Thanks again. I will recheck all files and try your suggestions this weekend and report you back.
Em Qui, 2013-10-24 às 19:39 -0400, Douglas N Greve escreveu: 
areyou loading the label (output of mri_cor2label) or did you create an 
annotation? Try loading the label. Then try loading 
LeftHippoBody_surf.mgh. If that does not look ok, check the registration 
between binLeftHippoBody.mgz and subj1 with --regheader

doug

On 10/24/2013 06:40 PM, Marcos Martins da Silva wrote:
> Hi, Doug
> Thanks again for your help.
> Using the command tksurfer suj1 lh surfHippo, I get the surface loaded 
> in tksurfer in the same way that I get in freeview. The only 
> difference is that the terminal window output is more verbose and that 
> is valuable when investigating this kind of situation. I am attaching 
> a screenshot. I got this just after I used tksurfer to import an 
> annotation (lh.surfHippo + hippo.annot.png).
> The screenshot show just a few vertices with color. Indeed this is 
> similar to what we see in freeview, except that in this last tool all 
> vertices not in label appears in black and tksurfer preserves the gray 
> color.
> At terminal output  we can see tksurfer expects the surface refers to 
> lh.white. That is not the case, I guess. I think it helps explain the 
> terminal window output we see in freeview and also in tksurfer when I 
> try to load the annot file. It seems we have lots of vertices in annot 
> file that both tools cannot find in surface file and at the same time 
> we have lots of vertices in my surface file not described in the annot 
> files. At least now I can understand the situation. It puzzles me 
> because the surface, binary masks, labels and annotations were created 
> from the same source: the posterior*.mgz files created by recon-all 
> --hippo-subfields. But, well, I probably misunderstood something in 
> documentation and lost my way in some point. I hope you can help me 
> with the correct steps to be followed. I still dream of showing the 
> hippocampus in a similar way we do with cortex when we load lh.pial 
> and lh.aparc.annot.
> Thank you for your help and attention.
> Cheers,
> Marcos.
> Em Qui, 2013-10-24 às 12:40 -0400, Douglas N Greve escreveu:
>> Can you load it properly in tksurfer?
>>
>>
>> On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote:
>> >
>> > 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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