Is *binLeftHippoBody.mgz a volume label or a surface label? If a volume label, map it onto the surface with mri_vol2surf, the run mri_cor2label *specifying --surf
doug
On 10/17/13 5:00 PM, Marcos Martins da Silva wrote:
Hi, Doug Thank you for your answer.
I am trying cor2label as you suggested. First of all I am afraid to say that website documentation and help from the own command are a bit different so I got a little confused. But the following command worked: *mri_cor2label --i binLeftHippoBody.mgz --id 1 --l 2.leftBody*
Using freeview I could load the hippocampus volume and 2.leftBody as a ROI. I attached a screenshot that also included 1.leftHead and 3.leftTail, generated in the same way. When I tried to concatenate the 3 labels into an annot file I got an error:
*mris_label2annot --s bert --h lh --ctab HippoColorLUT.txt --l 1.leftHead.label --l 2.leftBody.label --l 3.leftTail.label --a lefthippo* *Loading /home/marcos/freesurfer/subjects/bert/surf/lh.orig* *1 16711680 leftHead* *ERROR: 1.leftHead.label, n=0, vertex -1 out of range*
When I checked label file generated by mri_cor2label the first collumn (vertex number) contains only *-1* as value. It seems that when you use mri_cor2label it does not preserve or even recover the vertex number. It also seems I need the correct vertex number in label file to use mris_label2annot Just to rule out a problem with the hippocampal subfield files I tried the example command (extracted from command help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number.
Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label?
Cheers, Marcos
Em Qua, 2013-10-16 às 20:34 -0400, Douglas Greve escreveu:
I think you need to use mri_cor2label (not very well named:) doug
On 10/16/13 4:24 PM, Marcos Martins da Silva wrote:
Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.h... ) and, unless I am wrong, it seemed to me that mri_label2vol could be the tool to get it. If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. Thanks in advance for any help. Cheers, Marcos.
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