Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas.
Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation?
-Sincerely, June.
In QDEC, there is not a way to do this, but you can do it from the command line. If you cd to where the qdec output is (it might be a folder called Untitled in your $SUBJECTS_DIR), then run
mri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
This will only take a minute or so to run. In each contrast folder, there will be a file called cache.th13.abs.sig.cluster.summary with a list of clusters and a file called cache.th13.abs.y.ocn.dat which will have a column for each cluster and a row for each subject. You can compute statistics from this.
Note that the clusters found this way should be the same as with qdec, but might not be if the threshold parameters are not identical.
doug
On 07/02/2014 04:14 AM, June k. wrote:
Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas.
Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation?
-Sincerely, June.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
Thank you for your advice. It works like magic. I have one more question. In qdec gui, I found some small areas in two-group comparision with two discrete variables (diagnosis and gender) and two nuisance variables (ICV, age). Then processed monte-carlo simulation with 1.3 abs. ->Finally got three significant areas
Now your code gave me the mean thickness of three areas. However, When I run stats with SPSS, (independent group t-test, ANCOVA using GLM multivariate), the p-value is far from significant (.05).
Is there any mistake, or I ran wrong stats with SPSS?
Again, Thanks for your advice : ) -June
On Jul 2, 2014, at 11:28 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
In QDEC, there is not a way to do this, but you can do it from the command line. If you cd to where the qdec output is (it might be a folder called Untitled in your $SUBJECTS_DIR), then run
mri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
This will only take a minute or so to run. In each contrast folder, there will be a file called cache.th13.abs.sig.cluster.summary with a list of clusters and a file called cache.th13.abs.y.ocn.dat which will have a column for each cluster and a row for each subject. You can compute statistics from this.
Note that the clusters found this way should be the same as with qdec, but might not be if the threshold parameters are not identical.
doug
On 07/02/2014 04:14 AM, June k. wrote:
Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas.
Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation?
-Sincerely, June.
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/
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.
On 07/03/2014 08:01 PM, June k. wrote:
Dear Douglas,
Thank you for your advice. It works like magic. I have one more question. In qdec gui, I found some small areas in two-group comparision with two discrete variables (diagnosis and gender) and two nuisance variables (ICV, age). Then processed monte-carlo simulation with 1.3 abs. ->Finally got three significant areas
Is this a problem?
Now your code gave me the mean thickness of three areas. However, When I run stats with SPSS, (independent group t-test, ANCOVA using GLM multivariate), the p-value is far from significant (.05).
Is there any mistake, or I ran wrong stats with SPSS?
You have to make sure to use exactly the same model. I don't know how to do this in SPSS. I can step you through the process in matlab. doug
Again, Thanks for your advice : ) -June
On Jul 2, 2014, at 11:28 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
In QDEC, there is not a way to do this, but you can do it from the command line. If you cd to where the qdec output is (it might be a folder called Untitled in your $SUBJECTS_DIR), then run
mri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
This will only take a minute or so to run. In each contrast folder, there will be a file called cache.th13.abs.sig.cluster.summary with a list of clusters and a file called cache.th13.abs.y.ocn.dat which will have a column for each cluster and a row for each subject. You can compute statistics from this.
Note that the clusters found this way should be the same as with qdec, but might not be if the threshold parameters are not identical.
doug
On 07/02/2014 04:14 AM, June k. wrote:
Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas.
Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation?
-Sincerely, June.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 http://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 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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
June k.