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
