Please read the help of ExploreASL_Import for more information
Import Parameters
Input parameters of ExploreASL can be specified in the DataPar.json file of the corresponding study. Required and optional parameters are displayed in the table below and in the ExploreASL DataParTemplate.json.
Environment Parameters
FSL
Parameter
x.bAutomaticallyDetectFSL
Description
Boolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized.
Example
n/a
Required
optional
Default
disabled
Make NIfTI 4D DICOM
Parameter
x.MakeNIfTI4DICOM
Description
Boolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file, e.g. for implementation in PACS or other DICOM archives.
Example
n/a
Required
n/a
Default
n/a
Study Parameters
Name
Parameter
x.name
Description
String for the name of the study.
Example
AD-study
Required
optional
Default
n/a
Root directory
Parameter
x.D.ROOT
Description
Path to analysis root folder where data is stored.
Example
/home/hjmutsaerts/TestDataSet
Required
optional
Default
pwd
Regular Expression
Parameter
x.subject_regexp
Description
String with regular expression for ExploreASL to find subjects by foldername.
Example
^\d{3}$ for three digits
Required
required
Default
n/a
Exclusion
Parameter
x.exclusion
Description
Cell with list of subjects to exclude.
Example
{'005' '018'}
Required
optional
Default
empty
Sessions
Parameter
x.SESSIONS
Description
Use this to define sessions.
Example
{'ASL_1' 'ASL_2'}
Required
optional
Default
{'ASL_1'}
Session Options
Parameter
x.session.options
Description
This is how the sessions will be called. For FEAST, this should be {'non-crushed' 'crushed'}.
Example
{'baseline' 'drug'}
Required
optional
Default
n/a
Inclusion List
Parameter
x.ForceInclusionList
Description
Use this field if you want to use a selection of subjects rather than taking all available subjects from directories.
Example
load(fullfile(x.D.ROOT,'LongitudinalList.mat'))
Required
optional
Default
use all subjects
M0 Parameters and Options
Conventional Processing
Parameter
x.M0_conventionalProcessing
Description
Boolean, use the conventional M0 processing (per consensus paper). 1 = standard processing, 0 = new image processing (improved masking & smoothing).
Example
n/a
Required
optional
Default
0
M0
Parameter
x.M0
Description
Choose which M0 option to use. Options: separate_scan = for a separate M0 NIfTI (needs to be in the same folder called M0.nii), 3.7394*10^6 = single M0 value to use, UseControlAsM0 = will copy the mean control image as M0.nii and process as if it was a separately acquired M0 image (taking TR etc from the ASL4D.nii). Make sure that no background suppression was used, otherwise this option is invalid.
Example
n/a
Required
required
Default
n/a
GM Scale Factor
Parameter
x.M0_GMScaleFactor
Description
Add additional scale factor to multiply the M0 image by. This can be useful when you have background suppression but no control/M0 image without background suppression. If you then know the M0 scalefactor for the GM, you can use the control image as M0 and use this parameter to scale back what was suppressed by background suppression. Note that there is no option for separate tissue scaling (e.g. WM & GM), because ExploreASL pragmatically smooths the M0 a lot, assuming that head motion and registration between M0 & ASL4D will differ between patients and controls.
Example
n/a
Required
optional
Default
1
M0 Position in ASL Scan
Parameter
x.M0PositionInASL4D
Description
Indicates the position of M0 in TimeSeries, if it is integrated by the vendor in the DICOM export. Will move this from ASL4D.nii to M0.nii.
Example
Philips 3D GRASE = [1 2] (first control-label pair), Siemens 3D GRASE = 1 (first image), GE 3D spiral = 2 (where first image is PWI & last = M0)
Required
optional
Default
no M0 in timeseries
Sequence Parameters
Background Suppression Pulses
Parameter
x.Q.BackGrSupprPulses
Description
Used to estimate decrease of labeling efficiency. Options: 0 = (no background suppression), 2 = labeling efficiency factor 0.83 (e.g. Philips 2D EPI & Siemens 3D GRASE), 4 = labeling efficiency factor 0.81 (e.g. Philips 3D GRASE), 5 = labeling efficiency factor 0.75 (e.g. GE 3D spiral).
