13 Nov
2014
13 Nov
'14
6:42 p.m.
ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar
2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
:
Hi Doug, so I made contrast matrices and stored them in mystudy, and then ran selxavg3-sess per subject. I defined three different contrasts (in three mat files), but selxacg3-sess only gives me one analysis, it seems to be an F-test. When I do isxconcat-sess after that, I get six ces files per analysis (I presume one for each of my predictors), not three (number of contrasts).
Is there a way for me to force selxavg3-sess to actually compute the contrasts that I want?
Thanks, Caspar
2014-11-13 12:16 GMT-05:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
I don't know whether that will work or not. If it runs, you can compare
the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>:
Hi Doug, I am a little bit confused about the variance. Shouldn't the relevant variance be the variance over the differences, not the mean variance over all? Of course at the level of ces and cesvar, I do not have access to the timepoint by timepoint differences anymore. Is there another way to do this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > just to clarify: > If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would > compute > ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) > and > cesvar=mean(cesvar(taskreg(1,2,3,4,5,6))) > > Is that correct? > Thanks, Caspar > > > 2014-11-11 13:19 GMT-05:00 Bill Taylor <bt@cs.wisc.edu <mailto:bt@cs.wisc.edu> > <mailto:bt@cs.wisc.edu <mailto:bt@cs.wisc.edu>>>: > > Sorry, Though we do have freesurfer pipelines we run in Madison, I > responded to wrong email. > > Bill Taylor > Center for High Throughput Computing > Computer Sciences > University of Wisconsin, Madison > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > I'll start the process thursday. > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > >> It will be the same as the DOF of the individual contrasts > (don't sum them). > >> > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > >>> ok, I will try that. How do I get the degrees of freedom? > Thanks! Caspar > >>> > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>:
> >>> > >>> > >>> Actually, you can still do each contrast individually. > Each will > >>> produce > >>> ces and cesvar files. Take the difference between the > ces files > >>> and the > >>> average of the cesvar files, then feed the result into > mri_glmfit FFX > >>> > >>> doug > >>> > >>> > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > >>> > Hi Doug, > >>> > I wanted to follow up on this. Would you be able to > provide a > >>> > workaround for contrasting multiple taskregs against > each other? Is > >>> > there something I can try in the meantime? Thanks, Caspar > >>> > > >>> > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M.Schwiedrzik
> >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>: > >>> > > >>> > Hi Doug, > >>> > thanks for your reply. I would like to feed the > differences > >>> into a > >>> > FFX group analysis, so I think I will need to > resort to your > >>> > workaround. It would be great if you could provide > that. Thanks! > >>> > Caspar > >>> > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>: > >>> > > >>> > > >>> > To get sig maps for an individual, this is > problematic > >>> but I > >>> > could > >>> > probably come up with a work-around. For a group > >>> analysis, you can > >>> > simply compute each taskreg separately, then > subtract > >>> the two > >>> > prior to > >>> > running mri_glmfit. > >>> > doug > >>> > > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik > wrote: > >>> > > Hi! > >>> > > A quick follow-up: > >>> > > I have a taskreg file with 6 continuous > predictors. I > >>> would > >>> > like to > >>> > > run specific contrasts, e.g., predictor 1 vs. > >>> mean(predictor > >>> > 2:6). > >>> > > From what I gather, selxavg3-sess will run > automatic > >>> > contrasts on > >>> > > taskregs, but the automatic contrasts are > against > >>> baseline. > >>> > This is > >>> > > not what I need at this point. > >>> > > mk-contrast-sess does not like what I am > putting in > >>> because > >>> > I do not > >>> > > have a paradigm file in which condition > numbers are > >>> specified. > >>> > > Is there a way to compute specific contrasts > between > >>> multiple > >>> > > taskregs, and if not, is there a workaround? > >>> > > Thank you very much, Caspar > >>> > > > >>> > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>>>>: > >>> > > > >>> > > Hi! > >>> > > I have several external regressors in my > analysis > >>> that I > >>> > configure > >>> > > with -taskreg in mkanalysis-sess > (something like > >>> -notask > >>> > -taskreg > >>> > > nameoffile 6). > >>> > > I was wondering how to set up > mkcontrast-sess to > >>> > contrast these > >>> > > regerssors given that I do not have a > paradigm > >>> file for > >>> > them. > >>> > > Can I just do something like -a 1 -c 2 > -c 3 -c 4 -c 5? > >>> > > > >>> > > Thanks, Caspar > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > _______________________________________________ > >>> > > Freesurfer mailing list > >>> > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > >>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > >>> > > >>> > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > <http://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/
> >>> > > >>> >
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> >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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 <http://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
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