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>
To: Leon <leonado78@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 <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
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.

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