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
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
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.
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 *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 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
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
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 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 _______________________________________________ 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.
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
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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
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 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.
OK, I have the data. Can you send me the exact command line I need to run to replicate your results? No shell variables or wild cards ...
On 06/04/2012 02:44 PM, Leon wrote:
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 http://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
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto: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>
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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 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 <mailto: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 <mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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 http://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
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto: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>
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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 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 <mailto: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 <mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 7, 2012 2:03 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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 http://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
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto: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>
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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 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 <mailto: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 <mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
________________________________ From: Leon leonado78@yahoo.com To: Douglas N Greve greve@nmr.mgh.harvard.edu Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 7, 2012 10:52 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 7, 2012 2:03 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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 http://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
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto: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>
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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 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 <mailto: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 <mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
________________________________ From: Leon leonado78@yahoo.com To: Douglas N Greve greve@nmr.mgh.harvard.edu Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 7, 2012 10:52 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 7, 2012 2:03 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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 http://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
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto: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>
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto: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 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 <mailto: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 <mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@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:* 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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto: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
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*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
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*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
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*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 mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto: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
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Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 1:32 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@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:* 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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
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*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
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
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*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
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*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
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*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 mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto: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
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Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
________________________________ From: Leon leonado78@yahoo.com To: Douglas N Greve greve@nmr.mgh.harvard.edu Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 3:48 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 1:32 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon
*To:* Douglas N Greve greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the
annotation file was transferred from the
subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@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:* 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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto: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
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto: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 mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto: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
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The information in this e-mail is intended only for the person to whom it is
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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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax:
617-726-7422
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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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
What is your command line and what is the terminal output? doug
On 8/27/12 7:57 PM, Longchuan Li wrote:
Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
*From:* Leon leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 3:48 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 1:32 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *To:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@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:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>>
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*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
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*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
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<mailto: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
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Hi, Doug Here is the output from my log file and my command. I have been running this command many times and sometimes the job got killed, but sometimes they finished without error.
/usr/local/sge/bitc/spool/node13/job_scripts/77912: line 7: 30345 Killed /home/lli/freesurferv51/bin/mri_label2vol.linux --offset 1 --annot /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/label/rh.randomroi300_WithoutMedialWall.MacaqueYerkes6_to_RVJ8_Preuss_20111115.annot --temp /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/brain.mgz --subject RVJ8_Preuss_20111115 --hemi rh --fillthresh 0 --proj frac 0 0.5 0.05 --o /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/rh.randomroi300_WithoutMedialWall_Ribbon.MacaqueYerkes6_to_RVJ8_Preuss_20111115_fill0_projs0_proje0.5_projin0.05.nii.gz --identity
Many thanks in advance!
Longchuan
________________________________ From: Douglas Greve greve@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 27, 2012 3:47 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What is your command line and what is the terminal output? doug
On 8/27/12 7:57 PM, Longchuan Li wrote:
Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
From: Leon leonado78@yahoo.com To: Douglas N Greve greve@nmr.mgh.harvard.edu Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 3:48 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, June 8, 2012 1:32 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that
ftp site. When you run
it, add "--offset 1". This will change the
segmentations IDs to go from
1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed
that the missing ROI in
the volume space is vertex_0 (see attached).
Totally there are 162
entries in the annotation file, but only 161
left in the volume file
after transferring the annotation file to the
volume using
mri_label2vol and the intensity value ranges
from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I
was told that the image
for the previous mail is too big.
*From:* Leon leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when
using mri_label2vol to
transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it.
The ROIs ending with 2 and
5s have been correctly labeled and have
volumes now after running the
fixed version of
mris_make_face_parcellation. However, there is still
one ROI missing in the volume data that is
located at the top of the
postcentral gyrus after the annotation file
was transferred from the
subject's surface to the volume using
mri_label2vol. I checked the
index of the ROI yesterday (I am at home now
and do not have access to
the data) and I remember the index of the
missing ROI is vertex_0 and
the location of the ROI is identical as the
one in the picture I
attached in the previous email. Do you think
it might be because the
mri_label2vol overlooks the index of 0, as
the intensity value in the
volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Leon leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when
using mri_label2vol to
transfer ic2.tri
Hi Leon, I found the problem.
mris_make_face_parcellation was actually
merging several units together. You can get a
fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@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:* 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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
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mailto:freesurfer@nmr.mgh.harvard.edu
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*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
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>>
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto: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 mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto: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>
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The information in this e-mail
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The information in this e-mail is
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<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
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Bugs:
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The information in this e-mail is intended
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Bugs:
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The information in this e-mail is intended only for the
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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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Longchuan, when I asked for the terminal output, I meant the stuff that gets printed to the screen when the command runs. Try running it outside of your script to capture the output. Also, does the old program require 20G ? doug
On 08/27/2012 04:20 PM, Longchuan Li wrote:
Hi, Doug Here is the output from my log file and my command. I have been running this command many times and sometimes the job got killed, but sometimes they finished without error.
/usr/local/sge/bitc/spool/node13/job_scripts/77912: line 7: 30345 Killed /home/lli/freesurferv51/bin/mri_label2vol.linux --offset 1 --annot /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/label/rh.randomroi300_WithoutMedialWall.MacaqueYerkes6_to_RVJ8_Preuss_20111115.annot --temp /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/brain.mgz --subject RVJ8_Preuss_20111115 --hemi rh --fillthresh 0 --proj frac 0 0.5 0.05 --o /home/lli/freesurferv51/subjects/RVJ8_Preuss_20111115/mri/rh.randomroi300_WithoutMedialWall_Ribbon.MacaqueYerkes6_to_RVJ8_Preuss_20111115_fill0_projs0_proje0.5_projin0.05.nii.gz --identity
Many thanks in advance!
Longchuan
*From:* Douglas Greve greve@nmr.mgh.harvard.edu *To:* Longchuan Li leonado78@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, August 27, 2012 3:47 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What is your command line and what is the terminal output? doug
On 8/27/12 7:57 PM, Longchuan Li wrote:
Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
*From:* Leon leonado78@yahoo.com mailto:leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 3:48 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu mailto:greve@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 8, 2012 1:32 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *To:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@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:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto: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
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*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
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*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
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<mailto: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
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-
Bruce Fischl -
Douglas Greve -
Douglas N Greve
-
Leon -
Longchuan Li