fMRI Primer

DTI data analysis (in progress!)

MedINRIA is a powerful program to use for analyzing and displaying DTI data. It also is useful for overlaying multiple image types (i.e. MRI,fMRI,DTI) atop one another. This is useful when using an fMRI cluster as a DTI seed. It is also allows you to use high-resolution images as your base image.

Analyzing DTI data in MedINRIA-Importing from Dicom

Put all of the dicom images from the DTI run into one folder. Make sure there is nothing else in the folder except the DTI images.

Open MedINRIA and go to Modules–> Image Viewer

Click the ‘Import’ button and then the ‘Next’ button. On the top left corner of the ‘DICOM Importer Wizard’ is the ‘Open folder’ button. Click this button and point the browser to the folder that contains the DTI images.

Once they load, highlight the series and click the “split” and then the “save all” button. Finally, click “finish” and wait for the volumes to save and load. The program creates one Analyze image for each DTI gradient direction.

Analyzing DTI data in MedINRIA-Creating a new project

Now you can go to Modules–> DTI Track, and Click the upper left button to “Create a new .dts”.

Select all of the analyze images created by the Dicom Import Wizard.

Next you will need to load a .bvec file with the gradient directions from the scan. This file can be generated with MRICron:.

Using MRICron to get direction values:

To extract the gradient directions from raw dicom images, use a utility called dcm2nii which is installed along with the MRIcron package. This converts the dicom to analyze (which we do not need), and produces a .bvec file that has the direction info.

Get analyze activation map into MedINRIA

Step 1:
From BV space: To go from BV space to MedINRIA space, use fslswapdim with the options z x -y on both the SPGR and the activation map (or the exported to analyze .vmr amd .vmp files).
From FSL/SPM space: To go from FSL/SPM space to MedINRIA space, use fslswapdim with the options x -y z on both the SPGR and the activation map (or the exported to analyze .vmr amd .vmp files).

Step 2:
Use FLIRT with a 6 parameter rigid body transform to register the first volume of the DTI image with the spgr image. Use the high-resolution SPGR as the base image.

Be sure to check the result…you may have to limit the search angle of the x and y dimensions.

Step 3:
Apply the inverse of this transformation to the activation map and/or spgr images to get them into the DTI space.

To do this, press the UTILS button on the FLIRT menu and them choose “Invert FLIRT transform”. Choose the .mat file created during step 2. Apply the inverse transformation to the maps you want to bring into MedINRIA.

Loading SPGR in MedINRIA
Select “Open Volume”

Loading fMRI map in MedINRIA

Select “Open Map”, then adjust the significance value.

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