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 To: Leon leonado78@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
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 *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 fischl@nmr.mgh.harvard.edu mailto:fischl@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:* 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> 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
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