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--- tools:preprocessmprage [2025/08/04 14:27] – created will
+++ tools:preprocessmprage [2025/08/04 14:38] (current) – will
@@ Line 1: / Line 1: @@
 ====== preprocessMprage (Hallquist pipeline) ======
-''preprocessMprage'' is a prerequisite for [[:tools:preprocessfunctional|Preprocess Functional (Hallquist pipeline)]]. It is analogous to [[https://www.nipreps.org/smriprep/|smriprep]]: skullstrips and MNI-aligns the anatomical/structural T1w image.
+''preprocessMprage'' is a prerequisite for [[:tools:preprocessfunctional|Preprocess Functional (Hallquist pipeline)]]. Code is https://github.com/LabNeuroCogDevel/fmri_processing_scripts/ and on rhea in ''/opt/ni_tools/fmri_processing_scripts''.
+It is analogous to [[https://www.nipreps.org/smriprep/|smriprep]]: skullstrips and MNI-aligns the anatomical/structural T1w image.
 Important files include:
@@ Line 7: / Line 9: @@
   * ''mprage_brain.nii.gz'' -- skull stripped
   * ''mprage_warpcoef.nii.gz'' -- voxelwise nonlinear warp file for/using [[:tools:fsl]]'s ''fnirt''
+===== mp2rage =====
+The mp2rage from 7T projects ([[:grants:7t]] and [[:grants:SPA]]) have inhomogeneities/bias field that complicate skullstripping.
+See [[:grants:7t:mr:anat]]
+ Workarounds
+  * skullstrip the INV component instead of the combined UNIDEN or use [[:tools:freesurfer]]'s output. In either case, use ''-ss_method freesurfer=/path/toskullstrip'' or invert the mask and use ''-post_bet_skullmask''
+  * SPM correction via VS's [[projects:mtrsnr#analysis_pipelinestructural_image_processing|Correct UNI for B1+ transmit field biases]]
+  * try ''-strong_bias -unifize -ss_method ROBEX''
 ===== QA/QC =====
@@ Line 14: / Line 28: @@
 The most likely failure is during skullstripping.
-{{:tools:pasted:20250804-142647.png}}
+{{:tools:pasted:20250804-142647.png?200}}
 ==== Failure example ====
-{{:tools:pasted:20250804-142657.png}}
+{{:tools:pasted:20250804-142657.png?200}}
 Inspecting further with ''afni'', using ''$'' keypress to toggle the overlay/underlay slider
-{{:tools:pasted:20250804-142703.png}}
+{{:tools:pasted:20250804-142703.png?200}}
+===== Options =====
+<code>
+----------------------------------------------
+preprocessMprage is a shell script that computes the nonlinear warp of a
+  participant's structural scan to a standard stereotaxic template (e.g., MNI).
+It is intended to be run within an mprage directory containing raw data (or a
+  nifti of the raw data if you use the -n option).
+The basic pipeline is:
+) Convert dicom files to NIFTI
+) Optional bias field correction to reduce spatial variation in intensity
+       due to coil sensitivity. Particularly important for 32-channel T1 images.
+) Brain extract the structural image
+) Warp structural to standard stereotactic space using affine (linear)
+      transformation: flirt. (Used only for warp coefficients)
+) Warp structural image to stereotactic space using nonlinear transformation
+       with fnirt. Affine coefficients from the linear warping are used as
+       starting values (helps optimization). In the case of MNI, uses FSL's
+       config file with optimal parameters for fnirt. In the case of Talairach,
+       use a custom settings file adapted from FSL's MNI configuration.
+Command line options:
+  -b -bet_opts: bet options. Passes value to fsl bet (brain extraction).
+        Must be quoted (e.g., -b "-f 0.7"). Defaults to "-R -f 0.5 -v"
+  -bright_skull: apply a correction to reduce the intensity of bright voxels in the skull prior to FNIRT.
+        Skull voxels that are bright (esp. near top of brain) can lead to artifactual stretching in FNIRT.
+        This correction is recommended if the skull is noticeably brighter (2-3x) than brain voxels.
