[Freesurfer] fsaverage and mni305

Hi, I'm trying to figure out how to go from a coordinate in mni305 space to a vertex index in fsaverage. In the README file that comes with fsaverage it's stated that surface coordinates are in talairach space, so they align with the MNI305 volume (and the talairach.xfm is the identity). But

Re: [Freesurfer] cerebellum not segmented well

did you check to see if the skull stripping worked? On Fri, 30 Mar 2007, deepa preeti wrote: Hi, I am trying to segment a few scans with freesurfer. Unfortunately, they failed during autorecon2 - the cerebellum not well segmented and the inferior portion looks very bright. I have attached

[Freesurfer] cerebellum not segmented well

Hi Bruce, I checked the skullstripping, the image is good with intact cerebellum. I have attached the skull stripping image as well. I wonder why the inferior regions of the cerebellum looks very bright and they are not included in subcortical segmentation resulting in failed segmentation. Any

Re: [Freesurfer] cerebellum not segmented well

can you put the orig.mgz on our file drop? On Fri, 30 Mar 2007, deepa preeti wrote: Hi Bruce, I checked the skullstripping, the image is good with intact cerebellum. I have attached the skull stripping image as well. I wonder why the inferior regions of the cerebellum looks very bright and

[Freesurfer] stc-sess -fsd error

FSFast folks, I am setting up an analysis stream and I am having an issue with stc-sess. If I leave my funcs in a folder called 'bold' the script works. stc-sess -i fmc -o fmcstc -so siemens -s c01 -d . However, we have multiple studies for each participant and I would like to use the '-fsd'

Re: [Freesurfer] stc-sess -fsd error

Yes, you are correct. I've just fixed it in dev and stable, live on the next update. On Fri, 30 Mar 2007, Avram Holmes wrote: FSFast folks, I am setting up an analysis stream and I am having an issue with stc-sess. If I leave my funcs in a folder called 'bold' the script works. stc-sess

Re: [Freesurfer] stc-sess -fsd error

Doug, I'm running on non-MR center server. Is there a quick way to update that script on our system without downloading the entire package again? Thanks, Avram Avram Holmes Department of Psychology Harvard University 1210 William James

Re: [Freesurfer] fsaverage and mni305

What do you mean by the actual 3d coordiantes in the mesh? The RAS coord is the MNI305 coord. You can have tksurfer display it with View-Information-VertexMNITal. In this case it will be the same as the RAS. The Talairach coord is the MNI coord adjusted with Mathew Brett's algorithm, which is

Re: [Freesurfer] stc-sess -fsd error

I've put the new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc-sess doug On Fri, 30 Mar 2007, Avram Holmes wrote: Doug, I'm running on non-MR center server. Is there a quick way to update that script on our system without downloading the entire package

[Freesurfer] optseq help

Hello, I am trying to use the optseq command for 2 conditions of 30 trials each with TR = 2 optseq -ntp 120 -TR 2 -npercond 30 30 -tpercond 3 3 -nsessions 3 -label critical independent -o TestFile I get the following result: -0.0001 3.000 critical 4.0001 3.000

Re: [Freesurfer] fsaverage and mni305

I think tksurfer reports the coords of the white surface roberto toro wrote: On 3/30/07, Doug Greve [EMAIL PROTECTED] wrote: What do you mean by the actual 3d coordiantes in the mesh? The RAS coord is the MNI305 coord. You can have tksurfer display it with View-Information-VertexMNITal. In

Re: [Freesurfer] optseq help

Have you tried using optseq2? Haven't used optseq in a long time:). Mithra wrote: Hello, I am trying to use the optseq command for 2 conditions of 30 trials each with TR = 2 optseq -ntp 120 -TR 2 -npercond 30 30 -tpercond 3 3 -nsessions 3 -label critical independent -o TestFile I get the

[Freesurfer] control points and voxel segmentation stats

Hi, I understand that it is possible to use control points to fix intensity normalization, so that volumes which were not selected as white matter can be manually selected as white matter. Is it possible to de-select volumes which were determined as white matter in freesurfer, even though it

[Freesurfer] QDEC

Hello developers, How can I get access to QDEC? Regards Chacko. Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=listsid=396546091

Re: [Freesurfer] QDEC

Hi Chacko, how did you hear about qdec? It's still in development - check back in a couple of months and maybe we'll have a beta. cheers, Bruce On Fri, 30 Mar 2007, Chacko Cherian wrote: Hello developers, How can I get access to QDEC? Regards Chacko.

Re: [Freesurfer] control points and voxel segmentation stats

Hi Trina, not really. Is this the aseg.mgz of the wm.mgz that you are talking about? Bruce On Fri, 30 Mar 2007, Trina Kok wrote: Hi, I understand that it is possible to use control points to fix intensity normalization, so that volumes which were not selected as white matter can be