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. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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> >>>> 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. >>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
