[Freesurfer] T2 pial

Dear FreeSurfer experts, First of all, congrats for this new 5.2 stable version. My name is Eduard, and I'm trying to perform de T2 pial refinement in a pre-processed subject with the B0 image from a DTI. I used that command: recon-all -autorecon3 -T2pial -s ACC019/ -T2

Re: [Freesurfer] T2 pial

of: mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii Nick On Wed, 2013-04-17 at 13:04 +, Eduard Vilaplana Martinez wrote: Dear FreeSurfer experts, First of all, congrats for this new 5.2 stable version. My name is Eduard, and I'm trying to perform de T2 pial refinement

[Freesurfer] Gender as a nuisance factor

Dear Freesurfer experts, I'm performing a group analysis in Qdec correlating a biological marker and the CTh, and I would like to covariate the gender and age effect, i.e. ideally get rid of both effects and isolate the biological marker effect. So, I understand that the age effect is (at

[Freesurfer] Longitudinal stream

Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you

[Freesurfer] PETsurf - point-spread function in ADNI

Dear Freesurfer experts, I'm processing ADNI PET data (AV45 and AV1451) in a surface-based approach following your guidelines (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). Do you guys have any experience with ADNI data? I would like to apply partial volume correction but I don't know

[Freesurfer] 5.3v migration

Dear FS experts, We are planning to update all our subjects from de 5.1v to 5.3v. Our subject database processed with the 5.1v is really big so we are thinking about ways to not start over new. Is there any way to take advantage of the 5.1v segmentations? We have been thinking about using a

[Freesurfer] PVC on DTI

Dear Freesurfer experts, Does anyone have any experience on surface PVC in DTI? Concretely, I'm analysing cortical mean diffusivity (all on surface) and I am wondering whether the PVC pipeline for PET (petsurfer) would work on that case. Thanks for your help, Edu V.

[Freesurfer] PETSURFER - smooth question

Dear FS experts, I've been working with the proposed pipeline, but I still have a doubt regarding the degree of smooth to be applied to the final surfaces prior to the analyses. The first question is that, given a "standard" PET scanner, with a PSF between 5-8mm, what size smooth would you

[Freesurfer] mris_fwhm

External Email - Use Caution Dear freesurfer experts, I would like to ask you about the mris_fwhm script. What does the flag "--mask" exactly do? Suppose I would like to compute the effective smoothness of an mri dataset. Some subjects have zeros in some vertices, but instead

[Freesurfer] V6.1

Dear freesurfer experts, Some days ago I unexpectedly found a thread (about including the flair in the pipeline) in which you mentioned the v6.1. In my lab we are thinking about doing the major 5.1 to 6.0 upgrade, but given that we have a huge database of subjects N~2000) we are wondering