Hi, Doug.
Thanks again for all your attention.
I am trying to show the head, body and tail segments on the hippocampal surface. Each with one color. I thought the best way to do it would be creating an annot file with 3 surface labels one for each segment. The approach, concatenation of hippo-subfields -> binarize -> tesselation -> smooth, I used gave me a realistic hippocampal surface. I could also segment that concatenated volume into head, body and tail but I do not know how to convert these segments into surface labels.

Unfortunately mapping on the hippo surface did not work too, unless I did something wrong. Could you please check if the following commands are correct? Perhaps all I need is to add or remove one parameter.

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

Cheers,
Marcos.


Em Qua, 2013-10-30 às 10:47 -0400, Douglas N Greve escreveu: 
I've lost track of what you are trying to do. Can you just sample it on 
to your hippo surface?
doug



On 10/29/2013 08:05 PM, Marcos Martins da Silva wrote:
> I did several tests but I got no luck. But, I guess I know the reason: 
> when you use mri_vol2surf the tool needs a reference surface (lh.white 
> is default, if you do not use --surf argument). The problem is that 
> lh.white, lh.orig and lh.pial all exclude hippocampus. I loaded a 
> volume (orig.mgz) with the p-labels corresponding to left hippocampal 
> head, body and tail. Then I alternatively loaded the surfaces lh.orig, 
> lh.pial and lh.surfhippo. I am attaching screenshots with lh.orig and 
> lh.surfhippo. Registering seems good among volumes, surfaces and 
> p-labels. But hippocampus is completely excluded from lh.orig while 
> lh.pial includes just a few vertices in hippocampal region. On the 
> other side the lh.surfhippo perfectly matches the hippocampus.
> So, I guess I would need a different approach or a different surface 
> file that includes the hippocampus. I hope you can help me solve this. 
> Thank you for all your attention.
> BTW, I am not sending the lh.pial screenshot due to list's 500 K 
> restriction, but I can send you if you want to see.
> Cheers,
> Marcos
> 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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