+  -check_dependencies: what tools are avaible on this system. Exit w/ status 0 if everything needed is found
+  -cleanup: cleanup intermediate files not needed for further processing.
+  -cleanup_only: run cleanup of intermediate files, then exit. (after checking files)
+  -custom_brainmask: a NIfTI image containing a custom brain mask to be used instead of running a skull strip internally.
+        Must be the same dimensions as the structural scan. Technically, this can even be a skull-stripped volume such that
+        non-zero values are used to mask the structural image.
+  -cut_zindex Z:  keep index Z to end. use Z1-Z2 to specify range. (e.g. '0-100' to keep up until 100 instead of 100 and up)
+        useful when brain is only part of image.
+  -d -delete_dicom: delete or archive DICOM files. Options are -d n ("no": leaves DICOM
+        untouched), -d y ("yes": deletes DICOM files), -d a ("archive":
+        compresses files into archive file: mprage_dicom.tar.gz. If not
+        passed, user will be prompted for action. Can also use "yes", "no", and "archive."
+  -deface: use pydeface to remove face and maybe also hands and arms near the face (esp. babies)
+  -deneck: remove from the neck down with local remove_neck.py (implemented for baby data)
+  -fnirt_mask: controls how dilated the --refmask is for fnirt. Changing this may help with undesirable stretching at edge. Options:
+  	vtight: no dilation of template brain mask
+	tight: 1x dilation (-dilF) of mask
+	normal: 2x dilation (-dilF -dilF) of mask (default)
+	loose: 3x dilation (-dilF -dilF -dilF) of mask
+  -grad_unwarp: a file containing gradient nonlinearity coefficients for a SIEMENS scanner (e.g., trio.coeff.grad).
+        Structural image will be corrected for gradient distortion prior to transformation to template.
+  -h -help: print command help
+  -log: Name for log file that documents each command that is run. Default: preprocessMprage.log
+  -n -nifti: skip DICOM conversion and start with specified NIFTI file.
+        Example: -n mprage.nii.gz (will complete bet, flirt, and
+        fnirt, but skip DICOM -> NIFTI conversion).
+  -no_bias: skip bias field correction.
+  -no_robustfov: skip robustfov neck cleanup
+  -o -output: output file name. The filename for the final warped mprage image.
+        Defaults to mprage_nonlinear_warp_<referenceName>.nii.gz
+  -p -dicom: file pattern for dicom MR files. Defaults to "MR*". Please enclose the pattern in quotes or it may not function properly
+  -post_bet_skullmask: provide a mask to remove extra skull even after skull stripping. likely created by hand using afni's draw plugin
+        See https://labneurocogdevel.github.io/tuts/afni_draw
+  -r -template_brain: reference brain. Currently supports "MNI_2mm", "MNI_FSL_2mm", "SPM_2mm", "Tal_2mm", 1YO_2mm, neo_2mm.
+        Default is "MNI_2mm".
+  -startover: ignore .preprocessmprage_complete. useful if changing/adding arguments like "-ss_method bet -b '-f .6 -R'"
+  -ss_method: skull-stripping method used to create final brain-extracted data. Default is fnirt-inv. Options:
+        fnirt-inv: uses the template brain mask warped onto the subject's brain to define brain mask
+        bet: uses the bet program (FSL) to skull strip (also respects -bet_opts).
+dSkullStrip: uses the 3dSkullStrip program (can pass additional parameters using -bet_opts).
+        noisy: use @NoisySkullStrip
+        ROBEX: uses the ROBEX program (which doesn't accept any parameters).
+        freesurfer=/path/to/subj/mri/brainmask.mgz
+  -strong_bias: used for images with very strong bias fields
+  -unifize:  run afni's 3dUnifize on input mprage
+  -use_old_mni: support legacy preprocessing
+  -w -warpres: resolution of warp basis (nonlinear neighborhood size) in mm. Default is 8 mm.
+  -weak_bias: used for images with little and/or smooth bias fields (cf. fsl_anat). This is the default.
+Example call: preprocessMprage -r MNI_2mm -b "-R -f 0.5 -g 0.2" -d a -o mprage_final.nii.gz -w 6
+----------------------------------------------
+</code>