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 <leonad...@yahoo.com> > *To:* Douglas N Greve <gr...@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 <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 > <mailto:gr...@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:* 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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> <mailto: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>>> > > <mailto: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>>> > > >> <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 <leonad...@yahoo.com > <mailto:leonad...@yahoo.com> > > <mailto:leonad...@yahoo.com <mailto:leonad...@yahoo.com>> > > >> <mailto: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>> > > <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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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> > <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 > 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 > > > > _______________________________________________ > 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
