[Freesurfer] Extracting time series from aparc.a2009s+aseg.mgz

Hi FSusers, Is there a way to extract averaged BOLD signal from the identified cortical regions in aparc.a2009s+aseg.mgz. Thanks Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

It will still work. from mri_cor2label --help : Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc). John Gelburg wrote: > thanks, but isn't COR volume and my ANALYZE image is not the same thing? > >

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

thanks, but isn't COR volume and my ANALYZE image is not the same thing? On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve wrote: > try mri_cor2label > > John Gelburg wrote: > >> Hi, >> >> I have ANLYZE binary mask which I would like to convert to FreeSurfer >> labels. Is there any more automatic w

Re: [Freesurfer] Colortable in annotations

Thanks, that should be helpful. Is there a way to use mris_anatomical_stats on the .annot file that the cluster correction creates within the qdec analysis folder, or do I need to map the annotation to a subject in order to use mris_anatomical_stats? If I try to run mris_anatomical_stats on th

Re: [Freesurfer] Colortable in annotations

or you can use the -c option of mris_anatomical_stats to extract the colortable from the .annot file, edit the colors in that colortable, and then specify that colortable with the -colortable option of tksurfer. n. On Fri, 2010-04-09 at 14:49 -0400, Douglas N Greve wrote: > The only "easy" way to

Re: [Freesurfer] Processing of brains with malformations of cortical development

Hi Diego, it depends on the extent of the abnormality. As PPJ pointed out they have done some of this, as have we. cheers Bruce On Fri, 9 Apr 2010, Diego Herrera wrote: > Hello > > Do you know how would theorically behave Freesurfer with pathologic brains > with malformations like polymicrogir

Re: [Freesurfer] Processing of brains with malformations of cortical development

Or this link: http://www3.interscience.wiley.com/journal/122368840/abstract --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.br --- Novo Netfilter Small Business

Re: [Freesurfer] Processing of brains with malformations of cortical development

Take a look at this paper of our group: https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.b

[Freesurfer] Processing of brains with malformations of cortical development

Hello Do you know how would theorically behave Freesurfer with pathologic brains with malformations like polymicrogiria, schizencephaly, etc. Also, do you have experience with subtle malformations like Focal Cortical Dysplasia (FCD)? Recently, we tried recon-all in a polimicrogiric brain obtaining

Re: [Freesurfer] CEPHES ERROR: fdtrc domain error

It could be a scaling issue. Try normalizing the ICV by the mean. doug Lars M. Rimol wrote: > > Hi, > > I get this error message when running glm_fit (v.3.02): > > CEPHES ERROR: fdtrc domain error (I see you've handled this error > message before, but there was no solution there: > http

Re: [Freesurfer] Colortable in annotations

The only "easy" way to do it is to create individual labels for each cluster (using the label option or mri_annotation2label), then use mris_label2annot and specify your own color table. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I am running cluster corrections on data and attemp

[Freesurfer] Colortable in annotations

Hi all, I am running cluster corrections on data and attempting to display the resulting cluster maps. Is it possible to make all of the clusters in an annotation the same color? And if so, how? As it stands now, all of the clusters are given a different color. Thanks for your help, Natha

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

try mri_cor2label John Gelburg wrote: > Hi, > > I have ANLYZE binary mask which I would like to convert to FreeSurfer > labels. Is there any more automatic way to do it than loading it as an > overlay and then selecting manually as a label? > > Thanks for help, > John > -

Re: [Freesurfer] Analyze 7.5 hdr into .mat file

Try pulling out the matrix and saving as version 4, something like M = HDR.M; save('subject.mat','M','-v4') doug SG KIM wrote: > I want to import anlayze75 with a right direction (still). > > I have those files: > > subject.hdr > subject.img > > > And got warnings as: > -

[Freesurfer] mri_label2vol: how to make the opposite direction?

Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John ___ Freesurfer mailing list Freesurfer

[Freesurfer] CEPHES ERROR: fdtrc domain error

Hi, I get this error message when running glm_fit (v.3.02): CEPHES ERROR: fdtrc domain error (I see you've handled this error message before, but there was no solution there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11602.html) I'm using a model with two groups,