Archived FMRI pipeline: Difference between revisions

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== NOTE: this page needs cleaning up and filling in!==
==About fMRI data and file types==
Raw fMRI data is saved in .dcm (dicom) files. Typically these .dcm files correspond to individual slices, and the resulting 3D image (or a time-series of 3D images) is saved in a .nii (nifti) file. Raw dicom files can be transformed into nifti format using SPM (a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data) or other software such as MRIcro or Freesurfer. (Note that, when handling neuroimaging data, you need to take special care that the orientation of the images is correct.)
 
==Standard Preprocessing Steps & The Pipeline==
NOTE THAT THIS IS NOT THE MOST UPTO DATE PIPELINE, which is why we don't link to the relevant code here. We have kept this section for reference, and since the main preprocessing steps are standard, the documentation may be a useful guide.
PLEASE SEE SECTION ON MOTION (below) for the new pipeline (which can be downloaded from the secure wiki).
 
The input to the pre-processing pipeline must be provided in nifti (.nii) format (see section above). The following PDF [[http://bcni.psychol.cam.ac.uk/~pv226/fmri_preprocessing.pdf]] describes 6 broad stages of fMRI preprocessing:
 
'''Signal preprocessing'''
 
1. Preprocessing of anatomical images
 
2. Preprocessing of functional images
 
3. Anatomical standardization of functional images


==About fMRI data and file types==
4. Removal of noise signal
Raw fMRI data is saved in .dcm (dicom) files. Typically these .dcm files correspond to individual slices, and the resulting 3D image (or a time-series of 3D images) is saved in a .nii (nifti) file. Raw dicom files can be transformed into nifti format using SPM (a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data) or other software such as MRIcro.
 
'''Network construction'''
 
5. Construction of nodes: Parcellation
 
6. Construction of links
 
NB: The pipeline ends once the full, weighted adjacency matrix is defined. Network analyses need to be carried out separately.
 
 
'''The pipeline uses the following software packages:'''
 
* AFNI (Analysis of Functional NeuroImages - made by the NIH)  


Note that, when handling neuroimaging data, you need to take special care that the orientation of the images is correct.
* FSL (FMRIB Software Library - made by the FMRIB in Oxford)


==Preprocessing in SPM==
* WMTSA (Wavelet Methods for Time-Series Analysis - a Matlab or R program for computing frequency-band specific “wavelet” correlations) . A very basic tutorial on wavelets can be found here: [[http://person.hst.aau.dk/enk/ST8/wavelet_tutotial.pdf]]. For details on the wavelet toolbox in MATLAB, read: [[http://web.mit.edu/1.130/WebDocs/wavelet_ug.pdf]].
In what follows, we describe the broad stages of fMRI preprocessing, and how they are implemented in SPM. Note that SPM saves the data after each intermediate step in newly created files with relevant prefixes.


===Slice-timing Correction===
Note that it saves the data after each intermediate step in newly created files with relevant prefixes.
This step corrects for the time-delay between the acquisition of different slices. In order to correct for this, the user needs to provide the following information:


===== -loading the data =====
===== - the number of slices (e.g. 32)=====
===== - TR=====
===== - TA=====
===== - the order in which slices were acquired (e.g.. bottom to top, interleaved: 2:2:32 1:2:31)=====
===== - a reference slice=====
===== - a filename prefix (this is used to prefix the new files created at the end of this preprocessing step, saving the slice-time corrected data)=====


===Rigid body Correction===
==The Motion Problem==
This step estimates, characterises and broadly corrects for the effect of head-motion. It is also the step at which one can exclude subjects with excessive head-motion (e.g. more than a voxel size). The four options at this stage are
In short, the 'motion problem' refers to the recent (2012) discovery that even tiny head-motion can lead to severe artifacts in connectvitiy analyses of resting state fMRI data. We have recently set up a 'task-force' to try to better understand and deal with this problem. The task-force holds regular meetings to keep efforts integrated and the key ideas emerging from these meetings will be logged on a parallel (secure) wiki which also contains benchmark data and useful code generated along the way:
===== -estimate =====
===== -reslices =====
===== -estimate and reslice =====
===== -realign and unwrap =====


===Registration to Standard Space===
[https://wiki.cam.ac.uk/bmuwikisecure/Motion_Task-Froce_Meetings_and_Related_Code Secure Wiki]
This is the 'Normalize' option in SPM. Chose source image, template (EPI), method, image size, voxel size (2x2x2).
===Regressing out head motion, CSF, white matter & physiological signals===
In SPM, this is done under '1st level analysis' -> 'Data and design' -> 'Multiple regression'.


==Parcellation==
==Wavelet Decomposition==
==The question of smoothing==
Required before VBM. Important for finding activations regions. Not used when parcellating (for network analysis).
==Back To Main Page==
==Back To Main Page==
[[Main Page]]
[[Main Page]]

Latest revision as of 10:53, 10 May 2018

About fMRI data and file types

Raw fMRI data is saved in .dcm (dicom) files. Typically these .dcm files correspond to individual slices, and the resulting 3D image (or a time-series of 3D images) is saved in a .nii (nifti) file. Raw dicom files can be transformed into nifti format using SPM (a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data) or other software such as MRIcro or Freesurfer. (Note that, when handling neuroimaging data, you need to take special care that the orientation of the images is correct.)

Standard Preprocessing Steps & The Pipeline

NOTE THAT THIS IS NOT THE MOST UPTO DATE PIPELINE, which is why we don't link to the relevant code here. We have kept this section for reference, and since the main preprocessing steps are standard, the documentation may be a useful guide. PLEASE SEE SECTION ON MOTION (below) for the new pipeline (which can be downloaded from the secure wiki).

The input to the pre-processing pipeline must be provided in nifti (.nii) format (see section above). The following PDF [[1]] describes 6 broad stages of fMRI preprocessing:

Signal preprocessing

1. Preprocessing of anatomical images

2. Preprocessing of functional images

3. Anatomical standardization of functional images

4. Removal of noise signal

Network construction

5. Construction of nodes: Parcellation

6. Construction of links

NB: The pipeline ends once the full, weighted adjacency matrix is defined. Network analyses need to be carried out separately.


The pipeline uses the following software packages:

  • AFNI (Analysis of Functional NeuroImages - made by the NIH)
  • FSL (FMRIB Software Library - made by the FMRIB in Oxford)
  • WMTSA (Wavelet Methods for Time-Series Analysis - a Matlab or R program for computing frequency-band specific “wavelet” correlations) . A very basic tutorial on wavelets can be found here: [[2]]. For details on the wavelet toolbox in MATLAB, read: [[3]].

Note that it saves the data after each intermediate step in newly created files with relevant prefixes.


The Motion Problem

In short, the 'motion problem' refers to the recent (2012) discovery that even tiny head-motion can lead to severe artifacts in connectvitiy analyses of resting state fMRI data. We have recently set up a 'task-force' to try to better understand and deal with this problem. The task-force holds regular meetings to keep efforts integrated and the key ideas emerging from these meetings will be logged on a parallel (secure) wiki which also contains benchmark data and useful code generated along the way:

Secure Wiki

Back To Main Page

Main Page