Re: [Freesurfer] Multimodality analysis in FreeSurfer

I've mapped cortical thickness and the myelination data onto the fsaverage, and also used general linear modelling to investigate the one sample group mean of myelination data og cortical thickness (not very useful since the mean thickness or myelination should never be 0) data separately. I w

[Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)

I'd be very grateful for any help provided on this matter. It has been close to three weeks since I started trying to compile freesurfer from its sources (CSV stable5) on 32bit ubuntu ver. 10.04. I followed to the letter the recipe outlined in: http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersG

Re: [Freesurfer] Advice for FreeSurfer developers

This is a good point. We should run the check right away. Right now, the subfield module runs at the end, which means that everything else has completed just fine, but we should definitely check at the very beginning and say: "either download the runtime or remove the subfield flag" Juan Eugen

[Freesurfer] travel grants for April workshop

Hello, Are there possibly any travel grants available to attend the Freesurfer workshop in April? It would greatly benefit my PhD studies to attend this workshop to learn more about structural techniques, however my PI does not have sufficient funds to send me. Thanks, Jasmin -- Jasmin Alves Pr

Re: [Freesurfer] geodesic distance calculation

Hi Desiree, I don't know how to do that (and hope someone else will help), but about your analysis: make sure you also do the inverse (map right to left). Then maybe average the distances. Else you could potentially introduce a lateral processing bias (by selecting one hemi as the target). Bes

[Freesurfer] email

jal...@usc.edu -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Multimodality analysis in FreeSurfer

I'm not sure what you mean. You say that you have mapped the thickness and myelin data into fsaverage space but then need to map the correlation into fsaverage. Isn't it already there? On 11/17/2015 10:33 AM, Silas wrote: > > Dear Freesurfer team, > > > I've scanned a group of subjects and gaine

[Freesurfer] Advice for FreeSurfer developers

Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime. Cheers, Ed On 17 Nov 2015, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Grev

Re: [Freesurfer] recon-all

Hi Doug, Thanks you very much for your great and detailed answered.   Kindly one more thing: when I am tring to run recon-all on "001.mgz" (under the folder mri/orig). If the fov is more than 256 ( e.g 320) recon-all failed. I checked the "recon-all.log" file and I found that it failed because

Re: [Freesurfer] Same Error in processing for local gyrification index

Dear all, I solved the problem posted earlier that was similar to a problem before. It was a matlab version problem. Conclusion : if *recon-all -localGI command* is stopping at make_roi_paths and you use matlab 2013 1. either switch to a older matlab version or 2. follow the instructions fro

[Freesurfer] Multimodality analysis in FreeSurfer

Dear Freesurfer team, I've scanned a group of subjects and gained structural and myelination data. Then, I've used mris_preproc to map the data onto the surface of fsaverage (and concatenating the data). I would like to investigate the correlation between cortical thickness and myelination by

Re: [Freesurfer] grossly abormal brain

Thanks very much, Bruce. I have 6Beta running now with -bigventricles and -fingerscrossed. Thanks very much, Anthony, for the reference. I'll fetch it and see what I can do as that approach is interesting from several angles for our work. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] grossly abormal brain

Don, if that doesn't work, try the procedure outlined in this paper, although it is rather involved: http://www.architalbiol.org/index.php/aib/article/viewArticle/1221 Anthony On 11/17/15 8:27 AM, Bruce Fischl wrote: Hi Don it's impossible to say. Certainly 6.0 will be your best bet as it h

Re: [Freesurfer] grossly abormal brain

Hi Don it's impossible to say. Certainly 6.0 will be your best bet as it handles enlarged ventricles much better. Try 6.0 beta with the -bigventricles flag and see how it goes cheers Bruce On Tue, 17 Nov 2015, Krieger, Donald N. wrote: A few cuts from a grossly abnormal scan are attached.

[Freesurfer] SNR Tracula

Thanks Barbara, that is what I was after. Cheers, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it

[Freesurfer] grossly abormal brain

A few cuts from a grossly abnormal scan are attached. Do you think freesurfer can effectively segment this one? If so, please point us in the right direction to get started with it. Thanks. - Don ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] geodesic distance calculation

Dear freesurfer experts, I'm analysing functional data using fsfast running under freesurfer-Linux-centos7_x86_64-dev-20150728. After streaming out the maximal activated cluster using mri_surfcluster, I want to calculate the geodesic distance between these vertices. Can I do this with mri

[Freesurfer] Problem with hippocampal subfields segmentation FS v6 - Solved

Hi, It seemed to be a problem with Java Runtime which I installed because it is required to do the hippocampal subfields segmentation. After starting the Matlab R2012a application itself the problem was gone. Cheers, Ed Begin forwarded message: From: "Gronenschild Ed (NP)" mailto:ed.gronensch.

[Freesurfer] R: R: Re: R: Re: R: Re: R: Re: average z-score of each subject from a common cluster

I have run cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary and I have obtained ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLowCWPHi NVtxs Annot 1 -3.595 110577865.93 11.8 39.4 -0.1 0.00620 0.00520 0.00720 1672 rostral

[Freesurfer] R: R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST

Thanks. But the MRS_mask should be in Tal, MNI or native? Now I'm using a masks that overlaps orig.nii.gz. Second, if I would like to create a sphere and use it as seed, there is a specific command line? Stefano >>Messaggio originale >>Da: gr...@nmr.mgh.harvard.edu >>Data: 9-nov-2015 2