-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this sig.mgh file from the qdec analysis? rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote:
Thanks Bruce!! now i wonder whether it is possible to get a table of all the
significant blobbs that i found in qdec that gives the size and average p value or some other way to find this out?
rosa -------- Original-Nachricht --------
Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
Hi Rosa,
you have to select them.
cheers, Bruce
On Tue, 4 Aug 2009, Rosa Steimke wrote:
HI, i have a question regarding qdec. If i load a designfile with 4
variables, but than i only select 1 for analysis, does qdec then
correct for the
other variables that i did not select? or do i have to select them?
thanks in advance!! rosa
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
cd $SUBJECTS_DIR/qdec find | grep "sig.mgh"
will show you the location of the sig.mgh files, one for each analysis.
On Tue, 2009-08-04 at 19:33 +0200, Rosa Steimke wrote:
-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this sig.mgh file from the qdec analysis? rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote:
Thanks Bruce!! now i wonder whether it is possible to get a table of all the
significant blobbs that i found in qdec that gives the size and average p value or some other way to find this out?
rosa -------- Original-Nachricht --------
Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
Hi Rosa,
you have to select them.
cheers, Bruce
On Tue, 4 Aug 2009, Rosa Steimke wrote:
HI, i have a question regarding qdec. If i load a designfile with 4
variables, but than i only select 1 for analysis, does qdec then
correct for the
other variables that i did not select? or do i have to select them?
thanks in advance!! rosa
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
sorry, somehome i cannot figure it out... find | grep -f "sig.mgh in my qdec map but it says that no such file exist. do i have to make it? thanks for your help! rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 13:40:07 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles in qdec
cd $SUBJECTS_DIR/qdec find | grep "sig.mgh"
will show you the location of the sig.mgh files, one for each analysis.
On Tue, 2009-08-04 at 19:33 +0200, Rosa Steimke wrote:
-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this
sig.mgh file from the qdec analysis?
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote:
Thanks Bruce!! now i wonder whether it is possible to get a table of all the
significant blobbs that i found in qdec that gives the size and
average p value or
some other way to find this out?
rosa -------- Original-Nachricht --------
Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
Hi Rosa,
you have to select them.
cheers, Bruce
On Tue, 4 Aug 2009, Rosa Steimke wrote:
HI, i have a question regarding qdec. If i load a designfile with 4
variables, but than i only select 1 for analysis, does qdec then
correct for the
other variables that i did not select? or do i have to select them?
thanks in advance!! rosa
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
Hi Rosa,
have you run the qdec analysis? It will create the sig.mgh (as well as many other things)
cheers, Bruce On Thu, 6 Aug 2009, Rosa Steimke wrote:
sorry, somehome i cannot figure it out... find | grep -f "sig.mgh in my qdec map but it says that no such file exist. do i have to make it? thanks for your help! rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 13:40:07 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles in qdec
cd $SUBJECTS_DIR/qdec find | grep "sig.mgh"
will show you the location of the sig.mgh files, one for each analysis.
On Tue, 2009-08-04 at 19:33 +0200, Rosa Steimke wrote:
-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this
sig.mgh file from the qdec analysis?
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote:
Thanks Bruce!! now i wonder whether it is possible to get a table of all the
significant blobbs that i found in qdec that gives the size and
average p value or
some other way to find this out?
rosa -------- Original-Nachricht --------
Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
Hi Rosa,
you have to select them.
cheers, Bruce
On Tue, 4 Aug 2009, Rosa Steimke wrote:
> HI, > i have a question regarding qdec. If i load a designfile with 4 > variables, but than i only select 1 for analysis, does qdec then
correct for the
other variables that i did not select? or do i have to select them?
> thanks in advance!! > rosa > > _______________________________________________ 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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
Hi, yes i have run the analysis and i found the sig.mgh file in the map of the contrast i am interested in. now i want to create a table with all significant clusters from my qdec analysis. i have learned that i need to use the mri_surfcluster command. however i am asked to specify a subject. but im not interested in single subjects, but in getting my qdec results into a tabel (all significant clusters (above .001) the amount of voxels and the average p value). or do i have to first run all the subjects seperatly?
thanks for all your help. rosa -------- Original-Nachricht --------
Datum: Thu, 6 Aug 2009 10:23:25 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: Nick Schmansky nicks@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles in qdec
Hi Rosa,
have you run the qdec analysis? It will create the sig.mgh (as well as many other things)
cheers, Bruce On Thu, 6 Aug 2009, Rosa Steimke wrote:
sorry, somehome i cannot figure it out... find | grep -f "sig.mgh in my qdec map but it says that no such file
exist. do i have to make it? thanks for your help!
