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.html ) 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. 

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.