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atlases
anatROIs comes with a predefined list of ROIs in MNI, and you can create your own too.
They can be downloaded by anyone from here. See the contents of the zip file in the table below:
| ATR_roi1_L.nii.gz | ATR_roi1_R.nii.gz | ATR_roi2_L.nii.gz | ATR_roi2_R.nii.gz | CGC_roi1_L.nii.gz |
| CGC_roi1_R.nii.gz | CGC_roi2_L.nii.gz | CGC_roi2_R.nii.gz | CST_roi1_L.nii.gz | CST_roi1_R.nii.gz |
| CST_roi2_L.nii.gz | CST_roi2_R.nii.gz | Callosal_ROIs.nii.gz | Callosum_midsag.nii.gz | FA_L.nii.gz |
| FA_R.nii.gz | FP_L.nii.gz | FP_L_peds.nii.gz | FP_L_peds2.nii.gz | FP_R.nii.gz |
| FP_R_peds.nii.gz | FP_R_peds2.nii.gz | FSL_MNI152_FreeSurferConformed_1mm.nii.gz | HCC_roi1_L.nii.gz | HCC_roi1_R.nii.gz |
| HCC_roi2_L.nii.gz | HCC_roi2_R.nii.gz | ICP_L_high.nii.gz | ICP_L_low.nii.gz | ICP_R_high.nii.gz |
| ICP_R_low.nii.gz | IFO_roi1_L.nii.gz | IFO_roi1_R.nii.gz | IFO_roi2_L.nii.gz | IFO_roi2_R.nii.gz |
| IFO_roi3_L.nii.gz | IFO_roi3_R.nii.gz | ILF_roi1_L.nii.gz | ILF_roi1_R.nii.gz | ILF_roi2_L.nii.gz |
| ILF_roi2_R.nii.gz | ILF_roi3_L.nii.gz | ILF_roi3_R.nii.gz | L_AntFrontal.nii.gz | L_Ant_Frontal.nii.gz |
| L_Arcuate_PostSegment.nii.gz | L_LateralParietal.nii.gz | L_Motor.nii.gz | L_Occipital.nii.gz | L_Occipital_copy.nii.gz |
| L_Orb_Frontal.nii.gz | L_Orbital.nii.gz | L_Parietal.nii.gz | L_PostParietal.nii.gz | L_Post_Parietal.nii.gz |
| L_SupFrontal.nii.gz | L_SupParietal.nii.gz | L_Sup_Frontal.nii.gz | L_Sup_Parietal.nii.gz | L_Temporal.nii.gz |
| L_VOF_ROI1.nii.gz | L_VOF_ROI2.nii.gz | MCP_L.nii.gz | MCP_R.nii.gz | OR_roi3_L.nii.gz |
| OR_roi3_R.nii.gz | R_AntFrontal.nii.gz | R_Ant_Frontal.nii.gz | R_Arcuate_PostSegment.nii.gz | R_LateralParietal.nii.gz |
| R_Motor.nii.gz | R_Occipital.nii.gz | R_Orb_Frontal.nii.gz | R_Orbital.nii.gz | R_Parietal.nii.gz |
| R_PostParietal.nii.gz | R_Post_Parietal.nii.gz | R_SupFrontal.nii.gz | R_SupParietal.nii.gz | R_Sup_Frontal.nii.gz |
| R_Sup_Parietal.nii.gz | R_Temporal.nii.gz | SCP_L_high.nii.gz | SCP_L_low.nii.gz | SCP_R_high.nii.gz |
| SCP_R_low.nii.gz | SLF_roi1_L.nii.gz | SLF_roi1_R.nii.gz | SLF_roi2_L.nii.gz | SLF_roi2_R.nii.gz |
| SLFt_roi2_L.nii.gz | SLFt_roi2_R.nii.gz | UNC_roi1_L.nii.gz | UNC_roi1_R.nii.gz | UNC_roi2_L.nii.gz |
| UNC_roi2_R.nii.gz | callosum_rough.nii.gz | eye_L.nii.gz | eye_R.nii.gz | midline_wedgebig.nii.gz |
Out of the box, these ROIs will be usable in the RTP-pipeline, the tool will convert them automatically to individual subject space.
If you want to use your own ROIs, you can draw them in MNI space (they should be in FSL_MNI152_FreeSurferConformed_1mm.nii.gz space, the file it is provided inside the zip above). Then, you can add them to the zip (and maybe remove the ROIs you don't want to have), and add the zip as input to the anatROIs container. You MNI ROIs will be in the output of the container in individual subject space.
We included several other atlases that will create ROIs that you can later use in RTPpipeline or fMRI or in any part of your analysis pipeline.
- HCP Atlas
- Wang Atlas
- Hippocampal and Thalamic segmentation
- Neuropythy
- Cerebellum atlas
- Mori atlas ROIs