I've put a new version of mri_label2vol at that ftp site. When you run
it, add "--offset 1". This will change the segmentations IDs to go from
1-162 instead of 0-161.
doug

On 06/08/2012 11:30 AM, Leon wrote:
> Hi, Douglas
>
> I checked the data this morning and confirmed that the missing ROI in
> the volume space is vertex_0 (see attached). Totally there are 162
> entries in the annotation file, but only 161 left in the volume file
> after transferring the annotation file to the volume using
> mri_label2vol and the intensity value ranges from 1 to 161.
>
> Thanks
>
> Leon
>
> PS: I am sending the message again because I was told that the image
> for the previous mail is too big.
>
> *From:* Leon <leonado78@yahoo.com>
> *To:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Thursday, June 7, 2012 10:52 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> transfer ic2.tri
>
> Hi, Douglas
>
> Thank you very much for taking care of it. The ROIs ending with 2 and
> 5s have been correctly labeled and have volumes now after running the
> fixed version of mris_make_face_parcellation.  However, there is still
> one ROI missing in the volume data that is located at the top of the
> postcentral gyrus after the annotation file was transferred from the
> subject's surface to the volume using mri_label2vol. I checked the
> index of the ROI yesterday (I am at home now and do not have access to
> the data) and I remember the index of the missing ROI is  vertex_0 and
> the location of the ROI is identical as the one in the picture I
> attached in the previous email. Do you think it might be because the
> mri_label2vol overlooks the index of 0, as the intensity value in the
> volumes starts with 1?
>
> I would appreciate your help on this.
>
> Leon
>
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Leon <leonado78@yahoo.com>
> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Thursday, June 7, 2012 2:03 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> transfer ic2.tri
>
> Hi Leon, I found the problem. mris_make_face_parcellation was actually
> merging several units together. You can get a fixed version from here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
> Let me know how it goes
> doug
>
> On 06/04/2012 02:44 PM, Leon wrote:
> > Hi, Douglas
> > I have uploaded the file to the system.
> > Also, my new results showed that  when  ic3.tri (instead of ic2.tri)
> > is used as the input, one ROI at the similar location is also missing.
> > Hope it will help you diagnose.
> >
> > Thanks
> > Leon
> >
> > *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > *To:* Leon <leonado78@yahoo.com <mailto:leonado78@yahoo.com>>
> > *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > *Sent:* Monday, June 4, 2012 1:00 PM
> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > transfer ic2.tri
> >
> > Can you upload the subject to our file drop system?
> >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> >
> >
> >
> >
> > On 06/04/2012 12:24 PM, Leon wrote:
> > > Hi, Douglas
> > >
> > > Thank you very much for the updated one. I tested the new codes and
> > > the problem is still there. The ID for the original version that
> > > generates a mask with one missing ROI is:
> > >
> > > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> > >
> > > I remember this is a version I downloaded from a link in FS archive.
> > >
> > > The ID for the one you sent to me is:
> > >
> > > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
> > >
> > > They look almost identical. Do you have any ideas what else may cause
> > > this issue and possible workaround?
> > >
> > > Thank you
> > >
> > > Leon
> > >
> > >
> > > *From:* Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > *Sent:* Friday, June 1, 2012 11:29 PM
> > > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > > transfer ic2.tri
> > >
> > >
> > > What version are you using? I fix a problem last Sept that might be
> > > like this. I've put a new version of mri_label2vol here:
> > >
> >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> > > Try this and let me know if it works.
> > > doug
> > >
> > >
> > > On 6/1/12 10:46 PM, Leon wrote:
> > >> Hi, Bruce
> > >> Here are my two command lines
> > >> For transferring the annot from the source template to the target
> > >> subject:
> > >>
> > >> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
> > >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
> > >> src_2_trg.annot --hemi rh --surfreg sphere.reg0
> > >>
> > >> Where sphere.reg0 is the registration from the target subject to the
> > >> source subject.
> > >>
> > >> For transfer them to the volume file:
> > >>
> > >> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp
> > >> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi
> > >> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz
> > >> --identity
> > >>
> > >>
> > >> Here is output for one of my transformations:
> > >>
> > >> Setting mapmethod to nnf
> > >> Source registration surface changed to sphere.reg0
> > >> Target registration surface changed to sphere.reg0
> > >> srcsubject = MacaqueA
> > >> srcval    = (null)
> > >> srctype    =
> > >> trgsubject = MacaqueB
> > >> trgval    =
> > >>
> >
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> > >> trgtype    =
> > >> srcsurfreg = sphere.reg0
> > >> trgsurfreg = sphere.reg0
> > >> srchemi    = rh
> > >> trghemi    = rh
> > >> frame      = 0
> > >> fwhm-in    = 0
> > >> fwhm-out  = 0
> > >> label-src  = (null)
> > >> label-trg  = (null)
> > >> OKToRevFaceOrder  = 1
> > >> Reading source surface reg
> > >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
> > >> Loading source data
> > >> Reading surface file
> > >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
> > >> reading colortable from annotation file...
