use stable5 Adam Nitenson wrote: > Hey Doug, > > Everything is working out well with this pathway....but beta2sxa is not > recognized as a valid command. I've sourced to nmr (Stable 4 if that > matters at all) and have been on the same terminal on which I've done the > previous steps. Any ideas? > > Specifically, I entered: > > beta2sxa -b 12ConT.13ConC.14SchC.17SchT.nii --nc 8 --nper 12 --o > h.12ConT.13ConC.14SchC.17SchT.nii > > (I have 4 groups, 2 conditions, 12 time points) > > -Adam > > >> Create two contrasts, A-vs-fixation and B-vs-fixation, then run >> isxconcat-sess separately for each group. This will create ces files for >> each contrast. There will be a ces file for each time point in the FIR; >> each of these will have a frame for all the members of the group. >> >> 1. Compute the mean of each time point >> mri_concat ces.000.nii --mean --o mean.ces.000.nii >> ... >> 2. Concat all the means into a single file: >> mri_concat mean.ces.???.nii --o all.mean.ces.nii >> >> This will give you 4 mean files, one for each group/condition. >> Concatenate them together: >> mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii >> g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii >> >> Now run >> >> beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o >> h.g1A.g1B.g2A.g2B.nii >> >> where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp >> is the number of time points in each waveform. >> >> you can then run >> >> tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii >> >> or tkmedit if these are volumes. >> >> doug >> >> >> Adam Nitenson wrote: >> >>> Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously. >>> >>> -Adam >>> >>> >>> >>>> Do you mean something like you have two conditions (say A and B) and >>>> two >>>> groups (say 1 and 2), you want to plot A1 and A2 instead of just A and >>>> B? >>>> >>>> Adam Nitenson wrote: >>>> >>>> >>>>> Hello Freesurfers, >>>>> >>>>> I'm been experimenting with creating timecourses for tksurfer and >>>>> tkmedit using the -hrf flag. However I've noticed that the h.nii files >>>>> created provide the HDR timecourse are only based on the original >>>>> analysis under which isxconcat-sess was run (in my case, error vs >>>>> correct). I was wondering if there was a way to tailor the timecourse >>>>> in such a way that, instead of plotting only the conditions of the >>>>> analysis, it would plot lines based on subject groups (e.g. Patients >>>>> and Controls from an fsgd file). >>>>> >>>>> Basically, is there a way that I can create an HDR timecourse plot >>>>> that can separate the data by groups that I can designate depending on >>>>> the type of anlaysis I wish to conduct? >>>>> >>>>> Thanks! >>>>> >>>>> Adam Nitenson, B.S. >>>>> Brain Genomics Lab >>>>> Massachusetts General Hospital >>>>> _______________________________________________ >>>>> 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 >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> >>>> >>> Adam Nitenson, B.S. >>> Brain Genomics Lab >>> Massachusetts General Hospital >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
