biac:analysis:resting_pipeline
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
biac:analysis:resting_pipeline [2012/05/31 16:16] – [Step 6] admin | biac:analysis:resting_pipeline [2012/07/09 18:59] – [Step 3] admin | ||
---|---|---|---|
Line 8: | Line 8: | ||
Usage: | Usage: | ||
resting_pipeline.py --func / | resting_pipeline.py --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: | ||
Line 18: | Line 17: | ||
4 - normalize data | 4 - normalize data | ||
5 - regress out WM/CSF | 5 - regress out WM/CSF | ||
- | 6 - bandpass | + | 6 - lowpass |
- | 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/ | ||
Line 29: | Line 34: | ||
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=/ | ||
-s 0,1,2,3, --steps=0, | -s 0,1,2,3, --steps=0, | ||
comma seperated string of steps. ' | comma seperated string of steps. ' | ||
Line 48: | Line 54: | ||
standard brain | standard brain | ||
--refcsf=FILE | --refcsf=FILE | ||
+ | standard brain | ||
+ | --refbrainmask=FILE | ||
standard brain | standard brain | ||
--refacpoint=45, | --refacpoint=45, | ||
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 | ||
--lpfreq=0.08 | --lpfreq=0.08 | ||
is .08hz | is .08hz | ||
Line 61: | Line 70: | ||
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 | ||
+ | parcellation output (default is to use | ||
+ | OUTPATH/ | ||
+ | to the correlation. | ||
+ | --dvarsthreshold=THRESH | ||
+ | If specified, this reprsents a DVARS threshold either | ||
+ | in BOLD units, or if ending in a ' | ||
+ | percentage of mean global signal intensity (over the | ||
+ | brain mask). | ||
+ | greater than this threshold will be excluded | ||
+ | (" | ||
+ | calculation is performed on the results of the last | ||
+ | pre-processing step, and is calculated as described by | ||
+ | Power, J.D., et al., " | ||
+ | correlations in functional connectivity MRI networks | ||
+ | arise from subject motion", | ||
+ | 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. | ||
+ | --motionthreshold=THRESH | ||
+ | If specified, any volume whose motion parameters | ||
+ | indicate a movement greater than this threshold (in | ||
+ | mm) will be excluded (" | ||
+ | correlation step. Volume-to-volume movement is | ||
+ | calculated per pair of neighboring volumes from the | ||
+ | three rotational and three translational parameters | ||
+ | generated by mcflirt. | ||
+ | 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. | ||
+ | only excluded during the final correlation, | ||
+ | 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. | ||
+ | --motionpar=FILE.par | ||
+ | specifies the .par file from which the motion | ||
+ | parameters are extracted. | ||
+ | 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. | ||
+ | met, then the script exits with an error. | ||
+ | to have no minimum. | ||
--cleanup | --cleanup | ||
</ | </ | ||
Line 89: | Line 153: | ||
* the functional run is meaned across time with fslmaths, then bet is applied. | * the functional run is meaned across time with fslmaths, then bet is applied. | ||
* 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 | ||
Line 110: | Line 174: | ||
==== 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 (" | ||
* 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