Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
tools:preprocessmprage [2025/08/04 14:36] – [preprocessMprage (Hallquist pipeline)] willtools:preprocessmprage [2025/08/04 14:38] (current) – will
Line 14: Line 14:
 ===== mp2rage ===== ===== mp2rage =====
  
-The mp2rage from 7T projects ([[:grants:7t]] and [[:grants:SPA]]) have inhomogeneities/bias field that complicate skullstripping. Workarounds+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''   * 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+  * 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''   * try ''-strong_bias -unifize -ss_method ROBEX''
 +
 +
 +===== QA/QC =====
 +
 +The pipeline provides ''qa_images'' for quality checking. And can be further inspected using a full nifti viewer like ''afni''.
 +
 +The most likely failure is during skullstripping.
 +
 +{{:tools:pasted:20250804-142647.png?200}}
 +
 +==== Failure example ====
 +
 +{{:tools:pasted:20250804-142657.png?200}}
 +
 +Inspecting further with ''afni'', using ''$'' keypress to toggle the overlay/underlay slider
 +{{:tools:pasted:20250804-142703.png?200}}
  
 ===== Options ===== ===== Options =====
Line 101: Line 119:
  
 </code> </code>
-===== QA/QC ===== 
- 
-The pipeline provides ''qa_images'' for quality checking. And can be further inspected using a full nifti viewer like ''afni''. 
- 
-The most likely failure is during skullstripping. 
- 
-{{:tools:pasted:20250804-142647.png}} 
- 
-==== Failure example ==== 
- 
-{{:tools:pasted:20250804-142657.png}} 
- 
-Inspecting further with ''afni'', using ''$'' keypress to toggle the overlay/underlay slider 
-{{:tools:pasted:20250804-142703.png}}