Re: [Freesurfer] Register Nifti files on Siemens raw data

2008-02-20 Thread Joerg Magerkurth
Hi Doug, What about the translations? I haven't found anything like -iid in mri_convert for the translation parameters. Can I take the -im MATRIX option? Assuming the Matrix contains the cosines in the first three columns and in the last the coordinates of the voxel in the corner, like the i

[Freesurfer] qdec vertex selection

2008-02-20 Thread James N. Porter
Howdy- I am working in qdec and having a problem selecting vertices. I can move the cross-hairs by entering a vertex number in the "Jump to vertex number" box, but I can't actually just click on the brain to get the vertex where I want it. Also, the ctrl-click function to pull up the scatterp

Re: [Freesurfer] Register Nifti files on Siemens raw data

2008-02-20 Thread Doug Greve
Use the --in_center option to spec the center of the volume. Joerg Magerkurth wrote: Hi Doug, What about the translations? I haven't found anything like -iid in mri_convert for the translation parameters. Can I take the -im MATRIX option? Assuming the Matrix contains the cosines in the firs

[Freesurfer] Obtaining cortical parcellations

2008-02-20 Thread Dan Dillon
Dear FreeSurfers, I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-auto

Re: [Freesurfer] Obtaining cortical parcellations

2008-02-20 Thread Allison Stevens
You can do: recon-all -cortparc -parcstats -s which will create the cortical parcellations and the associated stats file. (Note: -cortparc2 and -parcstats2 will use the alternative atlas). Steps like these can be found on the wiki, here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStable

[Freesurfer] qdec.table.dat & sample.levels for the tutorial data set

2008-02-20 Thread Gallo, Antonio (NIH/NINDS) [F]
Hi All, I'm trying to follow the FS Tutorial for Qdec/Group Analysis, but I was not able to find the qdec.table.dat and sample.levels for the tutorial data set. Could you please help me with this? Thanks a lot, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, R

Re: [Freesurfer] qdec.table.dat & sample.levels for the tutorial data set

2008-02-20 Thread Nick Schmansky
Antonio, Did you download the tutorial data file 'buckner_data- tutorial_subjs.tar.gz'? The qdec.table.data and sample.levels files are found in: buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/ You can get that data from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/D

[Freesurfer] surface co-ordinates

2008-02-20 Thread Mishkin Derakhshan
Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? 2. I am making the assumption that the lh.white and the lh.pial will always have the same number of indices and polygons. Can

Re: [Freesurfer] surface co-ordinates

2008-02-20 Thread Doug Greve
On Wed, 20 Feb 2008, Mishkin Derakhshan wrote: Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? These are "surface RAS" or "tkregister RAS". There is a power point present

Re: [Freesurfer] surface co-ordinates

2008-02-20 Thread Mishkin Derakhshan
On Wed, Feb 20, 2008 at 10:46 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > On Wed, 20 Feb 2008, Mishkin Derakhshan wrote: > > > Hi, > > > > 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate > > system are the xyz co-ordinates reported in? ie. is it the RAS > > co-ordinates of