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 <gr...@nmr.mgh.harvard.edu>
To: Leon <leonad...@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 <gr...@nmr.mgh.harvard.edu>
> *To:* Leon <leonad...@yahoo.com>
> *Cc:* FreeSurfer <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>
>
>
>
>
> 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 <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
> > *To:* 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 <fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>
> >> <mailto:fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>
> >> *To:* Leon <leonad...@yahoo.com <mailto:leonad...@yahoo.com>>
> <mailto:leonad...@yahoo.com <mailto:leonad...@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>>
> >> *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 <leonad...@yahoo.com
> <mailto:leonad...@yahoo.com>
> >> <mailto:leonad...@yahoo.com <mailto:leonad...@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>>
> >>> 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>>
> >> 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>>
> >> 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>>
> > 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 <mailto:gr...@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
>
>
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________
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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.
