what is your freeview command line? In the mri_label2vol command below,
where does the label come from?
On 03/28/2018 01:11 PM, gj wrote:
> 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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