NIMH Macaque Template
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NMT_v1.2
README.md

README.md

NMT - NIMH Macaque Template

For any issues or questions, contact Jakob Seidlitz at jakob.seidlitz@nih.gov or jms290@cam.ac.uk.

Description

The National Institute of Mental Health (NIMH) Macaque Template (NMT) is an anatomical structural MRI template of the macaque brain. It was created using the freely available software package ANTs. The NMT is technically the non-linear diffeomorphic average of T1-weighted Modified Driven Equilibrium Fourier Transform (MDEFT) scans from 31 adult rhesus macaque brains, generated by iteratively registering and averaging each individual subject to a common space. For more information on the template creation process, see our paper.

This README file provides an overview of the NMT MRI volume and its associated volume and surface files. Sample commands for visualizing the surfaces are listed as well, using SUMA from the AFNI software suite.

Citation

If you use this repository, please cite the paper below:

Seidlitz, J., Sponheim, C., Glen, D., Ye, F.Q., Saleem, K.S., Leopold, D.A., Ungerleider, L., Messinger, A. A population MRI brain template and analysis tools for the macaque. NeuroImage (2017). doi: 10.1101/105874

Download

To download from the terminal, navigate to the directory where you want to store the NMT repository. Then, copy and paste this command:

git clone http://github.com/jms290/NMT.git

Otherwise, on the NMT repository homepage, click the green button "clone or download"...

Alternatively, all files associated with the NMT may be downloaded straight from the AFNI website here

NMT Files

All volume and surface files are stored in the relatively universal nifti (.nii.gz) and gifti (.gii) formats, to be compatible with a plethora of software packages.

  • NMT volume (with skull) - NMT.nii.gz
  • NMT volume (without skull) - NMT_SS.nii.gz
  • NMT Masks
    • NMT Brain Masks
      • NMT Binary Brainmask NMT_brainmask.nii.gz
      • NMT cerebellum - NMT_cerebellum_mask.nii.gz
      • NMT olfactory bulb - NMT_olfactory_bulb_mask.nii.gz
      • NMT arterial blood vasculature - NMT_blood_vasculature_mask.nii.gz
      • NMT 4-tissue segmentation mask (including arterial blood vasculature) - NMT_segmentation_4class.nii.gz
    • NMT Probabilisitic Tissue Segmentation Masks
      • NMT Probabilisitic Brainmask NMT_brainmask_prob.nii.gz
      • Gray matter - NMT_segmentation_GM.nii.gz
      • White matter - NMT_segmentation_WM.nii.gz
      • Cerebral spinal fluid - NMT_segmentation_CSF.nii.gz
    • NMT Cortical Masks
      • NMT cortical cortical thickness mask - NMT_CT.nii.gz
      • NMT cortical gray matter mask - NMT_GM_cortical_mask.nii.gz
      • NMT cortical gray matter mask with white matter - NMT_GM_cortical_mask_withWM.nii.gz
  • NMT surfaces
    • Gray matter surface - [lh or rh].GM.gii
    • White matter surface - [lh or rh].WM.gii
    • Mid-cortical surface - [lh or rh].mid.gii
    • NMT surfaces (inflated)
      • Gray matter surface - [lh or rh].GM_inflated.gii
      • White matter surface - [lh or rh].WM_inflated.gii
      • Mid-cortical surface - [lh or rh].mid_inflated.gii
    • NMT surfaces (other)
      • Arterial blood vasculature - blood_vasculature.gii
      • Cerebellum surface - cerebellum.gii
  • Common Atlases
    • D99 Atlas Aligned to NMT - D99_atlas_1.2a_al2NMT.nii.gz
    • F99 Transformation Parameters (AFNI website)- /F99_volumetric_transformations

In the surfaces folder, there is a .spec file - NMT_both.spec, which is a text file used by SUMA to load in each of the left and right hemisphere surfaces above.

You will also find a folder called single_subject_scans/. This directory contains an example MRI script and tutorial for utilizing the NMT single-subject processing scripts (see Single-Subject Processing). Folders containing your MRI scans will need to be placed in the single_subject_scans/ folder before you can properly use the single-subject processing scripts.

Visualization in AFNI/SUMA

For those new to AFNI/SUMA, we recommend that you use the quick_view.csh script. This script will automatically open the NMT surfaces in SUMA and the NMT in AFNI.

