ROI analyses using FSL

March 27, 2013

Overview

- Creating ROIs- Creating atlas based ROIs- Creating functional ROIs- Drawing ROIs in FSLview

- Registering ROI in standard space to single subject space- Extracting data from the ROI (mean intensity, variance, zstat, and

timecourse)

Creating an atlas based ROI

- Each atlas is a single volume/mask, with regions delineated by intensities

- Using fslview, open the 2mm MNI standard brain

> fslview &

> File > Open Standard > /usr/local/packages/fsl-5.0.1/data/standard/ MNI152_T1_2mm_brain

- Add the AAL atlas (aal_MN_v4.nii) from /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/

>File > Open > /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MN_v4.nii

- Find the region you are interested in extracting (for example Right Precentral Gyrus)

- You can also use the atlas tools to help you with your anatomy:

>Tools > Toolbars > Atlas Tools

* Note the intensity of the region you will need this value to extract 

Extract ROI from atlas- For example: Extract right precentral gyrus ROI from the atlas using fslmaths

- Helpful hint: type fslmaths on the command line to see info on its usage

- On the command line:

fslmaths /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MNI_V4.nii –thr 2 –uthr 2 right_precentral

- Input is the full atlas image path

- thr: threshold input image (zero everything below)

- uthr: threshold input image (zero everything above)

- right_precentral is the output name, will be in folder you run the command from unless you specify a full path

Creating ROIs from Functional Activations- ROIs can be created in subject space using cluster masks from fsl 1st level

analyses to create individual functional ROI for each subject

- Example: from first level functional analyses> fslview &> File > Open > run02.feat/cluster_mask_zstat1.nii.gz

* Note the intensity of the region you will need this value to extract 

Creating ROIs from functional activations

fslmaths run02.feat/cluster_mask_zstat1.nii.gz –thr 6 –uthr 6 example_ROI

Create ROIs from functional activations

- ROIs can be created in standard space using cluster masks from fsl 3rd level analyses to create group ROIs that can be applied to each subject

Drawing ROIs using FSLview- Can be done in subject or standard space

- This example is in standard space

- fslview

- File > Create Mask

- Use pencil button to fill in voxels you want to have a value of 1

- File > Save

Register ROIs to subject space

If you create an ROI in standard space, and you want to extract information from the ROI in subject space (from a first level analysis), register the ROI to the subject’s preprocessed data

Since feat was already run, we know the transformation between the BOLD data and the MNI brain: run01.feat/reg/example_func2standard.mat

What we need is the inverse transformation matrix:

convert_xfm  inverse run02.feat/reg/example_func2standard.mat  omat run02.feat/reg/Std2Example_func.mat

Apply the transformation matrix to the ROI (for each subject separately)

flirt -in test_ROI.nii.gz -ref run02.feat/reg/example_func.nii.gz -applyxfm -init run02.feat/reg/Std2Example_func.mat -out run02.feat/reg/reg_test_ROI

Extracting data from ROIs

- This example uses the atlas based ROI after transforming to subject space

- Extract data from ROIs using fslstats using the following options:

–k (mask)

–m (output the mean)

- For example:

fslstats run02.feat/stats/zstat1.nii.gz –k run02.feat/reg/reg_test_ROI –m

gives you the mean zstat in that ROI for each subject

- Your inputs can be zstat images, magnitude of parameter estimate (cope images) variance of parameter estimate (varcope images)

- For DTI data, you can extract metrics such as mean FA on a subject by subject basis from a WM ROI

- Extracting mean time series from ROI

- Time series data comes from (preprocessed) filtered_func_data.nii.gz in a first level .feat directory

- use function fslmeants

fslmeants -i filtered_func_data -o meants.txt -m my_mask

Extracting data from ROIs