Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi, and
mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi, and
mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Are you sure the label was generated on fsaverage? Does it look ok if you run
tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label
On 07/22/2013 05:13 PM, Lingqiang Kong wrote:
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi, and
mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Yes. The input label looks fine on fsaverage.
But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem.
Lingqiang
Are you sure the label was generated on fsaverage? Does it look ok if you run
tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label
On 07/22/2013 05:13 PM, Lingqiang Kong wrote:
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi,
and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote:
Dear Freesurfer list,
I was converting a surface label from 'fsaverage' space to individual subjects and got this error:
###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------###
The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi
It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine.
Did anyone have this problem before or know how to resolve this? Thank you.
BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... in the archive but it was never followed up.
Lingqiang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote:
Yes. The input label looks fine on fsaverage.
But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem.
Lingqiang
Are you sure the label was generated on fsaverage? Does it look ok if you run
tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label
On 07/22/2013 05:13 PM, Lingqiang Kong wrote:
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi,
and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
what is the input label? How was it created? Does it have -1 as the first number on any line?
On 07/22/2013 03:54 PM, Lingqiang Kong wrote: > Dear Freesurfer list, > > I was converting a surface label from 'fsaverage' space to > individual > subjects and got this error: > > ###---------------------### > Performing mapping from target back to the source label > ERROR: srcvtxno = -1 < 0 > trgvtxno = 140122, dmin = 1000 > trgregxyz = 0, 0, 0 > This means that a vertex in the target surface could > not be mapped to a vertex in the source surface > because the xyz of the target is outside of the > range of the hash table > ###---------------------### > > The command I used was: > mri_label2label --srclabel $fsaverage_brain_label --trg > $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj > --regmethod surface --hemi $hemi > > It's worth noting that this subject is from a patient population > with > lesion and we had to manually edit the white matter and re-run > autorecon. > This error only happens for one hemisphere of this patient, the > other > hemi > is fine. > > Did anyone have this problem before or know how to resolve this? > Thank > you. > > BTW. I found this > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... > in the archive but it was never followed up. > > >
> Lingqiang
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Running autorecon3 fixed the mri_label2label conversion problem.
Thank you everyone!
L
yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote:
Yes. The input label looks fine on fsaverage.
But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem.
Lingqiang
Are you sure the label was generated on fsaverage? Does it look ok if you run
tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label
On 07/22/2013 05:13 PM, Lingqiang Kong wrote:
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote:
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011).
No. The first number of all lines are integers ranging from 5 to 132000.
Just adding some details:
- when we first ran recon did the same label conversion and
mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now.
- the label conversion ERROR: srcvtno=-1 happens only on one hemi,
and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity.
Thank you.
Lingqiang
> what is the input label? How was it created? Does it have -1 as the > first number on any line? > > On 07/22/2013 03:54 PM, Lingqiang Kong wrote: >> Dear Freesurfer list, >> >> I was converting a surface label from 'fsaverage' space to >> individual >> subjects and got this error: >> >> ###---------------------### >> Performing mapping from target back to the source label >> ERROR: srcvtxno = -1 < 0 >> trgvtxno = 140122, dmin = 1000 >> trgregxyz = 0, 0, 0 >> This means that a vertex in the target surface could >> not be mapped to a vertex in the source surface >> because the xyz of the target is outside of the >> range of the hash table >> ###---------------------### >> >> The command I used was: >> mri_label2label --srclabel $fsaverage_brain_label --trg >> $my_subject_brain_label --srcsubject fsaverage --trgsubject >> $mysubj >> --regmethod surface --hemi $hemi >> >> It's worth noting that this subject is from a patient population >> with >> lesion and we had to manually edit the white matter and re-run >> autorecon. >> This error only happens for one hemisphere of this patient, the >> other >> hemi >> is fine. >> >> Did anyone have this problem before or know how to resolve this? >> Thank >> you. >> >> BTW. I found this >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... >> in the archive but it was never followed up. >> >> >> >> Lingqiang > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
glad to hear it Bruce On Wed, 24 Jul 2013, Lingqiang Kong wrote:
Running autorecon3 fixed the mri_label2label conversion problem.
Thank you everyone!
L
yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote:
Yes. The input label looks fine on fsaverage.
But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem.
Lingqiang
Are you sure the label was generated on fsaverage? Does it look ok if you run
tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label
On 07/22/2013 05:13 PM, Lingqiang Kong wrote:
Yes. The label file is attached.
Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues.
Lingqiang
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: > The input label is one from a set published 1000 brain functional > connectivity label from the Buckner lab (Yeo & Krienen, et al., > 2011). > > No. The first number of all lines are integers ranging from 5 to > 132000. > > Just adding some details: > 1) when we first ran recon did the same label conversion and > mri_label2label worked fine. Later > we edited the white matter and added control points, and re-ran > autorecon2-cp and autorecon2-wm. The surface looked better after the > editing, but we have this label conversion problem now. > > 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, > and > mri_label2label haults. However, on the other hemi, although > mri_label2label runs through without reporting error, the converted > labels > on subject surface looks like gibberish and out of place. So it's > likely > there are problem with both hemis, but with different severity. > > Thank you. > > Lingqiang > >> what is the input label? How was it created? Does it have -1 as the >> first number on any line? >> >> On 07/22/2013 03:54 PM, Lingqiang Kong wrote: >>> Dear Freesurfer list, >>> >>> I was converting a surface label from 'fsaverage' space to >>> individual >>> subjects and got this error: >>> >>> ###---------------------### >>> Performing mapping from target back to the source label >>> ERROR: srcvtxno = -1 < 0 >>> trgvtxno = 140122, dmin = 1000 >>> trgregxyz = 0, 0, 0 >>> This means that a vertex in the target surface could >>> not be mapped to a vertex in the source surface >>> because the xyz of the target is outside of the >>> range of the hash table >>> ###---------------------### >>> >>> The command I used was: >>> mri_label2label --srclabel $fsaverage_brain_label --trg >>> $my_subject_brain_label --srcsubject fsaverage --trgsubject >>> $mysubj >>> --regmethod surface --hemi $hemi >>> >>> It's worth noting that this subject is from a patient population >>> with >>> lesion and we had to manually edit the white matter and re-run >>> autorecon. >>> This error only happens for one hemisphere of this patient, the >>> other >>> hemi >>> is fine. >>> >>> Did anyone have this problem before or know how to resolve this? >>> Thank >>> you. >>> >>> BTW. I found this >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.h... >>> in the archive but it was never followed up. >>> >>> >>> >>> Lingqiang >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>
>>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Lingqiang Kong