Hi, Doug
This new version works perfectly. I also did another annotation based on original hippocampal subfields (CA1, CA2_3, CA4_DG and the tail complement). I attached  screenshots showing the final result. Due to spatial disposition of the subfields I included 1screenshot to show superior aspect and a second for the inferior one. It was a long thread with a happy end. Thank you very much.
Cheers,
Marcos
Em Ter, 2013-11-12 às 16:35 -0500, Douglas N Greve escreveu: 
Hi Marcos, I have found and fixed the problem. As you suspected, the 
orig surface was being loaded instead of the surface you need. The fix 
is here (for centos6):

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_label2annot

Use the --surf option to specify your surface (without hemi designation, 
eg, surfHippo )

If you need it for another platform, let me know and I'll put it on-line 
after our nightly build

doug


On 11/06/2013 12:07 PM, Marcos Martins da Silva wrote:
> Hi, Doug
> Thank you for fast feedback.
> Answering your question, the annotation file I produced works but it 
> is not adequate because it has lots of unmapped vertices and this 
> generates thousands of warning lines when using freeview or tksurfer. 
> And generating all this terminal output steals some time. So a bit of 
> each of your options you asked about. Investigating the problem I 
> noticed that:
> 1- The first lines output on terminal during mris_annot2label includes 
> this one: *Loading /home/marcos/freesurfer/subjects/suj1/surf/lh.orig*
> 2- I guessed this confirmed my suspicions that mris_annot2label was 
> considering another file besides my labels when generating the annot file
> 3- Since it was not possible to use something like --ref to point to 
> lh.surfHippo, I tried a workaround. I know it was a dirty and low blow 
> but... it worked great. I saved lh.orig as real_lh.orig and copied 
> lh.surfHippo to lh.orig. This way, mris_annot2label would be 
> considering my hippo surface instead of lh.orig while creating the 
> annotation file. Using this approach mris_info says the annot file and 
> the surface have the same number of vertices. Both Freeview and 
> tksurfer loaded the surface and the annot files with no warning 
> messages and ad quick as it should be.
> 4- Checking 
> https://github.com/neurodebian/freesurfer/blob/master/mris_label2annot/mris_label2annot.c 
> , I confirmed that ?h.orig is hardcoded:
>
> // Read the surf   
> sprintf(tmpstr,"%s/%s/*surf/%s.orig*",SUBJECTS_DIR,subject,hemi); 
>   printf("Loading %s\n",tmpstr);   mris = MRISread(tmpstr);
>
> Just as a suggestion, perhaps you could add a --ref parameter to 
> mris_label2annot, while keeping ?h.orig as default.  That would allow 
> a consistent pathway (vol2surf -> cor2label -> label2annot ->freeview) 
> with all steps considering the same files.
>
> I guess the command and warning lines I mentioned in my last message 
> and you asked are no more necessary but they follow anyway. I just 
> restricted the terminal output to final lines for simplicity it would 
> be really huge.
>
> freeview -f lh.surfHippo:annot=$SUBJECTS_DIR/suj1/label/lh.Hippo
>
> MRISreadAnnotationIntoArray: vertex index out of range: 122882 
> i=00000000, in_array_size=11627
>     annot file: /home/marcos/freesurfer/subjects/suj1/label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122883 
> i=00000000, in_array_size=11627
>     annot file: /home/marcos/freesurfer/subjects/suj1/label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122884 
> i=00000000, in_array_size=11627
>     annot file: /home/marcos/freesurfer/subjects/suj1/label/lh.Hippo.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 122885 
> i=00000000, in_array_size=11627
>     annot file: /home/marcos/freesurfer/subjects/suj1/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)
> ippo.annot
> in_array_size=11627
>
> Thank you very much, Doug
> Cheers,
> Marcos
>
>
> Em Qua, 2013-11-06 às 10:25 -0500, Douglas N Greve escreveu:
