[Freesurfer] orientation of the data

Hello experts, I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse

Re: [Freesurfer] orientation of the data

Hi Jan, what was your input data? Bruce On Mon, 3 May 2010, Janani Dhinakaran wrote: > Hello experts, > > I've been having some trouble with the talairach during recon. I followed > previous instructions and checked the rawavg image and found that it was in > wrongly oriented. > The sagittal pic

Re: [Freesurfer] orientation of the data

I have also been getting error messages, after Talairach correction using tkregister2 *...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010 /usr/local/freesurfer/subjects/FS060828cr/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms

Re: [Freesurfer] orientation of the data

what format is your input data in? On Mon, 3 May 2010, Ilana Hairston wrote: > I have also been getting error messages, after Talairach correction using > tkregister2 > > *...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010 > /usr/local/freesurfer/subjects/FS060828cr/mri > > talairach_a

[Freesurfer] Vertices to matrix coordinates

Hi all, I checked quite a number of previous posts, but still can't seem to figure out what the vertices numbers given by read_annotation in matlab stand for. My questions are: - In what reference frame are they? - How do I convert them to coordinates in my original structural image (an x * y

Re: [Freesurfer] Vertices to matrix coordinates

The coordinate system is not easy to explain in an email. There are power point slides on our wiki about the geometry used. To get from surface xyz to column, row, slice in the orig.mgz, first get a matrix from the orig.mgz with mri_info --tkrvox2ras orig.mgz this will be 4x4, multiply the inv

Re: [Freesurfer] Vertices to matrix coordinates

Dear Doug, Thanks a lot for the fast reply. I got it to work with your tips. The missing link for me was especially that I could get the vertices locations by using read_surf over the mgz file. Instead of the fmri_info rotation matrix I can also use the matrix from the nii-file, can't I? They a

[Freesurfer] Incorporating T2 and T1 images in recon-all

Dear FreeSurfers, I have 2 identical structural scans for my subjects: one is T1-weighted and the other is T2-weighted. Is it possible to pass both scans to recon-all? The T1-scans are rapidly acquired MEMPRAGEs, and recon-all seems to be having some difficulty distinguishing cortex from dura a

Re: [Freesurfer] Incorporating T2 and T1 images in recon-all

Hi Dan, our tools don't currently suppor this, although Koen Van Leemput (ccd) may have something. cheers Bruce On Mon, 3 May 2010, Dan Dillon wrote: > Dear FreeSurfers, > > > > I have 2 identical structural scans for my subjects: one is T1-weighted and > the other is T2-weighted. Is it possib

[Freesurfer] contrast correction

Hi there, We have been doing contrast correction using mri_nu_correct.mni (e.g., mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2). My question is, after subsequent corrections (control points, white matter) do we need to specify nu2.mgz as the target file fo

[Freesurfer] mris_preproc thickness vs functional data

Hello All, I have a question regarding the actual command issued under the mris_preproc wrapper. I noticed that when I ran the recon-all -qcache to resample the different anatomical measures like thickness etc to fsaverage, one of the step is the following - mri_surf2surf --srcsubject 068 --

[Freesurfer] Submitting Files for Review

Dear All I want to send a file will an example of the segmentation of the Pallidum, as discussed previously, which I want refined in general for my OCD project. Do you generally want only the subject file folder with contents, or the mgz file only? Also when uploading from South Africa, what is th