Navigate to the directory where you have stored the NMT repository. Then follow these steps:

afni -niml &

This will start AFNI and tell AFNI that a connection with SUMA is imminent. Load in NMT.nii.gz as the underlay if it is not loaded automatically. Then, back in the terminal, run:

suma -spec ./NMT_both.spec -sv ./NMT.nii.gz &

This should start SUMA, and you should see the left and right WM surfaces. To switch to a different set of surfaces, move your cursor into the SUMA window and toggle the "." key. For other navigational shortcuts and tools, see the SUMA documentation.

Toggle the "t" key to open the connection between AFNI and SUMA. You should see various outlines on the NMT volume in AFNI that correspond with the surfaces loaded into SUMA. To edit or remove the outlines in AFNI, toggle the "Control Surface" button in the AFNI GUI.

Now that AFNI and SUMA are linked, this will allow you to visualize any data (i.e. overlay) from the NMT volume on the surface. Note that only the voxels which intersect the surface outlines will be plotted on the surface. As such, we suggest using the "mid" surface for the visualization of any functional MRI data. For more information about using AFNI interactively, see this slide show.

Atlases in the NMT

We provide the D99 atlas nonlinearly warped to the NMT, found in the atlases/D99_atlas/ directory. Before viewing the D99 atlas, we recommend running the NMT_env.csh script so that AFNI can recognize the D99 atlas aligned to the NMT as an atlas. Atlases may be further warped to the single subject space (see Single-Subject Processing) or utilized in the NMT for ROI-based analyses. Use of the D99 atlas should be accompanied with the following citation:

Three-dimensional digital template atlas of the macaque brain
Reveley, Gruslys, Ye, Glen, Samaha, Russ, Saad, Seth, Leopold, Saleem
Cerebral Cortex, Aug 2016.

Furthermore, we include the rigid, affine, and diffeomorphic (non-linear) tranformations to the NMT from the F99 template here. An example command to align the F99 atlas to the NMT (using AFNI's 3dNwarpApply command) is provided below:

3dNwarpApply -nwarp 'Macaque.F99UA1.LR.03-11_SurfVol_shft.1D \
 Macaque.F99UA1.LR.03-11_SurfVol_shft_al2std_mat.aff12.1D \
 Macaque.F99UA1.LR.03-11_SurfVol_shft_WARP.nii.gz' \
 -source {F99_atlas_name}  -ainterp NN -short \
 -master NMT.nii.gz -prefix F99_atlas_al2NMT.nii.gz

To go from the NMT to the F99 simply reverse the order of the transformations and add the INV() to each transformation file:

3dNwarpApply -nwarp 'INV(Macaque.F99UA1.LR.03-11_SurfVol_shft_WARP.nii.gz) \
INV(Macaque.F99UA1.LR.03-11_SurfVol_shft_al2std_mat.aff12.1D) \
INV(Macaque.F99UA1.LR.03-11_SurfVol_shft.1D)' \
-source NMT.nii.gz -ainterp NN -short \
-master {F99_atlas_name} -prefix NMT_in_F99_atlas.nii.gz

Single-Subject Processing

Along with the NMT dataset, we provide scripts to automated the processing of single subjects. See the paper as well as the table in the supplemental material for more information. Below is the usage for each script.

For help with using the single-subject processing tools, we recommend running our example script, align_and_process_tutorial.csh in the Example_Subject/ folder. This script will run the NMT processing scripts on our Example_Subject so that you can see how the scripts should be run and the format of the output files.

-Only a reconstructed T1-weighted scan/volume is needed (either AFNI (.BRIK/.HEAD) or NIFTI (.nii or .nii.gz) format)

NMT_subject_align

The NMT_subject_align script generates the rigid (6 parameter), affine (12 parameter), and non-linear (voxelwise) transformations to and from the NMT. The NMT_subject_process and NMT_subject_morph scripts depend on these transformations.

