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
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