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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