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>
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 <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>
>_______________________________________________
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu
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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
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dispose of the e-mail._______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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