Not sure if you've done this, but if you run AFNI's @SUMA_Make_Spec_FS
command it will convert all .mgz files to .nii. These can then be loaded
as an overlay in AFNI. If you open the @SUMA_Make_Spec_FS command in a
text editor, there is a line (387 in my editor) to edit which files to
convert,
You can load the segmentation as both a segmentation and an input volume
in tkmedit, eg
tkmedit subject orig.mgz -aux gmroi_volume.nii.gz -seg gmroi_volume.nii.gz
You can then see the number of each of your segmentations in the Aux
field when you click on your segmentation. There's probably an
Hi Paul, I'm not sure I understand. What does 3dcalc have to do with the
LUT?
doug
On 02/25/2013 05:13 PM, Paul Beach wrote:
> Hi Doug. Thank you for the e-mail.
>
> I do, actually, have a 'next step' problem.
>
> I've been able to get ROIs drawn in tksurfer into an augmented
> aparc+aseg file
Hi Paul, do you still have a problem that needs to be solved?
doug
On 02/18/2013 04:39 PM, Paul Beach wrote:
> Thank you for forwarding this.
>
> I realize I need to further clarify my issue as well.
>
> With the help of Doug Greve I've taken hand made ROIs in tksurfer,
> repackaged them into a
Hi Ziad,
Thank you so much for the suggestions. However, I'm not really sure how to
utilize any of them...So I guess more detailed help would be necessary for
me to follow these suggestions. Sorry.
I've also never actually used SUMA. Previously I was just using a 3dcalc
command to bring aseg ROIs
Thanks Ziad
Bruce
On Feb 19, 2013, at 10:42 PM, ziad wrote:
> Hello Paul,
>
> There are a couple of ways I can think of bringing the new ROIs to AFNI land
> from FreeSurfer. I can suggest the following, with the assumption that you
> seek to dump the average time series from single-subject
Thank you for forwarding this.
I realize I need to further clarify my issue as well.
With the help of Doug Greve I've taken hand made ROIs in tksurfer,
repackaged them into a new annotation, and repackaged that into a new aseg
file for an average subject. Now (and this is where I'm stuck) I'm try
Hi Paul
we usually call those labels and have an ascii label file format. Not
sure how to get that into AFNI, but I'm zure Ziad (ccd) knows.
cheers
Bruce
On Mon, 18
Feb 2013, Paul Beach wrote:
Hi there,
Through the help of the Freesurfer Q&A staff I've been able to get ROIs
drawn in tksurf
