[Freesurfer] Maps showing correlations between structural measures

Hello FreeSurfer experts, I came across a paper: http://www.sciencedirect.com/science/article/pii/S0166432815001837 where correlation maps between volume and gyrification are reported. I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures with volume and gyrification but I

Re: [Freesurfer] Interaction effects in QDEC

Great, thank you! Regards, Heidi Foo On Thu, 27 Apr 2017 at 12:17 AM, Douglas N Greve wrote: > Yes > > > On 04/26/2017 09:15 AM, Heidi Foo wrote: > > Dear Douglas, > > > > Thank you for your reply. Does this mean that if I were to have a > > continuous variable (i.e.

Re: [Freesurfer] Medial Surface Problem

Hi Mailing List, Still trying to solve the below medial surface problem. Does anyone have any ideas? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

glad it worked out :) On Wed, 26 Apr 2017, Patrycja Naumczyk wrote: Hi Bruce, thanks for a quick reply! mri_surf2surf worked fine just with specifying the target and source subjects, no registration file needed - much appreciated :) Best regards, Patrycja 2017-04-26 22:51 GMT+02:00 Bruce

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

Hi Bruce, thanks for a quick reply! mri_surf2surf worked fine just with specifying the target and source subjects, no registration file needed - much appreciated :) Best regards, Patrycja 2017-04-26 22:51 GMT+02:00 Bruce Fischl : > Hi Patrycja > > the standard

Re: [Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

Hi Patrycja the standard transform we use to fsaverage coordinates is surface-based (spherical). If you sample your EPI onto the surface, I believe you can use mri_surf2surf to transfer it from subject to fsaverage cheers Bruce On Wed, 26 Apr 2017, Patrycja Naumczyk wrote: Hello FS

[Freesurfer] FS-Fast's 'subject to fsaverage' registration files?

Hello FS experts, I have a question regarding FS-Fast processing. I have performed (successfully!) an FS-Fast single subject analysis. The results look fine in the fsaverage space, but I'm interested in viewing them in the subject space. Are the registration files used along the processing

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Hi Jared can you send us the full command line and screen output? cheers Bruce On Wed, 26 Apr 2017, Jared P Zimmerman wrote: Any chance I could get some help on this?  still having this problem On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman wrote:

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Any chance I could get some help on this? still having this problem > On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman > wrote: > > Hi FS Experts, > > I’m having trouble getting anatomical stats from a parcellation I made out of > scanner-space volume ROIs. I have

[Freesurfer] Extract time courses corresponding to a brain structure from an stc file

Dear Freesurfer experts, I would like to extract time courses of certain brain structures from the stc file in Matlab. Could someone please let me know how I can determine the lables of 10242 verices of my stc file? Or is there some matlab function that gives the time course of a barin structure.

Re: [Freesurfer] Interaction effects in QDEC

Yes On 04/26/2017 09:15 AM, Heidi Foo wrote: > Dear Douglas, > > Thank you for your reply. Does this mean that if I were to have a > continuous variable (i.e. Neuroinflammation) and a categorical > variable with 2 levels (i.e. gene positive and gene negative), > interaction can also be found

Re: [Freesurfer] Error when transforming aal.nii to lh.aal.label

In the mri_label2label command you have lh.aal.label as the input and output. Are you overwriting the input and so now it does not match the original subject? On 04/25/2017 09:23 PM, haidong wang wrote: > Hello FS experts, > I want to get the thickness of 90 ROIs of AAL using freesurfer.

Re: [Freesurfer] FS6.0 mri_surf2surf failure

I just tried it, and there was not a problem. Are you sure that hem.fsaverage.nii.gz has non-zeros in it? Can you send it to me? What platform are you using? On 04/26/2017 11:55 AM, dongnandi1 wrote: > > Dear FS experts, > > I’m trying to transform some files from fsaverage space to fsaverage5

Re: [Freesurfer] Fixing a left/right flip

I took a look at the xhemireg script and I feel like editing this to serve my purposes might be too tall of an order. However, I think I have a processing stream that will work — I want to make sure there’s nothing problematic about it. 1. Run recon-all on the properly oriented T1 images

[Freesurfer] FS6.0 mri_surf2surf failure

Dear FS experts, I’m trying to transform some files from fsaverage space to fsaverage5 space using mri_surf2surf(FS version: 6.0), however, it is weird that the results turn out to be all zeros on the fsaverage5 surface, the command line I used is : mri_surf2surf –srcsubject fsaverage –sval

Re: [Freesurfer] Filling in missing ventricles in WM

Hi Shane I can't really tell from the image. YOu can try setting some of the intensity bounds in mris_make_surfaces and mri_segment (eg. wlo, ghi and such). If you upload the subject I'll take a look cheers Bruce On Wed, 26 Apr 2017, Shane Schofield wrote: Hi Bruce, Thanks! The

Re: [Freesurfer] Filling in missing ventricles in WM

Hi Bruce, Thanks! The -bigventricles flag worked like a charm! But I have now run into other cases with fuzzy data and thin cortex that are not captured, such as the picture below: Any tips on filing them out? Thank you. On Sunday, April 23, 2017 3:41 PM, Bruce Fischl

Re: [Freesurfer] Interaction effects in QDEC

Dear Douglas, Thank you for your reply. Does this mean that if I were to have a continuous variable (i.e. Neuroinflammation) and a categorical variable with 2 levels (i.e. gene positive and gene negative), interaction can also be found using QDEC? Thank you. Best Regards, Heidi Foo On Wed, Jan