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biac:analysis:resting_pipeline [2012/05/31 16:16] – [Step 6] adminbiac:analysis:resting_pipeline [2012/07/09 19:02] – [Step 4] admin
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 Usage:  Usage: 
 resting_pipeline.py --func /path/to/run4.bxh --steps all --outpath /here/ -p func resting_pipeline.py --func /path/to/run4.bxh --steps all --outpath /here/ -p func
- 
  
 Program to run through Nan-kuei Chen's resting state analysis pipeline: Program to run through Nan-kuei Chen's resting state analysis pipeline:
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     4 - normalize data     4 - normalize data
     5 - regress out WM/CSF     5 - regress out WM/CSF
-    6 - bandpass filter +    6 - lowpass filter 
-    7 - produce correlation matrix from label file+    7 - do parcellation and produce correlation matrix from label file 
 +      * or split it up: 
 +         7a - do parcellation from label file 
 +         7b - produce correlation matrix [--func option is ignored if step 7b 
 +              is run by itself unless --dvarsthreshold is specified, and 
 +              --corrts overrides default location for input parcellation 
 +              results (outputpath/corrlabel_ts.txt)]
  
  
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                         run                         run
   -p func, --prefix=func   -p func, --prefix=func
-                        prefix for all resulting images, defaults to name of+                        prefix for all resulting images, defaults to name of                        
                         input                         input
 +  --t1=/path/to/BXH     bxh ( or nifti ) file for the anatomical T1
   -s 0,1,2,3, --steps=0,1,2,3   -s 0,1,2,3, --steps=0,1,2,3
                         comma seperated string of steps. 'all' will run                         comma seperated string of steps. 'all' will run
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                         standard brain                         standard brain
   --refcsf=FILE         pointer to CSF mask of reference image if not using   --refcsf=FILE         pointer to CSF mask of reference image if not using
 +                        standard brain
 +  --refbrainmask=FILE   pointer to brain mask of reference image if not using
                         standard brain                         standard brain
   --refacpoint=45,63,36   --refacpoint=45,63,36
                         AC point of reference image if not using standard MNI                         AC point of reference image if not using standard MNI
-                        brain                     +                        brain 
-  --betfval=0.5         f value to use while skull stripping. default is 0.5+  --betfval=0.4         f value to use while skull stripping. default is 0.4 
 +  --anatbetfval=0.5     f value to use while skill stripping ANAT. default is 0.5
   --lpfreq=0.08         frequency cutoff for lowpass filtering in HZ.  default   --lpfreq=0.08         frequency cutoff for lowpass filtering in HZ.  default
                         is .08hz                         is .08hz
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                         for the correlation search. default is the 116 region                         for the correlation search. default is the 116 region
                         AAL label txt file                         AAL label txt file
 +  --corrts=FILE         If using step 7b by itself, this is the path to 
 +                        parcellation output (default is to use 
 +                        OUTPATH/corrlabel_ts.txt), which will be used as input 
 +                        to the correlation. 
 +  --dvarsthreshold=THRESH 
 +                        If specified, this reprsents a DVARS threshold either 
 +                        in BOLD units, or if ending in a '%' character, as a 
 +                        percentage of mean global signal intensity (over the 
 +                        brain mask).  Any volume contributing to a DVARS value 
 +                        greater than this threshold will be excluded 
 +                        ("scrubbed") from the (final) correlation step.  DVARS 
 +                        calculation is performed on the results of the last 
 +                        pre-processing step, and is calculated as described by 
 +                        Power, J.D., et al., "Spurious but systematic 
 +                        correlations in functional connectivity MRI networks 
 +                        arise from subject motion", NeuroImage(2011).  Note: 
 +                        data is only excluded during the final correlation, 
 +                        and so will never affect any operations that require 
 +                        the full signal, like regression, etc. 
 +  --dvarsnumneighbors=NUMNEIGHBORS 
 +                        If --dvarsthreshold is specified, then 
 +                        --dvarsnumnumneighbors specifies how many neighboring 
 +                        volumes, before and after the initially excluded 
 +                        volumes, should also be excluded.  Default is 0. 
 +  --motionthreshold=THRESH 
 +                        If specified, any volume whose motion parameters 
 +                        indicate a movement greater than this threshold (in 
 +                        mm) will be excluded ("scrubbed") from the (final) 
 +                        correlation step.  Volume-to-volume movement is 