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 13:40:07 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles
in qdec
cd $SUBJECTS_DIR/qdec find | grep "sig.mgh"
will show you the location of the sig.mgh files, one for each analysis.
On Tue, 2009-08-04 at 19:33 +0200, Rosa Steimke wrote:
-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this
sig.mgh file from the qdec analysis?
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote:
Thanks Bruce!! now i wonder whether it is possible to get a table of all the
significant blobbs that i found in qdec that gives the size and
average p value or
some other way to find this out?
rosa -------- Original-Nachricht --------
> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) > Von: Bruce Fischl fischl@nmr.mgh.harvard.edu > An: Rosa Steimke rosasteimke@gmx.de > CC: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
>
> Hi Rosa, > > you have to select them. > > cheers, > Bruce > > On Tue, 4 Aug 2009, Rosa Steimke wrote: > > >> HI, >> i have a question regarding qdec. If i load a designfile with 4 >> > variables, but than i only select 1 for analysis, does qdec then
correct for the
> other variables that i did not select? or do i have to select them? > >> thanks in advance!! >> rosa >> >> > _______________________________________________ > 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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
Rosa,
qdec paints the results of a group study on the subject 'fsaverage', so the sig.mgh file is associated with that subject (the -qcache step of recon-all is what sampled each subjects data onto the fsaverage subject). you would specify 'fsaverage' as the subject with the mri_surfcluster command. you would use the ROI analysis procedure, described in the tutorials, if you want to work with data from your subject set directly.
Nick
t 14:16 +0200, Rosa Steimke wrote:
Hi, yes i have run the analysis and i found the sig.mgh file in the map of the contrast i am interested in. now i want to create a table with all significant clusters from my qdec analysis. i have learned that i need to use the mri_surfcluster command. however i am asked to specify a subject. but im not interested in single subjects, but in getting my qdec results into a tabel (all significant clusters (above .001) the amount of voxels and the average p value). or do i have to first run all the subjects seperatly?
thanks for all your help. rosa -------- Original-Nachricht --------
Datum: Thu, 6 Aug 2009 10:23:25 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: Nick Schmansky nicks@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles in qdec
Hi Rosa,
have you run the qdec analysis? It will create the sig.mgh (as well as many other things)
cheers, Bruce On Thu, 6 Aug 2009, Rosa Steimke wrote:
sorry, somehome i cannot figure it out... find | grep -f "sig.mgh in my qdec map but it says that no such file
exist. do i have to make it? thanks for your help!
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 13:40:07 -0400 Von: Nick Schmansky nicks@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fwd: Re: correction for behavioral varialbles
in qdec
cd $SUBJECTS_DIR/qdec find | grep "sig.mgh"
will show you the location of the sig.mgh files, one for each analysis.
On Tue, 2009-08-04 at 19:33 +0200, Rosa Steimke wrote:
-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" rosasteimke@gmx.de An: Douglas N Greve greve@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
thanks, but which input file do i have to use? where can i find this
sig.mgh file from the qdec analysis?
rosa -------- Original-Nachricht --------
Datum: Tue, 04 Aug 2009 12:46:49 -0400 Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
You can run mri_surfcluster on the sig.mgh for this kind of thing.
doug
Rosa Steimke wrote: > Thanks Bruce!! > now i wonder whether it is possible to get a table of all the significant blobbs that i found in qdec that gives the size and
average p value or
some other way to find this out? > rosa > -------- Original-Nachricht -------- > >> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) >> Von: Bruce Fischl fischl@nmr.mgh.harvard.edu >> An: Rosa Steimke rosasteimke@gmx.de >> CC: freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] correction for behavioral varialbles in
qdec
>> > > >> Hi Rosa, >> >> you have to select them. >> >> cheers, >> Bruce >> >> On Tue, 4 Aug 2009, Rosa Steimke wrote: >> >> >>> HI, >>> i have a question regarding qdec. If i load a designfile with 4 >>> >> variables, but than i only select 1 for analysis, does qdec then correct for the >> other variables that i did not select? or do i have to select them? >> >>> thanks in advance!! >>> rosa >>> >>> >> _______________________________________________ >> 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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Rosa Steimke