grateful if anyone can help out: I have exported MEG source data into w file format and would like to overlay this data on the anatomical MRI volume images i.e. like the images seen in the tkmedit viewer. Is this type of display possible, and if so what is the best way to do it? I've checked that the w files are easily visualized on the brain surfaces in the mne_analyze viewer and also in tksurfer, but when I try to overlay them onto tkmedit (either direct from terminal or through mne_analyze) I get this error: Error: Loading functional overlay .../*-rh.w. Couldn't load MRI volume. Tkmedit couldn't read the functional volume you specified. This could be because the volume wasn't found or was unreadable, or because a valid header type couldn't be find, or a registration file couldn't be found or opened. I assume that this error is because the w files are in surface format whilst tkmedit requires its overlays to be in volume format, so perhaps they need to be converted with mri_surf2vol - does anyone know what are the necessary arguments to acheive this with a w file? Alternatively, is there another way to show the w files, or other type of MEG source data format, on anatomical MRI volume images? Thanks for your help, Nela PS. I originally sent this query to the MNE mail-list, but perhaps this is really a freesurfer issue... ---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford

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libstdc++ problem
by Angel Wong 06 Jan '10

06 Jan '10

Hi Freesurfer experts We recently purchased a workstation with RedHat Enterprise Linux 5 installed. We then installed freesurfer (stable v4.5.0) on the workstation. But when we executed 'mri_convert' command, it prompted out the following errors: mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) Currently, our gcc version is 'gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)', and our libstdc++.so.6 found in /usr/lib64/ is redirected to libstdc++.so.6.0.8. This may explain why we cannot execute 'mri_convert' properly as our current versions of gcc and libstdc++ are a bit old. We have searched for libstdc++ rpm on the web, but we cannot find a suitable one for RHEL 5 (either we can find a libstdc++ rpm for Centos 5, but it doesn't provide version 'GLIBCXX_3.4.9' or above, or we can find one with 'GLIBCXX_3.4.11', but it only supports Fedora or OpenSuSE. So we would like to know if there is any way to solve the problem. Is there any source code of libstdc++ that we can build for RHEL 5, or any other better alternative solution for solving it? Thank you in advance. Angel

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How to make the average freesurfer surface in surfstat?
by leemon albert 06 Jan '10

06 Jan '10

Hey. The invidual Freesurfer surface and thickness file can be loaded into surfstat correctly. But the number of vertex varied a bit among subjects in Freesurfer. So when performing the surfstat analysis, I always met the error as follows. I am very curious how to fix it? Thank you in advance. avsurf = SurfStatAvSurf( filesboth ); 36 x 2 files to read, % remaining: 100 ??? Error using ==> plus Matrix dimensions must agree. Error in ==> SurfStatAvSurf at 36 surf.coord=fun(surf.coord,double(s.coord)); >> SurfStatReadSurf(filesboth(1,:)) ans = tri: [598010x3 int32] coord: [3x299009 double] >> SurfStatReadSurf(filesboth(2,:)) ans = tri: [621056x3 int32] coord: [3x310532 double] >> SurfStatReadSurf(filesboth(3,:)) ans = tri: [518412x3 int32] coord: [3x259210 double] Best wishes, -- Meng Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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skull strip question...
by Gonzalo Rojas Costa 05 Jan '10

05 Jan '10

Hi: The tissue located in volume index coordinates (164, 54, 137) approx in the skull stripped volume that I am sending, could produce an error in the cortical thickness values for example, or any other parameters that freesurfer computes ?... I uploaded the files through your upload web page... Sincerely, Gonzalo Rojas Costa

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