:orphan: .. _ahelp_fat_proc_map_to_dti: ******************* fat_proc_map_to_dti ******************* .. contents:: :local: | .. code-block:: none # ----------------------------------------------------------------------- This program is for bringing data sets into DWI space, with the particular thought that bringing anatomically-defined ROI maps or EPI data that are aligned to a subject's anatomical might be useful. This might be useful after having run FreeSurfer, for example. An affine transformation matrix between, say, a subject's T1w volume and a DWI reference volume is calculated, and then applied to follower data sets. The transformation can be applied either as 'NN' (-> for preserving integer values in sets) or as 'wsinc5' (-> if one has floating point values). The final dsets will reside in the DWI space. Yay. At the moment this program *assumes* that the input source ('-source SSS') and reference base ('-base BBB') are from the same subject, because only 12 DOF affine alignment is calculated (using 3dAllineate). Maybe something could be done with 3dQwarp in the future. Maybe. This program mainly assumes that the T1w and DWI reference volume have similar contrasts expected for standard sequences and healthy adult brains. This might still work for other applications, but caveat emptor (even more than usual!). This would *not* be recommended for aligning brains that aren't from the same subject. Ver. 2.32 (PA Taylor, Sep 27, 2021) # ---------------------------------------------------------------------- OUTPUT: + NIFTI file: aligned T1w volume. + NIFTI files: each follower DSET* ends up in the DWI/DTI space and has a respective name PREFIX_DSET*.nii.gz. + QC snapshots of the T1w volume overlaying the DWI reference volume, and also the T1w edges overlaying the ref vol. + QC snapshots of each of the follower dsets overlaying the DWI ref volume. # ---------------------------------------------------------------------- RUNNING: fat_proc_map_to_dti \ -source SSS \ -base DDD \ -prefix PPP \ {-followers_NN DSET01 DSET02 DSET03 ...} \ {-followers_wsinc5 DSET1 DSET2 DSET3 ...} \ {-followers_surf SURF1 SURF2 SURF3 ...} \ {-followers_ndset NDSET1 NDSET2 NDSET3 ...} \ {-followers_spec SPEC1 SPEC2 SPEC3 ...} \ {-matrix MMM} \ {-workdir WWW} \ {-no_cmd_out} \ {-no_clean} where: -source SSS :T1w volume (required); 'source' volume from which we are mapping, such as an anatomical volume in whose space ROIs might have been defined. SSS gets mapped into the '-base BBB' volume's space. -base BBB :DWI reference volume (required; should be from same subject as SSS), such as the b=0 (or minimally DWed volume), for aligning to; subbrick selections are allowed, so that dwi_dwi.nii'[0]', for example, would be allowed. This is the base dset for the alignment, with the purpose to bring other volumes into the DWI/DTI space (see the '-followers* ...' options, below). **NOTE**: BBB and SSS should be from the same subject by this function, because only affine alignment with 3dAllineate is performed! -prefix PPP :output prefix for files and snapshots. Required. -followers_NN DSET01 DSET02 DSET03 ... :apply the same transformation to 'follower' data sets; one or more dsets can be listed, with each assumed to overlay on the T1W source set. The 'NN' interpolation of 3dAllineate is applied to these dsets, so that integer values remain integer valued; thus, these might be dsets with ROI maps already created. NB: subbrick selectors are not allowed on the DSETs here at present. Labeltables attached to these dsets do get propagated, as well. -followers_wsinc5 DSET1 DSET2 DSET3 ... similar to the above '-followers_NN ...', except in this case the final applied mapping is 'wsinc5', which is appropriate, for example, for floating point values. Again, a list of one or more volumes (sans subbrick selectors) can be provided here. No labeltable is propagated for these sets (I doubt they would have one, anyways). -followers_surf SURF1 SURF2 SURF3 ... :similar to the above '-followers_* ...', except in this case the mapping is applied to surface dsets, such as '*.gii'. Per usual, a list of one or more surfaces can be provided here. -followers_ndset NDSET1 NDSET2 NDSET3 ... :similar to the above '-followers_* ...', except in this case the mapping is applied to '*.niml.dset' files, such as '*.annot.niml.dset'. Per usual, a list of one or more surfaces can be provided here. Prob wouldn't make sense to use this without using '-followers_surf ...'. -followers_spec SPEC1 SPEC2 SPEC3 ... :similar to the above '-followers_* ...', except in this case the mapping is applied to '*.spec' files. Per usual, a list of one or more surfaces can be provided here. Wouldn't make sense to use this without using both '-followers_surf ...' and '-followers_ndset ...' to map the dsets referred to in the file! -matrix MMM :one can apply a pre-made matrix that has been made by 3dAllineate previously. With this option. If you want. -cost CCC :one can apply any cost function CCC that is accepted by 3dAllineate. The default is for matching dsets of opposite contrast, such as a T1w to a b=0 DWI, which is like a T2w contrast (def: lpc). -warp xxx :one can set the linear affine warp type through the same warp arguments accepted by 3dAllineate: shift_only, shift_rotate, shift_rotate_scale, affine_general, etc. (def: affine_general). -workdir WWW :specify a working directory, which can be removed; (default name = '__WORKING_map_to_dti') -no_cmd_out :don't save the command line call of this program and the location where it was run (otherwise, it is saved by default in the ODIR/). -no_clean :do not delete temporary working directory (default is to remove it to save disk space). # ---------------------------------------------------------------------- EXAMPLE fat_proc_map_to_dti \ -source brain.nii \ -base dwi_dwi.nii.gz'[0]' \ -prefix indt \ -followers_NN aparc*_REN_*.nii.gz \ -followers_surf std.141.*gii \ -followers_ndset std.141.*niml.dset \ -followers_spec std.141.*.spec # -----------------------------------------------------------------------