Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
Sorry this didn’t seem to send the first time due to attachments most likely, so I’ll leave them out and let me know if you need to look at them.
On Jun 6, 2017, at 10:14 AM, Taylor Hilton BTH22@pitt.edu wrote:
Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H.
Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
<cache.th40.neg.sig.cluster.summary><recon-all.log>
Have you tried to view your label on the individual subject? If your original analysis was on cortical thickness, then there will be a *ocn*.dat file in the output with the values for each input subject and each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H.
Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just loaded up the label on a single subject, looks like it is fine, it's in the same position and squarely on the surface, it's a little skinnier but I'm guessing that's the difference of overlaying it on the subject. We tried looking at the ocn.dat file earlier and didn't find a significant difference between groups despite the output of mri_glmfit-sim (see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53380.html)
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Friday, June 9, 2017 9:48:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you tried to view your label on the individual subject? If your original analysis was on cortical thickness, then there will be a *ocn*.dat file in the output with the values for each input subject and each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7C420495d142b9409a021e08d4af3e4ae1%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=WgSHI656A9huYgLRXmSiuEHhkvHJ%2FmQbNP7%2F6lZqNas%3D&reserved=0
how did you do the test of the group diffs?
On 6/12/17 7:37 PM, Hilton, Benjamin Taylor wrote:
I just loaded up the label on a single subject, looks like it is fine, it's in the same position and squarely on the surface, it's a little skinnier but I'm guessing that's the difference of overlaying it on the subject. We tried looking at the ocn.dat file earlier and didn't find a significant difference between groups despite the output of mri_glmfit-sim (see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53380.html)
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Friday, June 9, 2017 9:48:50 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you tried to view your label on the individual subject? If your original analysis was on cortical thickness, then there will be a *ocn*.dat file in the output with the values for each input subject and each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H.
Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* 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
Okay I think I found a fix, but wanted to run it by you to see if it makes sense and for anyone else who might have this problem. I ran it with the thickness file specified under the -t argument, which I think makes it so that the program doesn't pick up anything that is subcortical when calculating the thickness average. Now the values seem reasonable, and look similar to when I use the thickness as an overlay in freeview. I'll post a sample of one of the commands I am running below.
mris_anatomical_stats -l s71765/label/rh.cluster-001.label -t s71765/surf/rh.thickness -b s71765 rh
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, June 13, 2017 1:52:58 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness {Disarmed}
how did you do the test of the group diffs?
On 6/12/17 7:37 PM, Hilton, Benjamin Taylor wrote:
I just loaded up the label on a single subject, looks like it is fine, it's in the same position and squarely on the surface, it's a little skinnier but I'm guessing that's the difference of overlaying it on the subject. We tried looking at the ocn.dat file earlier and didn't find a significant difference between groups despite the output of mri_glmfit-sim (see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53380.htmlhttps://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg53380.html&data=01%7C01%7CBTH22%40pitt.edu%7Cab6a52bd6f10440a55f108d4b22084d1%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=OwkZjONYT96jUWeigQL63zsmiPOK0ybiX%2BmSuVK%2Bldk%3D&reserved=0)
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: Friday, June 9, 2017 9:48:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you tried to view your label on the individual subject? If your original analysis was on cortical thickness, then there will be a *ocn*.dat file in the output with the values for each input subject and each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Hilton, Benjamin Taylor -
Taylor Hilton