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>
*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
<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
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
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.
