Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam, Can you can use the --mni flag? "Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)" Lilla On Wed, 1 Aug 2018, Peled, Noam wrote: I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't loc

Re: [Freesurfer] Sag T1 3D post-contrast

Hi John I've pushed a lot of post-contrast scans through and haven't had many issues. Have you checked the talairach? If you upload the dataset we will take a look cheers Bruce On Wed, 1 Aug 2018, John Absher wrote: External Email - Use Caution Has anyone else tried to do

Re: [Freesurfer] Surface editing: recon-all exited with errors

External Email - Use Caution Hi Andrew, Looks like that cleared the errors. Thank you both, -Eli From: Hoopes, Andrew Sent: Tuesday, July 31, 2018 3:09 PM To: Freesurfer support list Cc: Rockers, Elijah D. Subject: Re: [Freesurfer] Surface ed

Re: [Freesurfer] Mixed Block Event-related Design Optseq Question

sorry, it does not do mixed block event related On 07/31/2018 10:09 PM, Yu Han wrote: > > External Email - Use Caution > > > Hello experts, > > > We would like to use the optseq 2 to optimize a mixed block and > event-related design. Is it possible to use optseq for a mixed > desig

Re: [Freesurfer] Fwd: vertex MNI305 (ruopeng)

Actually, I think this is a better question for Ruopeng (cc'ed) On 07/31/2018 10:16 AM, Trisanna Sprung-Much wrote: > > External Email - Use Caution > > Hi there > > Still waiting for an answer to this! > > Thanks! > Trisanna > -- > Ph.D. Candidate > McGill University > Integrated Program

[Freesurfer] (no subject)

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Re: [Freesurfer] mri_cvs_register using fsaverage

Thanks Lilla! Just to be sure, when using the --mni flag, should I remove the --template flag? Also, is there any way I can calculate the registration directly to MNI305 and not MNI152? Thanks again, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu on be

[Freesurfer] (no subject)

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Re: [Freesurfer] mri_cvs_register using fsaverage

FYI, fsaverage is already in MNI305 space On 08/01/2018 11:14 AM, Peled, Noam wrote: > > Thanks Lilla! > > Just to be sure, when using the --mni flag, should I remove the  > --template flag? > > Also, is there any way I can calculate the registration directly to > MNI305 and not MNI152? > > > Th

[Freesurfer] Influence of control variables

External Email - Use Caution Dear Freesurfers, I am conducting a study on the link of cerebral structural measurements and psychopathological dimensions. At first, I investigated the link of structural markers and the respective dimension while controlling for the patient's age an

[Freesurfer] Thickness measurements.

External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a way to use white and pial surfaces not generated from the mris_make_surfaces to create thickness files? Mahalo, Ryan M Nillo Staff

Re: [Freesurfer] mri_cvs_register using fsaverage

Thanks for the clarification, I'm asking that because in the mri_cvs_register docs it's written that the --mni flag will "use the CVS atlas in MNI152 space as a target for registration". Thanks again, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu on beha

Re: [Freesurfer] mri_cvs_register using fsaverage

Yes, you can remove the template flag. And no, not at the moment. Thanks Lilla! Just to be sure, when using the --mni flag, should I remove the  --template flag? Also, is there any way I can calculate the registration directly to MNI305 and not MNI152? Thanks again, Noam __

Re: [Freesurfer] Thickness measurements.

yes, you can use the binary mris_thickness to compute the thickness cheers Bruce On Wed, 1 Aug 2018, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a

[Freesurfer] Problems associated segmentation results of hippocampal subfields

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/

[Freesurfer] PhD position avalaible in Torus, France : hisgh resolution Brainstem atlas

External Email - Use Caution Dear all, we have an open 3-year position for a PhD student in our lab in Tours, France beginning 2018, oct 1st. This student will work on a brainstem atlas from 11.7T exvivo MRI data. Details are included here : https://ibrain.univ-tours.fr/actual