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.
- recon-all --hippo-subfields
- mri_concat the posterior*.mgz to get the whole hippocampus
- 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.h... >> ) 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. >> >> _______________________________________________ >> Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.