Sorry, the b0dc.nii.gz should be the argument of --vsm (no need to use --exfdw).

On 09/12/2014 08:28 AM, Reza Rajimehr wrote:

Hi Doug,

So I am using a command like this:

epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46 --esp 0.31 --sigma 2 --perev

(note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because this command apparently does not have --o option)

Before running the above command, I have registered the mag and phasediff volumes to the template volume and I have generated new volumes (fid_mag and fid_phasediff) that are already in register with the template.

I have two steps remaining in preproc-sess, which are register-sess and rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two commands?

Both of those options are the same thing (I could not decide what to call it).

I assume that when I use the above flag(s), my EPI fmc volumes will be dewarped first, and then they will get registered to the anatomical and the surface, right? So I hope that when I view/check the result of registration with tkregister2 (for possible manual interventions), I will see the dewarped template ...?

Actually, tkregister2 does not take a VSM, so you will be looking at the nondewarped. You can use mri_vol2vol with the --vsm option to map the template into anatomical space and unwarp, then load that up in tkmedit to see the surfaces on the dewarped.

Finally what is the effect of specifying -b0dc in mkanalysis-sess?

It just tells it to use the B0 distortion corrected data.

Thanks, Reza

...

Hi,

I have a basic question, but the answer can be useful for others as well.

I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:

My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)

My EPI data: fmc.nii.gz files in run folders

Now I have three questions:

1. How can I unpack the fieldmap data? An example command ...

I think you get two series out, one magnitude and one phase, just convert those to nifti

...

2. How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an

example command would be very useful.

something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located)

...

3. How will the undistorted volumes be used later on in the FS-FAST

analysis stream?

When you run preproc-sess and mkanalysis-sess add -b0dc to the command line

...

Your help would be very much appreciated.

Thanks, Reza

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