[Freesurfer] TIV estimation with FreeSurfer

2006-10-27 Thread Joao Pereira
Dear all, I am posting the questions I made to Bruce without going through the list along with his reply. **I would still like to be sure about question 1)***, as it is central to my conclusions. If anyone has any other ideas, please let me know. >There are still a couple of questions in my mind

[Freesurfer] Head Points data files

2006-10-27 Thread Juranek, Jenifer
Hi, What are the file format requirements for the 2 files called to load head points - *.hpts and *.trans into tkmedit or tksurfer?   We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG system) with 248 sensor channels. I’d like to co-register my dipole locations wi

[Freesurfer] Aseg inforrmation

2006-10-27 Thread Ajith Kumar U
Hi Freesurfers, I have some questions about the aseg.stats file. What do the brainmask and brain segmentation volumes refer to? Is there a helpfile that defines these. Thanks Aju. ** Mr.Ajith Kumar U Junior Research Fellow, Department of Aud

Re: [Freesurfer] Aseg inforrmation

2006-10-27 Thread Jenni Pacheco
Hi Aju, The BrainMaskVOl in the aseg.stats file uses all of the voxels that are in the brainmask.mgz volume. the BrainSegVol uses all of the voxels that are labeled in the aseg.mgz segmentation. Jenni On Fri, 27 Oct 2006, Ajith Kumar U wrote: Hi Freesurfers, I have some questions about t

Re: [Freesurfer] TIV estimation with FreeSurfer

2006-10-27 Thread Bruce Fischl
yes, I agree that a new atlas might need a different scaling. And I also agree that the talairach_with_skull.lta should be adjusted relative to a volume with a skull on it, otherwise the eTIV wouldn't be right if there's atrophy. On Fri, 27 Oct 2006, Joao Pereira wrote: Dear all, I am postin

[Freesurfer] Slice Time Correction Error

2006-10-27 Thread Dan Dillon
    Hi all,  We are trying to implement a slice-time correction ('stc-sess -i fmc -o fmcstc -so siemens -s FPPREW01 -d .') but we get the following error...  INFO: set hdr.hist.orient to -1 /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional slicetimer -i /net/tucson/Raid/shared