Re: [Freesurfer] user specified output orientation using mri_convert?

It may be that tkmedit is doing the interpolation. Try running mri_diff with the --pixonly option. This just tests for differences in pixel value, excluding the geometry, etc. Michael Harms wrote: > > Command (FS v4.1.0) was just: > mri_convert --out_orientation input.nii output.nii > > Then, lo

Re: [Freesurfer] Difference in sub-cortical volumes

Hi Indika, the aseg.stats includes partial volume estimates, so it should be more accurate (and not the same as the result of mri_binarize) cheers Bruce On Fri, 5 Feb 2010, Walimuni, Indika S wrote: > Hi > I noticed in my FreeSurfer runs, that there is a significant volume > difference for su

[Freesurfer] Difference in sub-cortical volumes

Hi I noticed in my FreeSurfer runs, that there is a significant volume difference for sub-cortical structures obtained using the aseg.stat file and the mri_binaraize command. For example I got 14454mm3 for Thalamus-Proper (obtained by summing up the values for Left_Thalamus-Proper and Right-Thal

Re: [Freesurfer] user specified output orientation using mri_convert?

Command (FS v4.1.0) was just: mri_convert --out_orientation input.nii output.nii Then, loading both input.nii and output.nii into tkmedit, it is clear that the voxel values at the same cursor location do not match. (output.nii is clearly smoother, consistent with it being interpolated). thanks,

Re: [Freesurfer] user specified output orientation using mri_convert?

Michael Harms wrote: > Hi Doug, > > Is --reorder4 a new feature in one of the more recent releases? > (Currently, I'm using mri_convert from v4.1.0, and I don't see a -- > reorder4 flag). > Yes, it is. It is actually only in the dev version. > Also, can you please clarify what do you mean when

Re: [Freesurfer] user specified output orientation using mri_convert?

Hi Doug, Is --reorder4 a new feature in one of the more recent releases? (Currently, I'm using mri_convert from v4.1.0, and I don't see a -- reorder4 flag). Also, can you please clarify what do you mean when you said that -- out_orientation should not resample? If I take an nii file with this t

Re: [Freesurfer] user specified output orientation using mri_convert?

Sorry, I don't have anything that will reorder and change the geometry to be correct. You might be able to do it with --reorder4 (and not --reorder) in combination with --out_orientation. --out_orientation should not resample. doug Michael Harms wrote: > Hello Doug, > Is it possible using mri_

Re: [Freesurfer] sliver problem remains after going through relevant wiki page

the only thing i can suggest is to try our Ubuntu VirtualBox for Windows, which I know that tksurfer/tkmedit/qdec will work within (at least on the laptops and desktops i've seen it installed upon, it might none-the-less fail on other systems if there is an underlying graphics driver issue). its a

[Freesurfer] user specified output orientation using mri_convert?

Hello Doug, Is it possible using mri_convert to just reorder the way in which the data is stored, without any resampling of the actual voxel values? i.e., I have Siemen's MPRAGE DICOMs, and if run mri_convert, I get a default "PIL" orientation. I would like to just reorder the way in which the d

[Freesurfer] 2010 FSL & FreeSurfer course in Heidelberg, Germany

if you missed it the first time... > > We are pleased to announce the 2010 FSL & FreeSurfer course in > Heidelberg, Germany. It will run immediately before the Human Brain > Mapping conference, which will be in Barcelona - a 2-hour flight > from the Heidelberg area. The course is an official satel

[Freesurfer] use of Freesurfer in 2-4 year olds

Dear Freesurfer experts, We would like to use Freesurfer in a group of children 2-4 years of age. Is there a pediatric template in the works? How valid is it to use Freesurfer currently in this age group? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brai

[Freesurfer] multiple comparison correction using monte carlo

Hi, I have performed a linear mixed model analysis on surface data in AFNI using SUMA, resulting in each vertex having a p value. I would like to perform a multiple comparison correction using freesurfer, as an FDR approach in AFNI is to stringent (individual vertex statistical thresholds are low)