Align mask with EPI image

AFNI Message Board
1

I want to project the region of interest (ROIs) from [1] on my subjects’ surface and create a NIFTI file out of them. The ROIs are in 1d.dset format in AFNI. To do this, first, I mapped ROIs (e.g. v1_lh.1d.dset) on the subject surface (std.141.mysubj_lh.spec), which has been created in Freesurfer and converted to spec file using @SUMA_Make_Spec_FS, with the following command:

3dSurf2Vol -spec std.141.mysubj_lh.spec -surf_A lh.smoothwm -surf_B lh.pial -grid_parent mysubj_SurfVol.nii -sv mysubj_SurfVol.nii -map_func ave -f_steps 10 -f_index voxels -sdata_1D v1_lh.1d.dset -prefix v1_lh.nii.gz

The result was acceptable (figure below).

I want to align the NIFTI files from ROIs (e.g. v1_lh.nii.gz) with the EPI images. However, the structural image from @SUMA_Make_Spec_FS is not aligned with the EPI image. Would you please help me to align the masks (ROIs) with the EPI image?

  • One solution that comes to my mind is to align the structural image with the EPI image using align_epi_anat.py. Then use the transformation matrix form align_epi_anat.py to align masks with the EPI image, but I do not know how to use the transformation matrix to transform the masks.

[1] Probabilistic Maps of Visual Topography in Human Cortex; Liang Wang, Ryan E B Mruczek, Michael J Arcaro, Sabine Kastner

anat.jpg

2

A few ways to do this:

  1. Align your anatomical to the EPI dataset first, then redo Freesurfer processing using that anatomical dataset. Then repeat @SUMA_Make_Spec_FS, etc.

  2. Align EPI data to anatomical dataset as part of your processing with afni_proc.py. If you’re doing motion correction anyway, interpolation effects should be minimal.

  3. Align your anatomical to the EPI dataset using align_epi_anat.py. Then use that volume as the -sv volume option to align to experiment.

  4. Align your anatomical data to the EPI dataset using align_epi_anat.py. Transform the ROI data using the transformation computed with “3dAllineate -NN -1Dmatrix_apply” (using the transformation 1D file output from align_epi_anat.py).

3

Thank you, Daniel.
Item four worked for me. However, I used 3dresample after 3dAllineate, too. These are the commands I used:

align_epi_anat.py -anat brain.nii.gz -epi fmri.nii -epi_base 5 -volreg off -tshift off -anat_has_skull no -epi_strip None

3dSurf2Vol -spec std.141.brain.spec -surf_A smoothwm -surf_B pial -grid_parent brain.nii.gz -sv brain.nii.gz -map_func ave -f_steps 20 -f_index points -sdata_1D mask.1d.dset -prefix mask.nii.gz

3dAllineate -prefix align_mask.nii.gz -source mask.nii.gz -NN -1Dmatrix_apply brain_al_mat.aff12.1D

3dresample -master fmri.nii -prefix final_mask.nii.gz -input align_mask.nii.gz

4

Great. You can skip the resample step by specifying the -master dataset in 3dAllineate.

5

Thank you, Daniel.
I have a question. I checked the alignment of the mask and EPI images in ANFI and it seems that they are aligned, as in the figure below. However, when I checked them in ITK-SNAP, It seems that they are not aligned! Do you know why this is so?
I want to use the mask in CoSMoMVPA using cosmo_fmri_dataset and after checking the result with ITK-SNAP, I am not sure whether the mask and the EPI image are aligned are not.

For the both images:
Dimensions: 120x120x75
Voxel spacing: 1.75x1.75x1.75
Origin: -106.312x87.8681x-54.6848
for one of them:
Orientation: Oblique (Close to RPI)
and the other one:
Orientation: RPI

afni.png
afni.png334×713 94.6 KB

itk.png
itk.png659×651 46 KB

6

I think it’s likely this is an oblique dataset, and ITK-snap will show that differently than AFNI. You can remove the obliquity of copy of the dataset by doing this:

3dcopy mydset.nii.gz mydset_no_ob.nii.gz
3drefit -deoblique mydset_no_ob.nii.gz

Then view that dataset in ITK-snap with the same ROI data. In AFNI, you may want to save the dataset with a header attribute that will enforce a color map more suitable for ROIs with:
3drefit -cmap INT_CMAP myROIs.nii.gz

7

Thank you, Daniel.