> > >> colortable with 162 entries read (originally
> > >> /usr/local/freesurfer/lib/bem/ic2.tri)
> > >> Reading target surface reg
> > >> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
> > >> Done
> > >> Mapping Source Volume onto Source Subject Surface
> > >> surf2surf_nnfr: building source hash (res=16).
> > >> Surf2Surf: Forward Loop (61916)
> > >>
> > >> Surf2Surf: Dividing by number of hits (61916)
> > >> INFO: nSrcLost = 17467
> > >> nTrg121 = 61916, nTrgMulti =    0, MnTrgMultiHits = 0
> > >> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits
> > >> = 0.920927
> > >> Saving target data
> > >> Converting to target annot
> > >> Saving to target annot
> > >>
> >
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> > >> step2: writing the surface label to volume...
> > >> Number of labels: 0
> > >> Annot File:
> > >>
> >
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> > >> Template Volume:
> > >> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
> > >> Outut Volume:
> > >>
> >
> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
> > >> Registration File: (null)
> > >> Fill Threshold: 0
> > >> Label Vox Vol:  1
> > >> ProjType:      frac
> > >> ProjTypeId:    2
> > >> ProjStart:      0.3
> > >> ProjStop:      0.8
> > >> ProjDelta:      0.05
> > >> Subject:  MacaqueB
> > >> Hemi:    rh
> > >> UseNewASeg2Vol:  1
> > >> DoLabelStatVol  0
> > >> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> > >> Template RAS-to-Vox: --------
> > >> -1.000  -0.000  -0.000  160.000;
> > >> -0.000  -0.000  -1.000  160.000;
> > >> -0.000  1.000  -0.000  160.000;
> > >> -0.000  -0.000  -0.000  1.000;
> > >> Template Voxel Volume: 1
> > >> nHits Thresh: 0
> > >> Using Identity Matrix
> > >> RegMat: --------
> > >>  1.000  0.000  0.000  0.000;
> > >>  0.000  1.000  0.000  0.000;
> > >>  0.000  0.000  1.000  0.000;
> > >>  0.000  0.000  0.000  1.000;
> > >> Label RAS-to-Vox: --------
> > >> -1.000  0.000  0.000  160.000;
> > >>  0.000  0.000  -1.000  160.000;
> > >>  0.000  1.000  0.000  160.000;
> > >>  0.000  0.000  0.000  1.000;
> > >>  INFO: loading surface
> > >> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.white
> > >> nvertices = 61916
> > >> Reading thickness
> > >> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.thickness
> > >> Loading annotations from
> > >>
> >
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> > >> reading colortable from annotation file...
> > >> colortable with 162 entries read (originally
> > >> /usr/local/freesurfer/lib/bem/ic2.tri)
> > >> annotidmax = 162
> > >> Allocating Hit Volume (1013448704) voxels
> > >> nlabels = 162
> > >>
> > >> PVF (null)
> > >> Thesholding hit volume.
> > >> mri_label2vol done
> > >>
> > >> *From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>
> > >> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > >> *To:* Leon <leonado78@yahoo.com <mailto:leonado78@yahoo.com>
> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>>>
> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>
> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>>>
> > >> *Cc:* FreeSurfer <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>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >> *Sent:* Friday, June 1, 2012 8:02 PM
> > >> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > >> transfer ic2.tri
> > >>
> > >> Can you send us your command lines and screen output?
> > >>
> > >>
> > >>
> > >> On Jun 1, 2012, at 7:44 PM, Leon <leonado78@yahoo.com
> <mailto:leonado78@yahoo.com>
> > <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>>
> > >> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>
> <mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com>>>> wrote:
> > >>
> > >>> Hi, folks
> > >>>
> > >>> when I transferred the annotation file obtained using
> > >>> mri_make_face_parcellation based on ic2 (162 labels) to a volume
> > >>> file using mri_label2vol, I found that one ROI patch was missing in
> > >>> the volume file (see attached). I searched archives and the closest
> > >>> thread I could found is that somebody reported an ROI with the last
> > >>> index was missing in the mgz file after they were transferred from
> > >>> the annotation file to the volume file.
> > >>>
> > >>> Could someone help on this? If this happens to be a bug, is there
> > >>> any other strategy that will allow me to get a GM/WM ribbon without
> > >>> a hole on it?
> > >>>
> > >>> Many thanks in advance
> > >>> Leon
> > >>> <MissingROI.jpg>
> > >>> _______________________________________________
> > >>> 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>
> > <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>
> > <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.
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> 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>
> > <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>
> > <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
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >
> > _______________________________________________
> > 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>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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