 +                        calculated per pair of neighboring volumes from the 
 +                        three rotational and three translational parameters 
 +                        generated by mcflirt.  Motion for a pair of 
 +                        neighboring volumes is calculated as the maximum 
 +                        displacement (due to the combined rotation and 
 +                        translation) of any voxel on the 50mm-radius sphere 
 +                        surrounding the center of rotation.  Note: data is 
 +                        only excluded during the final correlation, and so 
 +                        will never affect any operations that require the full 
 +                        signal, like regression, etc. 
 +  --motionnumneighbors=NUMNEIGHBORS 
 +                        If --motionthreshold is specified, then 
 +                        --motionnumnumneighbors specifies how many neighboring 
 +                        volumes, before and after the initially excluded 
 +                        volumes, should also be excluded.  Default is 1. 
 +  --motionpar=FILE.par  If --motionthreshold is specified, then --motionpar 
 +                        specifies the .par file from which the motion 
 +                        parameters are extracted.  If you allow this script to 
 +                        perform motion correction, then this option is 
 +                        ignored. 
 +  --scrubkeepminvols=NUMVOLS 
 +                        If --motionthreshold or --dvarsthreshold are 
 +                        specified, then --scrubminvols specifies the minimum 
 +                        number of volumes that should pass the threshold 
 +                        before doing any correlation.  If the minimum is not 
 +                        met, then the script exits with an error.  Default is 
 +                        to have no minimum.
   --cleanup             delete files from intermediate steps?   --cleanup             delete files from intermediate steps?
 </code> </code>
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   * the functional run is meaned across time with fslmaths, then bet is applied.  the resulting mask is then applied to the entire run of data   * the functional run is meaned across time with fslmaths, then bet is applied.  the resulting mask is then applied to the entire run of data
   * if you find that bet is doing a poor job finding the edges you can adjust the intensity threshold with **--betfval**   * if you find that bet is doing a poor job finding the edges you can adjust the intensity threshold with **--betfval**
-    * this is equivalent of **-f** when actually running bet.  the default is 0.5, but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask ) +    * this is equivalent of **-f** when actually running bet.  the default is 0.4 (same as feat), but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask ) 
 +  * if provided T1 anatomical is skull stripped. **--anatbetfval** is used to control intensity threshold, the default is 0.5 (same as feat)
 ==== Step 4 ==== ==== Step 4 ====
   * normalize the data using flirt   * normalize the data using flirt
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   * if your subject has already been normalized during standard pre-processing of other runs, please provide the flirt matrix from pre-stats with **--flirtmat** ( most likely example_func2standard.mat)   * if your subject has already been normalized during standard pre-processing of other runs, please provide the flirt matrix from pre-stats with **--flirtmat** ( most likely example_func2standard.mat)
     * this will apply the previously determined flirt matrix to your functional data instead of trying to calculate a new matrix based on the functionals.  the matrix from pre-stats was likely calculated using a high-resolution anatomical, also this will assure that your resting state runs are in the same space as the other runs from your subject.     * this will apply the previously determined flirt matrix to your functional data instead of trying to calculate a new matrix based on the functionals.  the matrix from pre-stats was likely calculated using a high-resolution anatomical, also this will assure that your resting state runs are in the same space as the other runs from your subject.
 +  * if you've provided at T1 anatomical image then this sequence is followed:
 +    * func-2-t1
 +    * t1-2-standard
 +    * flirt matrices are concatenated to create func-2-standard
 +  * if no T1 is provided, then the functional is used for the flirt normalization
  
 ==== Step 5 ====  ==== Step 5 ==== 
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 ==== Step 7 ====  ==== Step 7 ==== 
   * if defaults are used, then the aal_MNI_V4 label file is used to extract the average timeseries for each of the 116 regions   * if defaults are used, then the aal_MNI_V4 label file is used to extract the average timeseries for each of the 116 regions
 +  * if --dvarsthreshold or --motionthreshold are specified, then the ROI-averaged timeseries are further filtered ("scrubbed") by removing timepoints that exceed the given thresholds
   * cross correlation coefficients are found for the entire matrix of 116x116 regions   * cross correlation coefficients are found for the entire matrix of 116x116 regions
   * this step produces 4 files:   * this step produces 4 files:
biac/analysis/resting_pipeline.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1