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. >> >> >> >> >>>>> >> >> >> >> >>>>> _______________________________________________ >> >> >> >> >>>>> Freesurfer mailing list >> >> >> >> >>>>>Freesurfer@nmr.mgh.harvard.edu >> >> >> >> >>>>><mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> >>>>><mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> >>>>><mailto: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> >> >> >> >> >>>><mailto: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. >> >> >> >> >>> >> >> >> >> >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> > >> >> >> >> >> > >> >> >> > >> > -- 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
