[Freesurfer] content of "subjects_dir"

Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of directories and files. If I set the environment so that my "subjects_dir" is not the default location, do I need to move any of the files in the original location to the new one?

[Freesurfer] viewing mri_glmfit FDR corrected results

Dear FreeSurfer experts, I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons. My question is about how do I correctly

Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

Hello Elijah, I want to extract this values like you did. How do I use the script doug recommended? Thanks Paul On Wed, Jun 21, 2017 at 11:47 AM, Elijah Mak wrote: > Thanks Doug! It works! > > Best Wishes, > Elijah > > On 21 June 2017 at 16:09:29, Douglas N Greve

[Freesurfer] Question mri_glmfit fwhm smoothing

Hi, I have a question about mri_glmfit. As an input, you give e.g. the stacked thickness data from all subjects, smoothed with a certain fwhm. But then as an output file, it gives an fwhm.dat file, which, at least in my case, contains another smoothing level. I noticed this because I ran

[Freesurfer] Subject with missing fMRI data

Hi List, I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Great, thank you! Best, Corinna On Thu, Jun 29, 2017 at 12:09 AM, Thomas Yeo wrote: > Hi Corinna, > > You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_ > JNeurophysiol11_SplitLabels.zip?dl=0 > > Regards, > Thomas > > > On Thu, Jun 29, 2017 at 5:45

[Freesurfer] Qdec error in analysis

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on

Re: [Freesurfer] CT DIOCMs

Hi Jon CT doesn't usually provide any gray/white contrast, so I don't think it can work. The dicom issue is a separate one. We should be able to read most dicoms, but of course this is the issue with an "evolving standard". cheers Bruce On Wed, 28 Jun 2017, John Anderson wrote: Dear

Re: [Freesurfer] Pial surface editing

sure, you can use whatever format we support - we will recognize it by the extension (e.g. .nii or .nii.gz). cheers Bruce On Tue, 27 Jun 2017, Michelle VanTieghem wrote: Hi Bruce,  The -gcut does not appear to make any difference on our skull stripping. I also saw that you can change flags