Re: [Freesurfer] Cortical gray matter surface area

Hi Will, I think lh.ribbon.mgz and lh.ribbon.mgz contain the volumes of the left and right cortical gray matter. You can extract a list of vectors on a 1 mm grid which fills these regions using mri_cor2label and count the vectors. Regards, Don Don Krieger, Ph.D. Department of Neurological Sur

[Freesurfer] Cortical gray matter surface area

Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 How abou

[Freesurfer] Questions about mri_make_bem_surfaces function

Hi experts I need use the mri_make_bem_surfaces function to generate the three surfaces from brain MRIs patient exam. I have installed Freesurfer and I have my series of MRIs in 001.mgz file. would be helpful if you could provide some material to use this function. regards -- *Gamaliel Huerta*

Re: [Freesurfer] tracula: bvec-error

Hi Robby, Try this (with the backslashes), applied only to bveclist, if that does not work, also to subjlist and dcmlist at the same time, and let me know please. I have started to process my data with a separate configuration file for every subject :( - as no combination of alterations to the

[Freesurfer] questions about qdec, group and age interaction

Dear all, I encountered several questions when using freesurfer. Although I searched carefully in this mailing list, I am still not very clear about some issues. My issues are described below: Based on a bunch of information, I know that before describing my results, I need to check whether there

Re: [Freesurfer] Change in the location/path and the name of subject

Hi Reza mostly it should be ok. I think some of the older register.dat files include a subject name and might need to be edited to be updated. Email us if anything goes wrong - there should be easy fixes. Bruce On Wed, 27 Aug 2014, Reza Rajimehr wrote: > Hi, > > I have got anatomicals of a su

Re: [Freesurfer] tracula: bvec-error

Dear Barbara, Unfortunately I haven’t found a solution yet. I’ll keep you up to date. Greetings, Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be On 01 Sep 2014, at 12:22, Barbara Kre

[Freesurfer] GLM: table with uncorrected clusters

Dear FS-community Thx to Doug I was able to successfully run a first analysis. However, I’d like to have a table of the uncorrected clusters. Is there any flag I can add to write these clusters to some sort of txt-file with the p-values etc.? I’m using the mri_glmfit command. Thanks, Best reg

Re: [Freesurfer] tracula: bvec-error

Dear all, Robby, are you still having the problem? Did you solve it? I am really having the same problem, just that I am using nifti files instead of dicoms. I am using the same version as Robby. Please find my command+output, trac-all.log and configuration file in the attachment. I would also app

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not n

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Mich