## page was renamed from FsTutorial/MultiModalRegistrationV5.1
## page was renamed from FsTutorial/MultiModalRegistration_freeview
#pragma section-numbers 1
[[Tutorials|Back to Tutorial Homepage]]<<BR>>[[FsTutorial|Back to Course Homepage]]<<BR>>[[FsTutorial/MultiModal_freeview|Back to Multimodal Tutorial List]]

##Other Multimodal Tutorials: [[FsTutorial/MultiModalDtiIndividual_freeview|B. Individual DTI Integration]], [[FsTutorial/MultiModalFmriIndividual_freeview|C. Individual fMRI Integration]], [[FsTutorial/MultiModalFmriGroup_freeview|D. Surface-based Group fMRI Analysis]]
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Other Multimodal Tutorials: [[FsTutorial/MultiModalFmriIndividual_freeview|Individual fMRI Integration]], [[FsTutorial/MultiModalFmriGroup_freeview|Surface-based Group fMRI Analysis]], [[FsTutorial/Diffusion_DtiIntegration|Diffusion and DTI Integration]]

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{{{#!html
<h1>Registration</h1>
}}}
The purpose of this multimodal tutorial is to get you acquainted with the concepts needed to perform multi-modal integration in !FreeSurfer using fMRI and DTI analysis. You will not learn how to perform fMRI or DTI analysis here; that knowledge is already assumed. The fMRI makes use of data from the Functional Biomedical Informatics Research Network (fBIRN, www.nbirn.net). <<TableOfContents(2)>>

== Preparations ==
=== If You're at an Organized Course ===
If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in ''every'' '''new''' terminal window (aka shell) you open throughout this  tutorial. Copy and paste the commands below to get started:

{{{
export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101
}}}
''To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command.''

These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into the directory within the SUBJECTS_DIR that you will use for this part of the tutorial. You can now skip ahead to the tutorial (below the gray line).

=== If You're Not at an Organized Course ===
If you are '''NOT''' taking one of the formally organized courses, then to follow this exercise exactly be sure you've downloaded the [[FsTutorial/Data|tutorial data set]] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. These are the commands that you need to run before getting started:

{{{
## bash
<source_freesurfer>
export TUTORIAL_DATA=<path_to_your_tutorial_data>
export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

## tcsh
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv TUTORIAL_DATA <path_to_your_tutorial_data>
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101
}}}
''Information on how to source [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer|FreeSurfer]] is located [[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup+&+Configuration|here]]''.

If you are not using the tutorial data you should set your {{{SUBJECTS_DIR}}} to the directory in which the recon(s) of the subject(s) you will use for this tutorial are located.

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== Basic Manual Registration ==
The purpose of this exercise is to:

 1. Familiarize you with the !FreeView and/or tkregister2 command interface.
 1. Show you how to make manual adjustments to the registration.
 1. Show you what a bad registration is and how hard it is to fix manually.

'''Option A''': Using FreeView

In order to use !FreeView, run the command below:

{{{
freeview -v template.nii \
$SUBJECTS_DIR/fbirn-anat-101.v4/mri/orig.mgz:visible=0 -f \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/lh.white:edgecolor=green \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/rh.white:edgecolor=green \
-viewport coronal
}}}
This should bring up an interface that looks like this:

{{attachment:FreeView.Snap1.sm.png||height="448",width="717"}}

 1. The grayscale image is the functional data.
 1. The green line is the white surface.
 1. Gray matter and CSF are bright while white matter is dark.

Notice how the surfaces do not line up with the  anatomy in the functional volume. You can turn the orig volume on and  off to see how much the registration is off. To do manual registration  in !FreeView, select the volume you want to adjust (in this case, choose  template) and then go to the 'Tools' menu and select 'Transform Volume'. Select the 'Translate' tab and  play around with the sliders until the surfaces follow the anatomy  better. You could play with the Rotation, as well.

{{attachment:FreeView.Snap2.png||height="410",width="386"}} {{attachment:FreeView.Snap3.png||height="413",width="389"}}

When you are happy  with your results, save the registration file ('Save Reg') and/or the resampled  volume ('Save Volume As'). If you would like to start over, you can choose 'Restore to  Original'. Note, !FreeView will save .lta type registration files.

