ROI analyses using FSL
合集下载
- 1、下载文档前请自行甄别文档内容的完整性，平台不提供额外的编辑、内容补充、找答案等附加服务。
- 2、"仅部分预览"的文档,不可在线预览部分如存在完整性等问题,可反馈申请退款(可完整预览的文档不适用该条件!)。
- 3、如文档侵犯您的权益，请联系客服反馈,我们会尽快为您处理(人工客服工作时间：9:00-18:30)。
- 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
> fslview & > File > Open Standard > /usr/local/packages/fsl5.0.1/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_atla s_templates/ >File > Open > /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pic katlas/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
Register ROIs to subject space
ROI analyses using FSL
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
Creating ROIs from functional activations
fslmaths run02.feat/cluster_mask_zstat1.nii.gz –thr 6 –uthr 6 example_ROI
Create ROIs from functional activations
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
fslmaths /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MNI_V 4.nii –thr 2 –uthr 2 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
- 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
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:
- 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
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
Drawing ROIs using FSLview
> fslview & > File > Open Standard > /usr/local/packages/fsl5.0.1/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_atla s_templates/ >File > Open > /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pic katlas/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
Register ROIs to subject space
ROI analyses using FSL
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
Creating ROIs from functional activations
fslmaths run02.feat/cluster_mask_zstat1.nii.gz –thr 6 –uthr 6 example_ROI
Create ROIs from functional activations
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
fslmaths /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MNI_V 4.nii –thr 2 –uthr 2 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
- 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
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:
- 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
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