[Freesurfer] Using mri_transform with output of bbregister

External Email - Use Caution Hi all, Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with. I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the

[Freesurfer] Dividing surface overlays

External Email - Use Caution Hi all, I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmw

Re: [Freesurfer] Incorrect SI/AP swap from bbregister

works. Thanks! Dylan > On Feb 23, 2022, at 9:15 AM, Tisdall, Dylan > wrote: > > Thanks for the help with my previous question on formatting the bbregister > command line. Now that I've got it running, I'm seeing that 1 of my two > subjects ends up with a 90 degree rotati

[Freesurfer] Incorrect SI/AP swap from bbregister

External Email - Use Caution Thanks for the help with my previous question on formatting the bbregister command line. Now that I've got it running, I'm seeing that 1 of my two subjects ends up with a 90 degree rotation (swapping SI and AP axes) when I try to register my 7T T1 or

Re: [Freesurfer] Subject ID error with bbregister

in the lta file? If so, it is probably > trying to get the subject from there. You can try putting the --s after > the --lta > > On 2/21/2022 3:43 PM, Tisdall, Dylan wrote: >> External Email - Use Caution >> >> Hi all, >> >> Quick question on a

[Freesurfer] Subject ID error with bbregister

External Email - Use Caution Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject

[Freesurfer] talairach.lta coordinate spaces

External Email - Use Caution Hi list, I'm trying to understand whether the talairach.lta transform is from the image-axes RAS to talairach or the scanner-axes RAS to talairach. Basically, if I rotate the imaging FOV and scan the same subject, should I expect that to change tala

[Freesurfer] Postdoc Positions at University of Pennsylvania

External Email - Use Caution Hi all, I'm recruiting postdoc follows for a couple of NIH-funded projects at the University of Pennsylvania. Projects include 1) development of motion-resilient methods for pediatric neuroimaging, and 2) ex-vivo/in-vivo 7T neuroimaging and analysi