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Distortion Correction at CFMRI
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CFMRI offers the use of custom wrapper scripts are used to prepare GE fMRI imaging data for use in the FSL topup distortion correction toolbox

After organizing the data to meet the input requirements of the FSL topup program, the data are automatically used as input in this popular method for estimating and correcting susceptibility induced distortions

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup 

CFMRI maintains a series of topup related scripts on all of our servers used by the imaging community 

fMRI Topup at CFMRI
===================

The most commonly used version of CFMRI topup code for fMRI data is "run_topup_hcpfmri"

Please see the description below for an example of how to effectively use this useful tool

.. image:: images/topup/fmri_topup.png
  :width: 700

fMRI Topup: Multiband Data (e.g., ABCD, HCP)
--------------------------------------------

Example Multiband Acquisition cfmricp_log.txt

.. code-block:: csh

   DICOMs
   
   p folder: p62
   exam #: e96
   patient id: example_mb_subject
   s1043: 3Plane_Loc_SSFSE
   s1045: CFMRI fwd ABCD
   s1046: CFMRI rvs ABCD
   s1047: rsfMRI_r1

   NIFTIs
   P0630_0927_53_rsfMRI_Run_#1.7_mbrecon.nii.gz

   

Example Topup Command

.. code-block:: csh

   run_topup_hcpfmri -d1 s1045 -d2 s1046 -i P0630_0927_53_rsfMRI_r1.7_mbrecon -o P0630_0927_53_rsfMRI_r1.7_mbrecon_topup


fMRI Topup: Non-Multiband Data
------------------------------

Example Non-Multiband Acquisition cfmricp_log.txt

.. code-block:: csh

   DICOMs
   
   p folder: p62
   exam #: e96
   patient id: example_mb_subject
   s1043: 3Plane_Loc_SSFSE
   s1045: SE_EPI_topup_fwd
   s1046: SE_EPI_topup_rvs
   s1047: rsfMRI_r1

   NIFTIs
   No nifti files
   

Example Topup Command

.. code-block:: csh

   run_topup_hcpfmri -d1 s1045 -d2 s1046 -i s1047 -o rsfMRI_r1_topup

Available Optional Input Arguments
----------------------------------

It is important to note that the default mode for this code will complete motion correction (3dVolreg) on the fMRI data and delete all temporary files (with the exception of the motion registration parameters)

In some cases, you may wish to complete motion correction using your own preferred packages and options 

Using the flag below, you can run the entire data prep and topup process without invoking the built-in motion correction option

.. code-block:: csh

  -nomoco

If you prefer to hold onto the temporary files created by our wrapper script:

.. code-block:: csh

   b02b0.cnf
   bothb0.nii.gz
   bothb0_rs.nii.gz
   bothb0_rs.topup_log
   cal_ap.nii.gz
   cal_pa.nii.gz
   epi.nii.gz
   epi_regb0.nii.gz
   epi_reg.nii.gz
   flist
   flist1
   motion.1D (preserved by default)
   my_acq_para.txt

You can add the following flags to your "run_topup_hcpfmri" command:

.. code-block:: csh

   -nocleanup 
   -tmpdir DirName #Specify your own directory name for the temporary files