Re: [Freesurfer] multi-slice timing correction

External Email - Use Caution Okay, I looked through the source code itself and I think I worked it out. preproc-sess calls on stc-sess, passing it both the sdf and the ngroups flags. stc-sess calls on stc.fsl, passing it both the sdf and the ngroups flags. stc.fsl calls on

Re: [Freesurfer] multi-slice timing correction

External Email - Use Caution looking further into the archives, I see that the -sdf flag can be used. I’m still uncertain about the -ngroups flag. I see at least a couple other users have asked about this but I don’t see a response. In the present case, if there are 60

[Freesurfer] mri_gtmpvc with amended aparc+aseg

Hello, I’ve been using PETSurfer for partial volume correction of PET images using the RBV option. I’m amending the parcellations/segmentations to add in extracortical areas of high PET signal (to prevent spill-in into the brain), and after adjusting the *ctab file this runs successfully.

Re: [Freesurfer] hippocampal subfield as CONN seeds

This will be a little tricky. How did you do the registration to MNI space? On 6/11/2019 1:36 AM, Nelson, Eric A wrote: External Email - Use Caution Hi all, I have successfully ran hippocampal subfields for a sample but would like to be able to use some of those subfields as seed

Re: [Freesurfer] label a ROI

Hi Francesca sorry, not sure if this got answered, but you should be able to create surface-based ROIs and run the analysis on them. cheers Bruce On Wed, 5 Jun 2019, Francesca Pentimalli wrote: External Email - Use Caution Dear Bruce,  Thank you very much for answering!

[Freesurfer] Correlate Dose Distribution with Cortical Thickness Change

External Email - Use Caution *We already send this email from a Medaustron email address but for some reason the response was blocked and cannot be seen anymore* Dear FreeSurfer Developers, We are doing research on cortical changes after radiation therapy to the brain. We are

[Freesurfer] Cerebellum and brainstem mask

External Email - Use Caution Dear Freesurfer devs, I would like to exclude from the T1 image those voxels that correspond to the cerebellum and brainstem. I tried to do this using the following commands although I am not completely sure if they are the right ones: 1. Extract

[Freesurfer] Yeo Atlas Download

External Email - Use Caution Dear Freesurfer Team, I cannot download the "Resting State Cortical Parcellation in nonlin MNI152 space" with several machines. Is there something wrong with the server? The error message is: Server Connection was reset. Thank you in advance, kind