Hi, Doug
Sorry for this late feedback.
Just so you can understand what is binLeftHippoBody.mgz I will explain its origin.
1) recon-all --hippo-subfields
2) mri_concat the posterior*.mgz to get the whole hippocampus
3) a custom octave routine to segment the whole hippocampus into head, body and tail. This routine preserves the probability values of the original posterior*.mgz
4) mri_binarize the whole hippocampus and its segments. So binLeftHippoBody.mgz is the binary mask of left hippocampal body.
5) mri-tesselate and mris_smooth the whole hippocampus binary mask to create a surface (lh.surfHippo)

Now that is the reason I would like to get the surface labels for head, body and tail. I would like to build a annot in order to display the colored segments over the whole hippocampus surface.
Your last tip was great and now I have vertex numbers at the labels files  and mris_label2annot works. It follows the commands I used to process the hippocampal body:
mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh --out_type mgh --hemi lh --regheader suj1 --surf surfHippo
mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo --id 1 --l lh.HippoBody.label

I put the --surf parameter pointing to lh.surfHippo because, if not, it would use lh.white (default). As I said it works but the results are not visually correct (see attached file). The surface loads on freeview with no problem but if I try to load the label representing the body or the annot with the 3 segments they do not appear. It seems only a small part of the vertices appears in blue. I also get the following output at the terminal window I used to start freeview:

MRISreadAnnotationIntoArray: vertex index out of range: 122882 i=00000000, in_array_size=11627
    annot file: ../label/lh.Hippo.annot
MRISreadAnnotationIntoArray: vertex index out of range: 122883 i=00000000, in_array_size=11627
    annot file: ../label/lh.Hippo.annot
MRISreadAnnotationIntoArray: vertex index out of range: 122884 i=00000000, in_array_size=11627
    annot file: ../label/lh.Hippo.annot
MRISreadAnnotationIntoArray: vertex index out of range: 122885 i=00000000, in_array_size=11627
    annot file: ../label/lh.Hippo.annot
reading colortable from annotation file...
colortable with 4 entries read (originally ../label/Hippo.ctab)
colortable with 4 entries read (originally ../label/Hippo.ctab)
=00000000, in_array_size=11627

Since the posterior*.mgz files are 0.5 x 0.5 x 0.5 mm I also tried to use mri_convert --vs 1 1 1, but it did not worked too.
I guess, or at least, I hope I am closer the image I want but I guess some more steps are necessary.
Thank you for any help.
Marcos



Em Qui, 2013-10-17 às 22:19 -0400, Douglas Greve escreveu:

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.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. 

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