Re: [Freesurfer] MNI152 to 305 conversion

2013-10-01 Thread Douglas N Greve
Hi Thomas, it loads properly for me. doug On 10/01/2013 08:21 PM, Thomas Yeo wrote: > Hi Doug, > > except Paul was saying the mni305.cor.mgz does not show up correctly > in freeview as well. Doesn't freeview handle header orientation > information properly? > > --Thomas > > On Wed, Oct 2, 2013 at

Re: [Freesurfer] MNI152 to 305 conversion

2013-10-01 Thread Thomas Yeo
Hi Doug, except Paul was saying the mni305.cor.mgz does not show up correctly in freeview as well. Doesn't freeview handle header orientation information properly? --Thomas On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve wrote: > Hi Paul, IMHO this is not a problem with the FreeSurfer output it

Re: [Freesurfer] MNI152 to 305 conversion

2013-10-01 Thread Douglas N Greve
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and

Re: [Freesurfer] MNI152 to 305 conversion

2013-09-30 Thread Douglas N Greve
View it in tkmedit to see if it is really a problem with your vol2vol command. doug On 09/30/2013 07:33 PM, Paul Beach wrote: > No. That was just a general example of how the image looks - from a > stock google image of an FSL brain (I'm not in the lab and so cannot > put up actual images

Re: [Freesurfer] MNI152 to 305 conversion

2013-09-30 Thread Douglas N Greve
Is this in tkmedit? On 09/30/2013 06:59 PM, Paul Beach wrote: > Hi Doug, > > Sorry, I should have been more specific. I meant for when one looks at > the resulting transformation in a sagittal view. > > More specifically... > Instead of this: > Inline image 1 > > It looks more like this (though m

Re: [Freesurfer] MNI152 to 305 conversion

2013-09-30 Thread Douglas N Greve
what do you mean the frontal lobe is pointing straight up? On 09/30/2013 02:32 PM, Paul Beach wrote: > Freesurfer experts, > > I'm attempting to utilize an archived e-mail's contents to resample > data in MNI152 to 305. > > The script I'm using is as follows: > /mri_vol2vol \/ > /--mov > /ext

[Freesurfer] MNI152 to 305 conversion

2013-09-30 Thread Paul Beach
Freesurfer experts, I'm attempting to utilize an archived e-mail's contents to resample data in MNI152 to 305. The script I'm using is as follows: *mri_vol2vol \* *--mov /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz \* *--targ FSL_MNI152_FreeSurferConformed_1mm