>> So is the problem that the annotation does not look good or is the
>> problem that you are getting a lot of warnings about unmapped vertices.
>> Please send the command lines that generate the warnings (and the
>> terminal output)
>> doug
>>
>>
>> On 11/06/2013 10:05 AM, Marcos Martins da Silva wrote:
>> > Hi, Doug
>> > Thanks again for your help.
>> > I am really glad to say I managed to get the labels and annotation
>> > file I wanted. See attached screenshot for result. There is one final
>> > problem I will explain ahead. The parameter that made this possible
>> > was *--ref*. So the final mri_vol2surf that made the trick was:
>> >
>> > mri_vol2surf --src binLeftHippoTail.mgz --out LeftHippoTail_surf.mgh
>> > --out_type mgh --hemi lh --regheader suj1 --surf surfHippo
>> > --projdist-max -2 0 .1 *--ref* binLeftHippoTail.mgz
>> >
>> > This way, using my binary mask both as source and reference I got the
>> > correct surface overlay to use as input in:
>> >
>> > mri_cor2label --i LeftHippoTail_surf.mgh --surf suj1 lh surfHippo --id
>> > 1 --l lh.HippoTail.label
>> >
>> > The --projdist parameter you suggested resulted in a a better image so
>> > I kept. Repeating this sequence for head and body I got what I wanted.
>> > It seems the problem was related to differences in space among the
>> > hipocampal subfields filesand orig.mgz (the default reference) perhaps
>> > because the first files are 0.5 x 0.5 x 0.5 mm^3 and orig.mgz is 1 x 1
>> > x 1 mm^3 or because the hippocampal subfields are generated from a
>> > strict region around the original hippocampal segments you find in
>> > aseg.mgz.
>> > Both Freeview and tksurfer can load the labels with no error message.
>> > Both can load the annotation file too. But at terminal window they
>> > show lots of vertices out of index (that is, present in lh.hippo.annot
>> > and absent in lh.surfHippo). Labels seem ok with about 12000 vertices
>> > if I sum the number of vertices in the 3 files because some vertices
>> > are present in more than 1 label but annot includes a huge amount of
>> > vertices mapped to unknown. It follows mris_info output.
>> >
>> > *mris_info --s suj1 lh surfHippo --a ../label/lh.Hippo.annot *
>> > *ERROR: ../label/lh.Hippo.annot has 122886 vertices, while
>> > /home/marcos/freesurfer/subjects/suj1/surf/lh.surfHippo has 11627
>> > vertices*
>> >
>> > It seems that mris_label2annot include a lot of unnecessary unknown
>> > vertices not present in my surface nor in the labels during its
>> > processing. It does not avoid using the annotation file but produces a
>> > huge amount of warning lines at terminal window. I guess
>> > mris)label2annot is using some other file as reference and seeing a I
>> > did not see any parameter I could add to restrict this behavior. I
>> > guess if I had something equivalent to --ref parameter as seem in
>> > mri_vol2surf I could have a better result. Alternatively, if I could
>> > process the annot file to trim the unmapped vertices I guess it would
>> > work too.
>> > This is the mris_label2annot I am using:
>> >
>> > *mris_label2annot --s suj1 --h lh --ctab ../label/Hippo.ctab --a Hippo
>> > --l ../label/lh.HippoHead.label --l ../label/lh.HippoBody.label --l
>> > ../label/lh.HippoTail.label --maxstatwinner*
>> >
>> > I hope you can help me in this final issue so we can finnish this
>> > thread. Thank you once more for your attention
>> > Cheers,
>> > Marcos.
>> > Em Seg, 2013-11-04 às 18:28 -0500, Douglas N Greve escreveu:
>> >> That vol2surf command might miss the values you want to sample. Try
>> >> adding --projdist-max -2 0 .1
>> >> This will sample from 2mm into the hippo out to the surface in .1mm
>> >> increments and then take the maximum value it finds
>> >> doug
>> >>
>> >> On 10/30/2013 03:08 PM, Marcos Martins da Silva wrote:
>> >> > 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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