[Freesurfer] Longitudinal processing clarification

(Questions for all, but maybe more directed towards Martin) I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any

Re: [Freesurfer] FreeSurfer & Matlab

Sorry -- appended the wrong version of 'mris_display. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA function [hf, hp, av_filtered] = mris_display(astr_mris,

Re: [Freesurfer] FreeSurfer & Matlab

Bruce Fischl wrote: (2) Import that surface onto Matlab and visualize it there. There is such a visualizer in the 'dev' tree of FreeSurfer -- called 'mris_display'. I've appended the relevant m files -- just save to a dir on your MatLAB path. -=R -- Rudolph Pienaar, M.Eng, D.Eng / email:

Re: [Freesurfer] FreeSurfer & Matlab

Thanks all. The reason to use start FreeSurfer within Matlab would be to, for example, build a kind of integrated GUI able to accomplish DICOM -> Surface Visualization. But, for my case, its not that necessary; running FreeSurfer externally is acceptable. Thanks again for your help, Raghav O

Re: [Freesurfer] FreeSurfer & Matlab

Hi Raghav, yes, people have done visualization of surfaces in matlab, maybe Thomas (ccd) can comment. As for 2, I'm not sure I understand what you mean. Why would you need to run freesurfer from within matlab? I guess you could use eval to run recon-all if you had to, but I wouldn't think you w

[Freesurfer] FreeSurfer & Matlab

Hi all, I am working on a project that aims to: (1) Use an MRI image, skullstrip and convert the brain volume to a surface (2) Import that surface onto Matlab and visualize it there. (3) On top of that surface in Matlab, add pictures of electrodes as well as 3D "heat maps" of neural activity.

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

Thank you all for the very good and detailed advice. We reran our cluster-wise correction after lowering the initial p-value (the one which is applied to the T-maps) to 0.01 or 0.001. Interestingly we then get the very same blob like in the FDR controlled approach (supramarginal gyrus). However,

Re: [Freesurfer] rebuild_gca_atlas.csh question

those command args are correct (no dash on either). your error appears to be something pertaining to your run environment (so i'm not sure i can help with that). n. On Mon, 2010-02-01 at 12:34 -0600, Guang Zeng wrote: > Hi, there, > > I am running rebuild_gca_atlas.csh now, and met a problem at

Re: [Freesurfer] group analysis with qdec

its possible to do 1). see the 'ROI Analysis' and 'Group Analysis' tutorials under: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial although doing this seems like 'double-dipping', or 'circular analysis'. 2) is possible, as it seems like an extension of 1). n. On Sun, 2010-01-31 at 14

[Freesurfer] rebuild_gca_atlas.csh question

Hi, there, I am running rebuild_gca_atlas.csh now, and met a problem at the first mri_ca_normalize step, my rebuild_gca_atlas.log file looks like below, \n\n mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /

Re: [Freesurfer] extracting brodmann labels

not just yet! they will in the next release. however, you can easily map the labels from the fsaverage subject (included in the freesurfer/subjects dir) to your subject with something like: foreach balabel (BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 V1 V2 MT) set cmd = (mri_labe

Re: [Freesurfer] extracting brodmann labels

HI Benjamin, they should be in each subject's label directory named things like lh.BA4p.label Bruce On Mon, 1 Feb 2010, Benjamin Groisser wrote: > Hello, > > I'm trying to extract freesurfer generated labels BA4a, BA4p, and BA6. > Are these labels (#404, 405, and 406) generated for each subjec

[Freesurfer] extracting brodmann labels

Hello, I'm trying to extract freesurfer generated labels BA4a, BA4p, and BA6. Are these labels (#404, 405, and 406) generated for each subject? If so, could you please tell me which file to extract them from? I don't fully understand how freesurfer organizes these labels compared to, say, cortical

Re: [Freesurfer] Problem starting

can you send us the output and the command line? On Mon, 1 Feb 2010, Janani Dhinakaran wrote: > Hello, > I'm operating freesurfer through a virtual box. I checked the memory space > it is around 4G. It's not starting. Any idea what I can do about it? > > __

Re: [Freesurfer] GM volume and cortical thickness

Hi Joe, I think we output a volume measure for the gray matter as well - we simply multiple the thickness by the surface area. cheers Bruce On Mon, 1 Feb 2010, keepmoon wrote: > Dear developer, > > I want to compare the grey matter volume by VBM to cortical thickness > by freesurfer. But i

[Freesurfer] GM volume and cortical thickness

Dear developer, I want to compare the grey matter volume by VBM to cortical thickness by freesurfer. But in this process, I meet a problem: how to change the points number of grey matter into the same with the vertex of thickness by freesurfer? Any help will be appreciated! Best

[Freesurfer] Problem starting

Hello, I'm operating freesurfer through a virtual box. I checked the memory space it is around 4G. It's not starting. Any idea what I can do about it? -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] Segment the grey matter volume

actually none of them are transformed to MNI coords. They are all in original (scanner) coords On Mon, 1 Feb 2010, leemon albert wrote: > Hey, thanks for your prompt reply. > > One more question, in subject/mri folder, only the Orig.mgz and T1.mgz > adjust the AC-PC alignment of the image to be