HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols
I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa
-------- Original-Nachricht --------
Datum: Fri, 24 Jul 2009 17:16:27 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa,
If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you.
You'll still have to load the results on your own in tksurfer by following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...
Nick
On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote:
HI! i have a question regarding multiple comparion correction in qdec. can i
use a clusterwise correction?
i found the following script for glm:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite
but i dont understand how i should apply it in qdec. what shoudl i use
as input directory?
rosa
Rosa,
Was this script generated after an analysis was successfully run? You will need to run an analysis first (ie, selecting your factors, etc, press Analyze, then select a contrast for display in the Display tab), then you can use the mri_glmfit-sim script generator feature.
I can't think of a reason why the design matrix and contrast matrix columns are different.
Nick
On Thu, 2009-07-30 at 11:17 +0200, Rosa Steimke wrote:
HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols
I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa
-------- Original-Nachricht --------
Datum: Fri, 24 Jul 2009 17:16:27 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa,
If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you.
You'll still have to load the results on your own in tksurfer by following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...
Nick
On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote:
HI! i have a question regarding multiple comparion correction in qdec. can i
use a clusterwise correction?
i found the following script for glm:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite
but i dont understand how i should apply it in qdec. what shoudl i use
as input directory?
rosa
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
I've seen this happen if two analyses were run using the same output directory. Some of the contrasts won't get deleted the 2nd time it is run.
doug
Nick Schmansky wrote:
Rosa,
Was this script generated after an analysis was successfully run? You will need to run an analysis first (ie, selecting your factors, etc, press Analyze, then select a contrast for display in the Display tab), then you can use the mri_glmfit-sim script generator feature.
I can't think of a reason why the design matrix and contrast matrix columns are different.
Nick
On Thu, 2009-07-30 at 11:17 +0200, Rosa Steimke wrote:
HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols
I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa
-------- Original-Nachricht --------
Datum: Fri, 24 Jul 2009 17:16:27 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa,
If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you.
You'll still have to load the results on your own in tksurfer by following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...
Nick
On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote:
HI! i have a question regarding multiple comparion correction in qdec. can i
use a clusterwise correction?
i found the following script for glm:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite
but i dont understand how i should apply it in qdec. what shoudl i use
as input directory?
rosa
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Rosa,
you can either delete the directory 'Untitled' before running the analysis (although I thought qdec did this already), or you should just set your Design Name to something other than the default 'Untitled' (which will save stuff in a directory of that name).
Nick
On Thu, 2009-07-30 at 12:29 -0400, Douglas N Greve wrote:
I've seen this happen if two analyses were run using the same output directory. Some of the contrasts won't get deleted the 2nd time it is run.
doug
Nick Schmansky wrote:
Rosa,
Was this script generated after an analysis was successfully run? You will need to run an analysis first (ie, selecting your factors, etc, press Analyze, then select a contrast for display in the Display tab), then you can use the mri_glmfit-sim script generator feature.
I can't think of a reason why the design matrix and contrast matrix columns are different.
Nick
On Thu, 2009-07-30 at 11:17 +0200, Rosa Steimke wrote:
HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols
I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa
-------- Original-Nachricht --------
Datum: Fri, 24 Jul 2009 17:16:27 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa,
If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you.
You'll still have to load the results on your own in tksurfer by following these instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwis...
Nick
On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote:
HI! i have a question regarding multiple comparion correction in qdec. can i
use a clusterwise correction?
i found the following script for glm:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite
but i dont understand how i should apply it in qdec. what shoudl i use
as input directory?
rosa
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
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 -
Nick Schmansky -
Rosa Steimke