Hi,
I loaded the 2mm MNI152 template and the mri_label2vol outputs in
mricron, and I saw that the labels are completely outside the template.
So, I know now to use freeview rather than the deprecated tkmedit so I
can also load the original atlas labels to check against (using the 2mm
MNI152 template as background) -- in any case, I don't even see the
labels, I guess because the ROIs/masks lie outside the display. I'm also
not sure what the equivalent of tkmedit's overlay-reg is for freeview? I
assume my not loading one is why I get the error, "Label coordinate out
of bound" when I try and load the original atlas labels (in fsaverage
space) on the MNI152 template?
Thank you!
Gina
P.S. Can't find a straightforward way to reply with the entire thread
when receiving only a digest from the listserv -- reply to the digest
takes the freesurfer-request address rather than the list address and
the button on the website for archives only gives the option of replying
directly to the person who posted)...what am I missing?
------------------------------
Douglas Greve dgreve at mgh.harvard.edu
Tue Mar 27 14:01:16 EDT 2018
how are you verifying that it is not in the right place? You should view
it on the 2mm MNI152 using freeview. Also, your label should be a label
in fsaverage space.
On 3/27/18 9:52 AM, gj wrote:
> Hi,
>
> Newbie question....I want to take FreeSurfer labels (from an atlas in
> fsaverage space) and convert it into a volumetric NIFTI mask. I ran the
> following command, but I must be missing something because the output is
> not in the right space (far too posterior):
>
> $FREESURFER_HOME/bin/mri_label2vol \
> --label $ll \
> --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
> --reg $FREESURFER_HOME/average/mni152.register.dat \
> --fillthresh .5 \
> --o $wd/${ll}.nii
>
> Am I perhaps supposed to first create the volumetric file without
> mapping into MNI space and then use tkregister2?
>
> Thanks in advance for any help or advice!
> Gina
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