Can you upload the subject to our file drop system? 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> > *To:* 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> >> *To:* Leon <leonad...@yahoo.com> <mailto:leonad...@yahoo.com> >> *Cc:* FreeSurfer <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>> 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> >>> 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. >> >> >> >> >> _______________________________________________ >> 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: 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
