[Freesurfer] Error map

Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces and display the difference between the 2surfaces ( like 'euclidian distance'). What I want is exactly that output

Re: [Freesurfer] bblabels??

mri_label2label maps them in whatever direction you specify. Someone else will have to answer the bblabels question as I don't know what it is cheers Bruce On Fri, 5 Apr 2013, Anupa AV wrote: Hello experts, I'm in a process to make coronal cuts using tksurfer Please help me with the

[Freesurfer] fsaverage mappings

hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the vertices in fsaverage4. is there an easy way to map those to vertices on to fsaverage/fsaverage5/... without going through surf2surf? something perhaps implemented in matlab

[Freesurfer] makelabels error

Hello, I am trying to adapt our ROIs used for tractography into a format that can be used in Freesurfer. I first used mri_cor2label to convert from nifti to .label format. When I run the following makelabels command: mri_label2label --srclabel

[Freesurfer] Problem running Tracula longitudinal analysis

I am trying to run Tracula on a single subject with two time points. I get the following Error below. I suspect it is because I am not setting my dmrirc file up correctly, but I cannot figure out what the error is. I've copied my dmrirc file below as well. Thanks, Dylan Command: trac-all -prep

Re: [Freesurfer] makelabels error

Hi Jeff have you looked at the labels? That error frequently means something is wrong in the coordinate transforms. Look at the label in the volume and see if it is where you think it should be. cheers Bruce On Sat, 6 Apr 2013, jwa...@nmr.mgh.harvard.edu wrote: Hello, I am trying to adapt

Re: [Freesurfer] Making mid-gray surfaces without mris_expand?

Hi Keith the average white/pial surface doesn't have any topological or smoothness constraints, which is why we don't really use it. Yes, mris_expand is slow, but that's precisely because it prohibits self-intersection. The good nes is that compared to the rest of the recon stream it doesn't

Re: [Freesurfer] fsaverage mappings

Hi Satra the first 12 vertices will be from the 0th order icosahedron, the next 30 from the 2nd order, etc Bruce On Sat, 6 Apr 2013, Satrajit Ghosh wrote: hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the

Re: [Freesurfer] Intensity Normalization

glad to hear it On Sat, 6 Apr 2013, Dan LaFreniere wrote: Hi Bruce, Apologies for the delay - was having some issues with the automatic moderator approval. That's good to hear, thank you for your help. You're spot on, the right temporal lobes appear to be in worse shape than the left.

Re: [Freesurfer] Making mid-gray surfaces without mris_expand?

Thanks for the reply. Maybe I'm not thinking deeply enough about this, but since there is a 1-to-1 mapping from white to pial vertices, is there a possibility of self-intersection in the average? -Keith On Sat, Apr 6, 2013 at 7:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Keith

Re: [Freesurfer] Making mid-gray surfaces without mris_expand?

yes, I think it can happen, although it's probably pretty rare On Sat, 6 Apr 2013, Keith Jamison wrote: Thanks for the reply.  Maybe I'm not thinking deeply enough about this, but since there is a 1-to-1 mapping from white to pial vertices, is there a possibility of self-intersection in the

Re: [Freesurfer] Tracula the inverse of TBSS results

I reinitialised the tracts and they all make sense now :) Hope to see you all at ISMRM. Sean Hatton Brain and Mind Research Institute University of Sydney. On 5/04/13 7:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: It's the pathstats.byvoxel.txt file. On Thu, 4 Apr 2013,