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Support for more than one run #13
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Is this going to be supported in the near future? Is there an alternate way to mimic this with current BROCCOLI version? |
Yes another user is also requesting it. 2015-08-17 15:09 GMT+02:00 ImmanuelSamuel notifications@github.com:
Anders Eklund, PhD |
Any idea on when you will be able to release it? I need to meet my deadline in a month and so i might start using FSL if this is going to take a long time. |
I will try to include it this week. 2015-08-17 15:43 GMT+02:00 ImmanuelSamuel notifications@github.com:
Anders Eklund, PhD |
I have now added support for several runs, and hope that I have found all To get the update, do a "git pull" in a linux terminal, while being in a For each run, 4 detrending regressors are added that are only "ON" for the FirstLevelAnalysis -runs 3 run1.nii run2.nii run3.nii T1.nii MNI.nii (if you only have 1 run you use the old syntax FirstLevelAnalysis run1.nii If there is one or several runs for which the subject did not do a certain regressors1.txt: NumRegressors 2 taskA_run1.txt regressors2.txt: NumRegressors 2 taskA_run2.txt regressors3.txt: NumRegressors 2 dummy.txt where dummy.txt only contains "NumEvents 0" Make use of -savedesignmatrix and -saveoriginaldesignmatrix to check if the 2015-08-17 16:01 GMT+02:00 Anders Eklund andek034@gmail.com:
Anders Eklund, PhD |
Would it be possible to add an ouput directory argument where the results can get saved? |
That option exists for other BROCCOLI function, but for some reason not yet 2015-08-20 0:21 GMT+02:00 ImmanuelSamuel notifications@github.com:
Anders Eklund, PhD |
I have now added -output option for FirstLevelAnalysis, if you for example run FirstLevelAnalysis -runs 3 bold1.nii.gz bold2.nii.gz bold3.nii.gz brain.nii.gz MNI152_T1_2mm_brain.nii.gz regressors1.txt regressors2.txt regressors3.txt contrasts.txt -output /home/andek/Data/subject1 all the results will be saved in the directory /home/andek/Data , and all the files will start with subject1 |
That works well. How do you do higher level analysis after this. FSL asks for registration before running higher level. Since the directory structure is different it complains. |
I don't know if you can run the group analysis through the FSL GUI, the You can use randomise in FSL to run a permutation test. First merge the fslmerge -t allcopes.nii.gz subject*_cope1.nii.gz then run randomise, e.g. for simple group mean randomise -i allcopes.nii.gz -o permtest -1 -c 2.3 -m In BROCCOLI you can use the function RandomiseGroupLevel, which also RandomiseGroupLevel allcopes.nii.gz -groupmean -mask Both randomise and RandomiseGroupLevel will generate new nifti files which 2015-08-20 17:12 GMT+02:00 ImmanuelSamuel notifications@github.com:
Anders Eklund, PhD |
See the following paper on permutation tests in neuroimaging, I prefer http://www.fil.ion.ucl.ac.uk/spm/doc/papers/NicholsHolmes.pdf 2015-08-20 17:30 GMT+02:00 Anders Eklund andek034@gmail.com:
Anders Eklund, PhD |
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