Usage

Create a directory in single_subject_scans/ directory in the NMT distribution, and copy the scans of the individual subjects into this new directory. Run this script using a single scan as input, along with the NMT and NMT_subject_align.csh in the parent directory, as below:

tcsh ../../NMT_subject_align.csh [subject] ../../NMT.nii.gz

If the brain has already been masked out from your subject (i.e., skull-stripped), utilize the skull-stripped version of the NMT (NMT_SS.nii.gz) as input to NMT_subject_align, as below:

tcsh ../../NMT_subject_align.csh [subject_without_skull] ../../NMT.nii.gz

We also provide the ability to automate the alignment of atlases through NMT_subject_align:

tcsh ../../NMT_subject_align.csh [subject] ../../NMT.nii.gz ../../atlases/D99_atlas/D99_atlas_1.2a_al2NMT.nii.gz

NMT_subject_align provides multiple outputs to assist in registering your anatomicals and associated MRI data to the NMT:

  • Subject scan registered to the NMT
    • mydset_shft.nii.gz - dataset center aligned to the NMT center
    • mydset_shft_al2std.nii.gz - dataset affine aligned to the NMT
    • mydset_shft_aff.nii.gz - dataset affine aligned to the NMT and on the NMT grid
    • mydset_warp2std.nii.gz - dataset nonlinearly warped to the NMT
  • Registration parameters for Alignment to NMT
    • mydset_composite_linear_to_NMT.1D - combined linear transformations to the NMT
    • mydset_shft_WARP.nii.gz - warp deformations to the NMT from nonlinear alignment only
  • Registration parameters for NMT Alignment to Subject
    • mydset_composite_linear_to_NMT_inv.1D - inverse of mydset_composite_linear_to_NMT.1D
    • mydset_shft_WARPINV.nii.gz - inverse of mydset_shft_WARP.nii.gz
  • Brain Atlas Aligned to Single Subject (Optional)
    • {atlas}_in_mydset.nii.gz - Specified Atlas or Mask Aligned to Single Subject

-NOTE: NMT_subject_align requires the AFNI software package to run correctly

Data aligned to your dataset can be easily warped to the NMT using NMT_subject_align outputs and AFNI's 3dNwarpApply and AFNI's 3dAllineate:

3dAllineate -1Dmatrix_apply {mydset}_composite_linear_to_NMT.1D \
	-source {newdset}+orig -master ../../NMT.nii.gz -final wsinc5 \
	-prefix {newdset}_in_NMT_aff.nii.gz
3dNwarpApply -nwarp {mydset}_shft_WARP.nii.gz -source {newdset}_in_NMT_aff.nii.gz \
	-master ../../NMT.nii.gz -ainterp wsinc5 -prefix {newdset}_in_NMT.nii.gz

To bring data from the NMT to your dataset, simply use the inverse transformations of the above commands:

3dNwarpApply -nwarp {mydset}_shft_WARPINV.nii.gz -source {newdset}+orig \
-master {mydset}+orig -prefix {NMTdset}_in_{mydset}_nl.nii.gz
3dAllineate -1Dmatrix_apply {mydset}_composite_linear_to_NMT_inv.1D -source {NMTdset}_in_{mydset}_nl.nii.gz \
-master {mydset}+orig -prefix {NMTdset}_in_{mydset}.nii.gz

When warping atlas or mask data, add the -ainterp NN flag to avoid warping artifacts.

NMT_subject_process

NMT_subject_process performs N4 bias field correction for normalizing intensity non-uniformities, and generates a brain mask (for skull-stripping) as well as probabilistic tissue segmentation masks (GM, WM, CSF).

Usage

bash ../../NMT_subject_process [subject]

Run this script from the directory where the NMT_subject_align output lies. This script will create a directory NMT_[subject]_process with the corresponding masks in the subject's anatomical space.

-NOTE: NMT_subject_process requires AFNI and ANTs to be installed

NMT_subject_morph

NMT_subject_morph uses the NMT's cortical GM mask to produce volumetric maps of cortical thickness, surface area, and mean and gaussian (i.e., intrinsic) curvature.

Usage

bash ../../NMT_subject_morph [subject]

Run this script from the directory where the NMT_subject_align output lies. This script will create a directory NMT_[subject]_morph with the corresponding masks in the subject's anatomical space.

-NOTE: NMT_subject_morph requires AFNI and ANTs to be installed

Troubleshooting

NMT_subject_process results in a inaccurately fit brainmask

In cases when NMT_subject_process does not produce a sufficient brainmask, we recommend manually warping the NMT's brainmask to your subject using the AFNI's 3dNwarpApply command:

3dNwarpApply -nwarp {mydset}_composite_WARP_to_NMT_inv.nii.gz -source ../NMT_brainmask.nii.gz \
-master {mydset}+orig -prefix NMTbrainmask_in_{mydset}.nii.gz -interp NN