Example
n/a
Required
required
Default
n/a
Readout Dimension
Parameter
x.readout_dim
Description
String specifying the readout type. Options: 2D for slice-wise readout, 3D for volumetric readout.
Example
n/a
Required
required
Default
n/a
Vendor
Parameter
x.Vendor
Description
String containing the vendor used. This parameter is used to apply the vendor-specific scale factors. Options: GE_product, GE_WIP, Philips, Siemens.
Example
n/a
Required
required
Default
n/a
Sequence
Parameter
x.Sequence
Description
String containing the sequence used. Options: 3D_spiral, 3D_GRASE, 2D_EPI.
Example
n/a
Required
required
Default
n/a
Labeling Type
Parameter
x.Q.LabelingType
Description
String containing the labeling strategy used. Options: 'PASL' (pulsed Q2-TIPS), 'CASL' (CASL/PCASL), Note: pulsed without Q2TIPS cannot be reliably quantified because the bolus width cannot be identified CASL & PCASL are both continuous ASL methods, identical quantification.
Example
n/a
Required
required
Default
n/a
Initial Post Labeling Delay
Parameter
x.Q.Initial_PLD
Description
Value of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice.
Example
1800
Required
required
Default
n/a
Labeling Duration
Parameter
x.Q.LabelingDuration
Description
Value of labeling duration (ms).
Example
1800
Required
required
Default
n/a
Slice Readout Time
Parameter
x.Q.SliceReadoutTime
Description
Value (ms) of time added to the PLD after reading out each slice. Other option = shortestTR; shortest TR enabled gives each sequence the minimal TR. This enables calculating slice delay per subject.
Example
31
Required
required for 2D ASL sequences
Default
n/a
Quantification Parameters
Lambda
Parameter
x.Q.Lambda
Description
Brain/blood water coefficient (mL 1H/ mL blood).
Example
0.32 (for GSP phantom)
Required
optional
Default
0.9
T2* of arterial blood
Parameter
x.Q.T2art
Description
T2* of arterial blood at 3T, only used when no M0 image (ms).
Number of modeled compartments for quantification. Options: 1 = a single-compartment quantification model (default by concensus paper), 2 = a dual-compartment quantification model.
Example
n/a
Required
optional
Default
1
Apply Quantification
Parameter
x.ApplyQuantification
Description
A vector of 1x5 logical values specifying which types on quantified images should be calculated and saved. Fields: 1) Apply ScaleSlopes ASL4D (xASL_wrp_Quantify, future at dcm2niiX stage), 2) Apply ScaleSlopes M0 (xASL_quant_M0, future at dcm2niiX stage), 3) Convert PWI a.u. to label (xASL_wrp_Quantify, future at xASL_wrp_Reslice?), 4) Quantify M0 a.u. (xASL_quant_M0, corrects for incomplete T1 relaxation), 5) Perform division by M0.
Example
ASL4D is an already quantified CBF image, disable all quantification '[0 0 0 0 0]'. To compare label but not CBF (e.g. label in vessels or sinus vs tissue): [1 1 1 1 0]. Note that the output always goes to CBF.nii.
Required
optional
Default
[1 1 1 1 1] = all enabled
Processing Parameters
Spike Removal Threshold
Parameter
x.SpikeRemovalThreshold
Description
Minimal t-stat improval needed to remove motion spikes.
Example
1 = effectively disabling spike removal
Required
optional
Default
0.01
Motion Correction
Parameter
x.motion_correction
Description
Boolean to perform motion correction in case of timeseries. Options: 1 = on, 0 = off.
Example
n/a
Required
optional
Default
1
Quality
Parameter
x.Quality
Description
Boolean specifying on which quality the pipeline should be run. Options: 1 = normal quality, 0 = lower quality, fewer iterations and lower resolution of processing for a fast try-out.
Example
n/a
Required
optional
Default
1
Delete Temporary Files
Parameter
x.DELETETEMP
Description
Boolean for removing the temporary files. Options: 0 = keeping all files, 1 = delete temporary files created by the pipeline.
