Hello Group,
We would like to create an ROI label in qdec and then run a correlation analysis with another factor to determine the relationship between thinning in the ROI and the measure of interest. Instead of looking at a single value from the ROI we want to look at the correlation across each vertex within the ROI. Basically we want to create a color map of the correlation within the ROI. Is this possible?
Thanks, Emily
You can run something like the following: mri_segstats --slabel fsaverage lh $SUBJECTS_DIR/fsaverage/label/lh.BA1.label --i y.mgh --sum junk --avgwf avgwf.dat
y.mgh is created by qdec and should be in the qdec output. avgwf.dat will be a text file with a value for each of your subjects. This is the data you want (I think).
doug
Emily Rogalski wrote:
Hello Group,
We would like to create an ROI label in qdec and then run a correlation analysis with another factor to determine the relationship between thinning in the ROI and the measure of interest. Instead of looking at a single value from the ROI we want to look at the correlation across each vertex within the ROI. Basically we want to create a color map of the correlation within the ROI. Is this possible?
Thanks, Emily
-- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski@gmail.com mailto:erogalski@gmail.com
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Doug,
I think what Emily wants to do is something like running mri_glmfit on an ROI (i.e., surface label drawn in QDEC). Then be able to display the results in tksurfer, showing flame-scale map results for only the ROI/label (not just singular values for the entire ROI/label). Would this be what the mri_glmfit '--label' flag is for?
-Derin
On Jan 26, 2010, at 10:53 AM, Douglas N Greve wrote:
You can run something like the following: mri_segstats --slabel fsaverage lh $SUBJECTS_DIR/fsaverage/label/lh.BA1.label --i y.mgh --sum junk --avgwf avgwf.dat
y.mgh is created by qdec and should be in the qdec output. avgwf.dat will be a text file with a value for each of your subjects. This is the data you want (I think).
doug
Emily Rogalski wrote:
Hello Group,
We would like to create an ROI label in qdec and then run a correlation analysis with another factor to determine the relationship between thinning in the ROI and the measure of interest. Instead of looking at a single value from the ROI we want to look at the correlation across each vertex within the ROI. Basically we want to create a color map of the correlation within the ROI. Is this possible?
Thanks, Emily
-- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski@gmail.com mailto:erogalski@gmail.com
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, that is what the --label (or --mask) is for. I don't think that QDEC has the ability to spec a label, but you can just run it from the command line too. Look in the glmfit output directory for a mri_glmfit.log file. This will have the mri_glmfit command line that was used. Just add the --label. Make sure that you are not doing a circular analysis (ie, don't do something like create a label of your activation, then correct for mult comp only in that label).
doug
Derin Cobia wrote:
Doug,
I think what Emily wants to do is something like running mri_glmfit on an ROI (i.e., surface label drawn in QDEC). Then be able to display the results in tksurfer, showing flame-scale map results for only the ROI/label (not just singular values for the entire ROI/label). Would this be what the mri_glmfit '--label' flag is for?
-Derin
On Jan 26, 2010, at 10:53 AM, Douglas N Greve wrote:
You can run something like the following: mri_segstats --slabel fsaverage lh $SUBJECTS_DIR/fsaverage/label/lh.BA1.label --i y.mgh --sum junk --avgwf avgwf.dat
y.mgh is created by qdec and should be in the qdec output. avgwf.dat will be a text file with a value for each of your subjects. This is the data you want (I think).
doug
Emily Rogalski wrote:
Hello Group,
We would like to create an ROI label in qdec and then run a correlation analysis with another factor to determine the relationship between thinning in the ROI and the measure of interest. Instead of looking at a single value from the ROI we want to look at the correlation across each vertex within the ROI. Basically we want to create a color map of the correlation within the ROI. Is this possible?
Thanks, Emily
-- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski@gmail.com mailto:erogalski@gmail.com
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Derin Cobia -
Douglas N Greve -
Emily Rogalski