'''Option B''': Using tkregister2

In order to use tkregister2 for this task, load a functional volume with the anatomical volume using:

{{{
tkregister2 --mov template.nii --s fbirn-anat-101.v4 \
 --regheader --reg myregister.dat --surf
}}}
The !FreeSurfer subject name  is "fbirn-anat-101.v4", and myregister.dat is the output registration (which does not exist yet). --regheader indicates to compute the initial registration from the information in the headers of the input volumes and not from the contents of a registration file, which is suitable when the volumes were acquired during the same scan session (ie, the head motion is minimal).

This should bring up an interface that looks like this:<<BR>> {{attachment:Registration.jpeg}} <<BR>>

Things to do:

 1. Click in the image window and hit the 's' key to toggle the surface on and off.
 1. Click on the "COMPARE" button to toggle between the functional and the anatomical. Note that the green surface is aligned with the anatomical.
 1. Change orientation by clicking on the "CORONAL", "SAGITTAL", and "HORIZONTAL" buttons.
 1. NOTE: DO NOT SPEND MORE THAN 5min DOING THIS STEP! Attempt to register the functional manually by adjusting the "TRANSLATE BRAIN" and "ROTATE BRAIN" sliders. Do NOT use "SCALE BRAIN".
 1. You can hit the "SAVE REG" button at any time to save a registration. (This will save a .dat type registration file.) If you hit it again, it will ask you if it is ok to overwrite it (it is).
 1. Close tkreg

== Automatic Registration ==
The purpose of this exercise is to show you how to use the automatic registration program (bbregister). To run, copy and paste this command into your shell:

{{{
  bbregister --mov template.nii --bold \
    --s fbirn-anat-101.v4 \
    --init-rr --lta register.lta
}}}
Notes:

 1. --bold indicates that the template has bold/T2 contrast (meaning that gray matter is brighter than white matter).
 1. --init-rr indicates that the [[mri_robust_register]] program will be used for registration.
 1. --lta indicates that the output registration file is register.lta (Note, currently register.dat will also be written into the output directory for backwards compatibility).
 1. This will take about 5 min (the same amount of time you spent manually, right?).

== View Automatic Registration ==
Look at the register.lta text file created:

{{{
cat register.lta
}}}
Click [[FsTutorial/MultiModalRegistration/RegisterFileLta|here]] to see an example.

In order to load a functional volume with the anatomical volume specifying the recently created automatic registration:

'''Option A''': Using !FreeView

{{{
freeview -v $SUBJECTS_DIR/fbirn-anat-101.v4/mri/orig.mgz \
template.nii:reg=register.lta -f \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/lh.white:edgecolor=green \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/rh.white:edgecolor=green \
-viewport coronal
}}}
Select the template volume and hit Alt+v to  switch between the template and orig or change the opacity value on the  top volume to observe the quality of the alignment. See how much better  the registration is now? How does it compare to your manual registration?

{{attachment:Registered.Snap.sm.png||height="428",width="684"}}

'''Option B''': Using tkregister2

{{{
tkregister2 --mov template.nii --reg register.dat --surf
}}}
Click back and forth between "TARGET" (the anatomical volume) and "MOVEABLE" (the automatically registered functional volume) to observe the quality of the alignment.

{{attachment:registerafter.jpeg}}

Notes:

 1. The subject is not specified since it is in the register.dat.
 1. --regheader is not used.

How does this registration look compared to your manual registration above? Can you make it any better?

##Other Multimodal Tutorials: [[FsTutorial/MultiModalDtiIndividual_freeview|B. Individual DTI Integration]] [[FsTutorial/MultiModalFmriIndividual_freeview|C. Individual fMRI Integration]], [[FsTutorial/MultiModalFmriGroup_freeview|D. Surface-based Group fMRI Analysis]]
----
Other Multimodal Tutorials: [[FsTutorial/MultiModalFmriIndividual_freeview|Individual fMRI Integration]], [[FsTutorial/MultiModalFmriGroup_freeview|Surface-based Group fMRI Analysis]], [[FsTutorial/Diffusion_DtiIntegration|Diffusion and DTI Integration]]

<<BR>>[[Tutorials|Back to Tutorial Homepage]]<<BR>>[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|Back to Course Homepage]]