I would redo everything with the new version. If you're mixing versions, I can't give you recommendations on what would work or not.
On 1/30/15 2:53 PM, Karahanoglu, Fikret Isik wrote: > We ran individual level analysis with the existing contrasts, which didn't > yield any incompatibility issues. > So all other contrasts must have been created with old version. > At that point what do you recommend? We continue with old version or redo > everything with new version? > isik > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, January 30, 2015 2:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized." > > This is analysis.info comes from an old version of FS and will not work with > 5.3. When you made new contrasts before, are you sure you used 5.3? > doug > > On 1/30/15 2:26 PM, Karahanoglu, Fikret Isik wrote: > > > We are just adding new analyses to a previous study, apparently, they didn't > run mkanalysis-sess. But, instead, they modified > analysis.info and analysis.cfg (attached) from another study with the same > design. But we had no problem before with other contrasts... > isik > > ________________________________________ > From: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] > on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>] > Sent: Friday, January 30, 2015 1:59 PM > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized." > > sorry, I wanted the mkanalysis-sess cmd, not the mkcontrast-sess > > On 1/30/15 1:50 PM, Karahanoglu, Fikret Isik wrote: > > > So we ran > > mkcontrast-sess -an RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c > 3 > > from the terminal. I attach the mkcontrast-sess.log and anlaysis.info. > isik > ________________________________________ > From: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] > on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>] > Sent: Friday, January 30, 2015 1:39 PM > To: > freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized." > > sorry, can you send me your mkanalysis-sess command line as well? You > can find it in the analysis.info file in the analysis folder > > On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote: > > > > Dear all, > > We are trying to make a new contrast for our GLM analysis, however we have > the following flag error. > > Is there any solution for this? > > Thank you > isik > > [schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an > RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3 > (standard_in) 1: syntax error > INFO: Found 4 Non-Null Conditions > INFO: Found Delays > Condition Weights: 1.00000000000000000000 -.50000000000000000000 > -.50000000000000000000 0 > mkcontrast -anadir RM_hard_easy_fake_error -wcond 1.00000000000000000000 > -.50000000000000000000 -.50000000000000000000 0 -sumconds -o > RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave > $Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $ > (standard_in) 1: syntax error > ERROR: Flag 1 unrecognized. > -anadir RM_hard_easy_fake_error -wcond 1.00000000000000000000 > -.50000000000000000000 -.50000000000000000000 0 -sumconds -o > RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave > ERROR running mkcontrast > mkcontrast -anadir RM_hard_easy_fake_error -wcond 1.00000000000000000000 > -.50000000000000000000 -.50000000000000000000 0 -sumconds -o > RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave > Fri Jan 30 12:07:42 EST 2015 > > > > _______________________________________________ > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.
