Hi Heena,
Could you zip up all of the data files in this example and share them so I can take a look?
You can use Oxfile without an account to upload files here:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=806832C3AC7CB2375D
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
Analysis Research Software Engineer
FMRIB, John Radcliffe Hospital
University of Oxford
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> On 13 Nov 2019, at 17:54, Heena Manglani <[log in to unmask]> wrote:
>
> Hi Taylor,
>
> Thanks for your response! Please see below for some follow-up questions:
>
> I co-aligned the runs using the steps you suggested but I co-aligned the res4d instead; I'm wanting to process the data with a joint model inclusive of preprocessing + regression of nuisance variables (consistent with this recent paper: Lindquist, M. A., Geuter, S., Wager, T. D., & Caffo, B. S. (2018). Modular preprocessing pipelines can reintroduce artifacts into fMRI data. Human Brain Mapping, 0(0). https://doi.org/10.1002/hbm.24528), and so would prefer not to have to use motion corrected aligned data, if possible. This is what I tried instead:
>
> #Pull out middle volume, register middle volumes, apply transformation matrix to run2 res4d
> 1) Preprocessed (motion and distortion correction of) both runs
> 2) fslroi run1/filtered_func_data run1_middle 227 1
> 3) fslroi run2/filtered_func_data run2_middle 227 1
> 4) flirt -dof 6 -in run2_middle -ref run1_middle -omat run2_to_run1_align.mat
> 5) flirt -in nuisance_run2/stats/res4d -ref nuisance_run1/stats/res4d -applyxfm -init run2_to_run1_align.mat -out run2_res4d_aligned
>
> #Align run1 to self.
> 6) fslroi run1/res4d run1/res4d_middle 227 1
> 7) flirt -dof 6 -in run1/res4d_middle -ref run1/filtered_func_data -omat run1_to_run1_align.mat
> 8) flirt -in run1/res4d -ref nuisance_run1/filtered_func_data -applyxfm -init run1_to_run1_align.mat -out run1_res4d_aligned
>
> Are there any ways to improve these steps? I wasn't sure if in step 8) using the filtered_func_data as the reference is most suitable given the difference in resolution between the res4d and the filtered_func which only has motion correction and distortion correction applied.
>
> Any thoughts would be much appreciated!
>
> Thanks!
> Heena
>
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