Dear Experts,
I am trying to "back-normalise" significant clusters identified in a qdec analysis (2 groups, thickness as main variable of interest) back into individual subjects so that I can derive cortical statisitcs.
As per previous posts I have been trying to use mri_cor2label but am running into some problems. My processing is as follows:
1) Identify file of interest which contains 3 clusters (labelled 1.000000 to 3.000000 as viewed in tksurfer and on qdec text output following analysis) significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot
2) mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
This produces a file called cluster2.label but when I try loading it into tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in menu system) I get the following error message which prevents me from double checking the label:
% ******************** 0 nonzero vertices found ********************
label stat field identically zero - setting to 1
1890 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
1617 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
My questions are:
1) Why does this occur ?
2) How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot to label files which I can then propagate to all subjects using mri_label2label).
Thanks.
Mahinda
Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find lh.aparc.a2009s and rh.aparc.a2009s under subjects/PT1/stats. I would like to know what is the difference between the two files? Thanks,Yawu
Now, I get it. lh means left side. :)Yawu
From: liuy88@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 5 Nov 2012 10:32:37 +0000 Subject: [Freesurfer] regional cortical thickness output
Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find lh.aparc.a2009s and rh.aparc.a2009s under subjects/PT1/stats. I would like to know what is the difference between the two files? Thanks,Yawu
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Hi Mahinda, you need to tell mri_cor2label that this is a surface with the --surf fsaverage lh white You can propagate this label to other subjects using mri_surf2surf.
doug
On 11/04/2012 10:08 PM, Mahinda Yogarajah wrote:
Dear Experts,
I am trying to "back-normalise" significant clusters identified in a qdec analysis (2 groups, thickness as main variable of interest) back into individual subjects so that I can derive cortical statisitcs.
As per previous posts I have been trying to use mri_cor2label but am running into some problems. My processing is as follows:
- Identify file of interest which contains 3 clusters (labelled
1.000000 to 3.000000 as viewed in tksurfer and on qdec text output following analysis) significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot
- mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
This produces a file called cluster2.label but when I try loading it into tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in menu system) I get the following error message which prevents me from double checking the label:
% ********************0 nonzero vertices found ********************
label stat field identically zero - setting to 1
1890 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
1617 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
My questions are:
Why does this occur ?
How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot
to label files which I can then propagate to all subjects using mri_label2label).
Thanks.
Mahinda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Thanks for quick reply. Does it make a difference if I use mri_label2label instead of mri_surf2surf for label propagation after I have used mri_cor2label ? Thanks.
M
On 5 Nov 2012, at 03:08, Mahinda Yogarajah y.mahinda@gmail.com wrote:
Dear Experts,
I am trying to "back-normalise" significant clusters identified in a qdec analysis (2 groups, thickness as main variable of interest) back into individual subjects so that I can derive cortical statisitcs.
As per previous posts I have been trying to use mri_cor2label but am running into some problems. My processing is as follows:
Identify file of interest which contains 3 clusters (labelled 1.000000 to 3.000000 as viewed in tksurfer and on qdec text output following analysis) significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot
mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
This produces a file called cluster2.label but when I try loading it into tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in menu system) I get the following error message which prevents me from double checking the label:
% ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 1890 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Couldn't assign 1617 vertices. 1617 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Couldn't assign 1617 vertices.
My questions are:
Why does this occur ?
How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot to label files which I can then propagate to all subjects using mri_label2label).
Thanks.
Mahinda
oops, sorry, I mean label2label not surf2surf doug
On 11/05/2012 03:48 PM, Mahinda Yogarajah wrote:
Dear Doug,
Thanks for quick reply. Does it make a difference if I use mri_label2label instead of mri_surf2surf for label propagation after I have used mri_cor2label ? Thanks.
M
On 5 Nov 2012, at 03:08, Mahinda Yogarajah <y.mahinda@gmail.com mailto:y.mahinda@gmail.com> wrote:
Dear Experts,
I am trying to "back-normalise" significant clusters identified in a qdec analysis (2 groups, thickness as main variable of interest) back into individual subjects so that I can derive cortical statisitcs.
As per previous posts I have been trying to use mri_cor2label but am running into some problems. My processing is as follows:
- Identify file of interest which contains 3 clusters (labelled
1.000000 to 3.000000 as viewed in tksurfer and on qdec text output following analysis) significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot
- mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
This produces a file called cluster2.label but when I try loading it into tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in menu system) I get the following error message which prevents me from double checking the label:
% ********************0 nonzero vertices found ********************
label stat field identically zero - setting to 1
1890 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
1617 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
Couldn't assign 1617 vertices.
My questions are:
Why does this occur ?
How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot
to label files which I can then propagate to all subjects using mri_label2label).
Thanks.
Mahinda
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freesurfer@nmr.mgh.harvard.edu
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yawu Liu