[Freesurfer] regenerating surfs after pial edits

Dear Freesurfer Experts, I am trying to create surfaces that can be used in afni/SUMA for cortical based inter-subject alignment. For most of my subjects your programs have worked perfectly. But I am having a problem for two subjects with dura residual from the skull stripping that is disotrt

[Freesurfer] Converting mgz to nii.gz

Dear all, I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation. I used for converting this .mgz image to .nii.gz the mri_convert as you can see below: mri_convert -

Re: [Freesurfer] problem applying morph with mri_vol2vol

Hi Greg, Have you tried to just apply the bbreg transformation to your tract to double check whether that registration is accurate? Lilla On Tue, 10 Jan 2012, Gregory Kirk wrote: Hi i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.

Re: [Freesurfer] Converting mgz to nii.gz

Hi Antonella, You should be able to just do mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz BTW, when resampling your FA data to CVS spac

[Freesurfer] control points

Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other

Re: [Freesurfer] control points

Hi Alana Have you tried changing the skull strip parameters? Cheers Bruce On Jan 16, 2012, at 6:33 PM, Alana Shepherd wrote: > Hello, > I am running version 5.0, and am finding in a few cases that some areas (most > commonly STG) are missing from the original brainmask - after adding contro

Re: [Freesurfer] control points

Hmmm. If you upload the subject we will take a look Bruce On Jan 16, 2012, at 9:53 PM, Alana Shepherd wrote: > On the brainmask the intensity within the STG wm is either slightly lower > than 110 or slightly higher, though at the exact location of the control > points it is 110. Similarly on

[Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

Hi All, I have a very small set of patients and I would like to compare the volumes of subcortical structures and thickness across the cortex to those of a large normative set. I don't need all the underlying data, just means and standard deviations. Is such a set of measures available? Than

Re: [Freesurfer] control points

Great, thanks. Do you need the brainmask plus surf ?h orig and/or aparc/aseg? Alana On 17/01/2012, at 2:09 PM, Bruce Fischl wrote: > Hmmm. If you upload the subject we will take a look > Bruce > > > > On Jan 16, 2012, at 9:53 PM, Alana Shepherd > wrote: > >> On the brainmask the intensity

Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15

Hi, was this problem ever resolved? I am seeing the same issue on my mac desktop. Thanks, Thomas On Mon, May 10, 2010 at 3:47 AM, Fred Dick wrote: > Hi Sebastian and Bruce > > thanks for the Sunday afternoon assists. Unfortunately, not a VNC problem > (am running it directly in X11, Xquartz 2

Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15

Attaching what I am seeing... On Tue, Jan 17, 2012 at 2:31 PM, Thomas Yeo wrote: > Hi, was this problem ever resolved? > > I am seeing the same issue on my mac desktop. > > Thanks, > Thomas > > > On Mon, May 10, 2010 at 3:47 AM, Fred Dick wrote: > >> Hi Sebastian and Bruce >> >> thanks for the