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 ās 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 ās 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
>>