[Freesurfer] how to separate any sub cortical region in freesurfer ?

how to separate any sub cortical region in freesurfer ? ___ 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 is

[Freesurfer] Fwd: qdec error

Dear Freesurfer Experts, Last week, I posted a question regarding the error during qdec. However, I did not receive any response yet. Could you give me a help to solve the problem? I am sincerely looking forward to receive your response soon. Best Regards, Seung-Gul Kang -- Forwarded

[Freesurfer] R: Re: R: Re: Map of covariance

Hi, on 4 groups, 1 covariate (4GV1) I run mri_glmfit using the following .mtx C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0

Re: [Freesurfer] bad midline cut

Dear Bruce, Did you get my email with the link for our problematic data? Best Regards, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is in

Re: [Freesurfer] Peripheral CSF

yes. The surface lives in a continuum and cannot necessarily be represented on a descrete grid On Sun, 1 Oct 2017, Fereshte wrote: I mean if the holes and handles are corrected in the aseg.mgz. You mean sampling the surfaces into the volume may cause topological defects?  On Sun, Oct 1, 201

Re: [Freesurfer] fwhm in area analysis

Hi FreeSurfer experts, To follow up on my early post, I am wondering if I use fwhm=15 to analyze area, mri_surfcluster reported that it cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/... is this normal? When I use fwhm=10, everything seems to be okay. Best, Daniel On Tue, Sep 26, 2017 a

Re: [Freesurfer] fwhm in area analysis

Hi FreeSurfer experts, I am wondering if I use fwhm=15 to analyze area, mri_surfcluster reported that it cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/... is this normal? When I use fwhm=10, everything seems to be okay. Best, Daniel On Tue, Sep 26, 2017 at 8:57 PM, Daniel Yang wrote:

Re: [Freesurfer] Peripheral CSF

I mean if the holes and handles are corrected in the aseg.mgz. You mean sampling the surfaces into the volume may cause topological defects? On Sun, Oct 1, 2017 at 11:04 PM Bruce Fischl wrote: > hmmm, not exactly sure what you mean, but the aseg is corrected with the > topologically corrected sur

Re: [Freesurfer] Peripheral CSF

hmmm, not exactly sure what you mean, but the aseg is corrected with the topologically corrected surfaces. Note that sampling them into the volume can change the topology though On Mon, 2 Oct 2017, angel angel wrote: I see. By the way is aseg.mgz the segmentation after surfaces ? I mean if th

Re: [Freesurfer] Peripheral CSF

I see. By the way is aseg.mgz the segmentation after surfaces ? I mean if the topology correction is considered. Thank you! On Sunday, October 1, 2017, Bruce Fischl wrote: > you can't get an accurate estimate of sulcal CSF from just a T1 as you > can't distinguish it from other things that are d

Re: [Freesurfer] Peripheral CSF

you can't get an accurate estimate of sulcal CSF from just a T1 as you can't distinguish it from other things that are dark, so we don't geenerate a label for it cheers Bruce On Sun, 1 Oct 2017, angel angel wrote: Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segm

[Freesurfer] Peripheral CSF

Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you! __