I want to project the region of interest (ROIs) from  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.
 Probabilistic Maps of Visual Topography in Human Cortex; Liang Wang, Ryan E B Mruczek, Michael J Arcaro, Sabine Kastner
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
Great. You can skip the resample step by specifying the -master dataset in 3dAllineate.
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:
Voxel spacing: 1.75x1.75x1.75
for one of them:
Orientation: Oblique (Close to RPI)
and the other one:
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