Re: [Freesurfer] [FSFAST]

Hello all, I would like to pose my question again in case it got missed. Thank you. WY On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin wrote: > Hi Doug, > > Is it possible to run retinotopy-like analysis to reveal areas in the > brain responsible for a certain phase of a presented stimuli? > Sa

Re: [Freesurfer] [FSFAST]

Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess -help to get more info On 3/20/18 4:28 AM, Walid Yassin wrote: Hello all, I would like to pose my question again in case it got missed. Thank you. WY On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin

[Freesurfer] Hippocampal Subfield Atlas

Hello, Does anyone know in which freesurfer folder I find the atlas corresponding to the following publication: "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MR"? Thanks, Roberto __

Re: [Freesurfer] Hippocampal Subfield Atlas

It’s in $FREESURFER_HOME/average/HippoSF/atlas But it’s not straightforward to visualize it… Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Rober

Re: [Freesurfer] mir_vol2surface registration file error

Hi Srishti, your volume maps are in some template space right? (the template you can open them on) This might be some MNI template space, but not necessarily the same the other people have used. You can register these to one another, e.g. with ANTS: Start ANTS in terminal > ants.sh 3 TheirTem

[Freesurfer] Brainstem registration

Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing, *I've had this posted but for some reason lost track of it so I'm uploading it again.* I have fMRI

[Freesurfer] POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING

POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA. The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusing on both clin

Re: [Freesurfer] Cortical volume parcellation

Bruce, I haven't used tksurfer before, but it seems like the best way to do what I need would be to edit the pre-existing labels in the fsaverage aparc+aseg image. What I want is almost exclusively from the superior and rostral-middle frontal labels already there, I just need to limit their ex

Re: [Freesurfer] Registering functional data between scan sessions

Awesome, thanks Doug! For clarity, I got it working with: bbregister --s --mov --reg day1func-to-day1anat.lta --init-fsl --bold bbregister --s --mov --reg day2func-to-day2anat.lta --init-fsl --bold bbregister --s --mov $SUBJECTS_DIR//mri/brain.mgz --reg day1anat-to-day2anat.lta --init

[Freesurfer] Functional Overlap Map

Hello Freesurfer experts, My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functiona

Re: [Freesurfer] Functional Overlap Map

I'm not entirely sure what you are doing. It sounds like you have 3 different conditions and want to find out where the activation for all conditions overlaps. But what you have done is to combine all conditions into a single condition, so you are seeing where the average activation is, which i

[Freesurfer] FreeSurfer for mouse brain

Dear FreeSurfer experts, I am currently trying to run FreeSurfer on a set of mouse brains and I have a few questions about it: 1. Is it possible to generate 2D surfaces from a set of structural scans on mouse brain in FreeSurfer? 2. Do the individual steps like Normalisation, Segmentation, Tesse