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| cal_img | Set Max/Min for nifti object by range of data |
| checkimg | Check if filename is character or nifti object |
| checkout | Determine of Q and S forms are consistent |
| check_file | Wrapper for getForms with filename |
| check_nifti | Check if nifti image or read in |
| cog | Image Center of Gravity |
| datatype | Change Data type for img |
| drop_img_dim | Drop Image Dimension |
| fast | FSL FAST |
| fast.help | FAST help |
| flirt | Register using FLIRT |
| flirt.help | FLIRT help |
| flirt_apply | Apply Warp from FLIRT |
| flirt_apply.help | FLIRT help |
| fnirt | Register using FNIRT |
| fnirt.help | FNIRT help |
| fnirt_with_affine | Register using FNIRT, but doing Affine Registration as well |
| fnirt_with_affine_apply | <brief desc> |
| fslbet | Use FSL's Brain Extraction Tool (BET) |
| fslbet.help | Help for FSL BET |
| fslbin | Binarize Image using FSL |
| fslbin.help | FSL Maths Help |
| fslcmd | FSL Command Wrapper |
| fslcog | Image Center of Gravity (FSL) |
| fsldir | Get FSL's Directory |
| fslerode | Erode image using FSL |
| fslerode.help | FSL Maths Help |
| fslfill | Fill image holes |
| fslfill.help | FSL Maths Help |
| fslhd | Get NIfTI header using FSL |
| fslhd.help | FSLhd help |
| fslhd.parse | Parse FSL Header |
| fslhelp | Wrapper for getting fsl help |
| fslmask | Mask image using FSL |
| fslmask.help | FSL Maths Help |
| fslmaths | FSL Maths |
| fslmaths.help | FSL Maths Help |
| fslmerge | Merge images using FSL |
| fslmerge.help | FSLMerge help |
| fslorient | FSL Orient |
| fslorient.help | fslorient help |
| fslrange | Get range of an image |
| fslrange.help | FSL Stats Help |
| fslreorient2std | FSL Orient to MNI |
| fslreorient2std.help | fslreorient2std help |
| fslsmooth | Gaussian smooth image using FSL |
| fslsmooth.help | FSL Maths Help |
| fslstats | FSL Stats |
| fslstats.help | FSL Stats Help |
| fslsub2 | Subsample image by factor of 2 |
| fslsub2.help | FSL Maths Help |
| fslswapdim | FSL Swap Dimensions |
| fslswapdim.help | fslswapdim help |
| fslthresh | Threshold an image |
| fslthresh.help | FSL Maths Help |
| fslval | Get value from FSL header |
| fslval.help | fslval help |
| fslview | Open image in FSLView |
| fslview.help | FSLView help |
| fsl_anat | FSL FAST |
| fsl_anat.help | fsl_anat help |
| fsl_applywarp | Apply Warp from FNIRT |
| fsl_applywarp.help | FSL applywarp help |
| fsl_biascorrect | FSL Bias Correct |
| get.fsl | Create command declaring FSLDIR |
| get.fsloutput | Determine FSL output type |
| get.imgext | Determine extension of image based on FSLOUTPUTTYPE |
| getForms | Get Q and S Forms of orientation matrix |
| have.fsl | Logical check if FSL is accessible |
| mask_img | Mask nifti Image |
| melodic | Run MELODIC ICA |
| melodic.help | MELODIC help |
| newnii | Resets image parameters for a copied nifti object |
| niftiarr | Make new nifti from array |
| nii.stub | Grab nii file stubname |
| onefile | Creates onefile specification |
| ortho2 | Orthographic Display, added options |
| rescale_img | Image Rescaler |
| robust_window | Window image based on quantiles of Image |
| susan | FSL SUSAN noise reduction |
| susan.help | FSL SUSAN Help |
| tempimg | Create temporary nii.gz file for FSL |
| voxdim | Gets Voxel Dimensions |
| window_img | nifti image windower |
| zero_trans | Change intercept to 0 and slope to 1 |
| zscore_img | Get Z-score over a margin of an img |