Example
n/a
Required
optional
Default
1
Skip if no FLAIR
Parameter
x.SkipIfNoFlair
Description
Boolean to skip processing of subjects that do not have a FLAIR image. These parameters can be useful when some data is still complete, but one would like to start image processing already. Options: 1 = skip processing of a subject that does not have a FLAIR image, 0 = do not skip anything.
Example
n/a
Required
optional
Default
0
Skip if no ASL
Parameter
x.SkipIfNoASL
Description
Boolean to skip processing of subjects that do not have a ASL image. Options: 1 = skip processing of a subject that does not have a ASL image, 0 = do not skip anything.
Example
n/a
Required
optional
Default
0
Skip if no M0
Parameter
x.SkipIfNoM0
Description
Boolean to skip processing of subjects that do not have a M0 image. Options: 1 = skip processing of a subject that does not have a M0 image, 0 = do not skip anything.
Example
n/a
Required
optional
Default
0
Segment SPM12
Parameter
x.SegmentSPM12
Description
Boolean to specify if SPM12 segmentation is run instead of CAT12 (OPTIONAL, DEFAULT = 0). Options: 1 = run SPM12, 0 = run CAT12.
Example
n/a
Required
optional
Default
0
Hammers CAT 12
Parameter
x.bHammersCAT12
Description
Boolean specifying if CAT12 should provide Hammers volumetric ROI results.
Example
n/a
Required
optional
Default
0
Fix Resolution
Parameter
x.bFixResolution
Description
Resample to a resolution that CAT12 accepts.
Example
n/a
Required
optional
Default
false
Registration Contrast
Parameter
x.bRegistrationContrast
Description
specifies the image contrast used for registration: 0 = Control->T1w, 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667), 2 = automatic (mix of both), 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV.
Example
n/a
Required
optional
Default
2
Affine Registration
Parameter
x.bAffineRegistration
Description
Specifies if the ASL-T1w rigid-body registration is followed up by an affine registration: 0 = affine registration disabled, 1 = affine registration enabled, 2 = affine registration automatically chosen based on spatial CoV of PWI.
Example
n/a
Required
optional
Default
2
DCT Registration
Parameter
x.bDCTRegistration
Description
Specifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account the x.bAffineRegistration must be >0 for DCT to run: 0 = DCT registration disabled, 1 = DCT registration enabled if affine enabled and conditions for affine passed, 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right.
Example
n/a
Required
optional
Default
0
Register M0 to ASL
Parameter
x.bRegisterM02ASL
Description
Boolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). It can be useful to disable M0 registration if the ASL registration is done based on the M0, and little motion is expected between the M0 and ASL acquisition. If no separate M0 image is available, this parameter will have no effect. This option is disabled automatically for 3D spiral: 0 = M0 registration disabled, 1 = M0 registration enabled (DEFAULT).
Example
n/a
Required
optional
Default
0
Use MNI as dummy Structural
Parameter
x.bUseMNIasDummyStructural
Description
When structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. With this option, the ASL module copies the structural templates to fool the pipeline, resulting in ASL registration to these templates. While the rigid-body parameters might still be found somewhat correctly, with this option it is advised to enable affine registration for ASL as well, since ASL and these dummy structural images will differ geometrically. When disabled, an error will be issued instead when the structural images are missing. 1 = enabled, 0 = disabled.
Example
n/a
Required
optional
Default
0
Masking
Parameter
x.S.bMasking
Description
Vector specifying if we should mask a ROI with a subject-specific mask (1 = yes, 0 = no), [1 0 0 0] = susceptibility mask (either population-or subject-wise), [0 1 0 0] = vascular mask (only subject-wise), [0 0 1 0] = subject-specific tissue-masking (e.g. pGM>0.5), [0 0 0 1] = WholeBrain masking (used as memory compression), [0 0 0 0] = no masking at all, [1 1 1 1] = apply all masks. Can also be used as boolean, where: 1 = [1 1 1 1], 0 = [0 0 0 0]. Can be useful for e.g. loading lesion masks outside the GM.