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>
To: Leon <leonad...@yahoo.com>
Cc: FreeSurfer <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> 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>
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