Hello all,
I'm after some general help in getting sensible CBF values from some ASL data we've got (PCASL, collected on a 3T Philips Ingenia). I've been doing a few runs on BASIL, which appear to have completed without error. However the CBF images I get from this (the "perfusion_calib.nii.gz" file) are too high, with GM pixels being in the ballpark of 150-200.
Any general input would be really welcome in case I'm doing something obviously incorrectly. I'm going to try and attach text files which have the .json and scanner setup info for the main ASL sequence and M0 image to this post. One thing I was thinking could be an issue was pixel scaling from DICOM to nifti being done differently between the ASL and M0 data, but the json files for each indicate that the Philips "float" values are used rather than the display scaling ones ("UsePhilipsFloatNotDisplayScaling": 1), and if I understand this correctly that would mean this shouldn't be causing any problems.
I've run BASIL in a few different ways and consistently get this "high" results, but the following is a typical setup. I have made some educated guesses / assumptions on some of these points which I will highlight in brackets. Any info without accompanying brackets I'm taking to be more confidently correct as it's gained directly from a setup file etc.
Input Data
Input image = the raw PCASL set (control/tag pairs, with control first. This is an educated guess but gives me sensible looking subtraction images with "positive" pixel values if I treat the data with this assumption).
Number PLDs = 1
Number repeats = 30
Grouping order / pair info = as described
Labelling = cASL/pcASL
Bolus duration = constant at 1.8
PLDs = 1.8
Readout = 2D multi-slice
Time per slice = 28.1 (this is a guess I may well be wrong on. Couldn't see this info in parameter files, and assuming it's the same as "echo spacing", "calculated" it from the echo train length variable according to the formula given in this jismail thread with the water value at 440 - https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;162ab1a3.1308 )
Multi-band = unticked (generally unsure here)
Structure
Here I say data is from "Independent structural data", and provide a bias-field corrected "whole" T1 image and accompanying brain-extracted version of that image. I do not tick to transform to standard space. Each of these images have been treated with fslreorient2std.
Calibration
Calibration image = the raw M0
M0 type = Proton Density
Sequence TR = 10.00
Calibration Gain = 1.00 (this is a guess and I do not currently know if the gain was any different between the M0 and ASL data)
Calibration mode = Reference region
Type = CSF
Mask = unticked
Reference T1 = 4.30 (I think this was the default value)
Sequence TE = 12.00 (i.e. the TE from the M0 sequence?)
Reference T2 = 750.00 (I think this was the default value)
Blood T2 = 150.00 (I think this was the default value)
Reference Image for sensitivity correction = unticked (?)
Distortion Correction = not enabled
Analysis
Output Directory = wherever
Brain Mask = not provided
Analysis to conform to "white paper" = unticked (?)
Initial parameter values = all left as defaults
Analysis options = the following are ticked: Adaptive spatial regularisation; Fix label duration; Partial Volume Correction; Motion Correction (?)
Sorry for this being a fairly in-depth post, but really appreciate any help.
Thanks very much everyone,
Iain
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JSON info
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.738,
"Manufacturer": "Philips",
"ManufacturersModelName": "Ingenia",
"InstitutionName": "Sheffield_University",
"InstitutionalDepartmentName": "MRI",
"DeviceSerialNumber": "42223",
"StationName": "PHILIPS-EO688RT",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "NCGS_VISIT_1",
"SoftwareVersions": "5.4.1_5.4.1.0",
"MRAcquisitionType": "2D",
"SeriesDescription": "M0_V5.4",
"ProtocolName": "M0_V5.4",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"],
"SeriesNumber": 401,
"AcquisitionTime": "09:52:4.290000",
"AcquisitionNumber": 4,
"PhilipsRWVSlope": 1.49011,
"PhilipsRWVIntercept": 0,
"PhilipsRescaleSlope": 1.49011,
"PhilipsRescaleIntercept": 0,
"PhilipsScaleSlope": 0.00263718,
"UsePhilipsFloatNotDisplayScaling": 1,
"SliceThickness": 7,
"SpacingBetweenSlices": 8,
"SAR": 0.011624,
"EchoTime": 0.012002,
"RepetitionTime": 10,
"FlipAngle": 90,
"CoilString": "MULTI_COIL",
"PartialFourier": 0.4375,
"PercentPhaseFOV": 100,
"EchoTrainLength": 35,
"PhaseEncodingSteps": 80,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 80,
"PixelBandwidth": 2055,
"PhaseEncodingAxis": "j",
"ImageOrientationPatientDICOM": [
0.999135,
-0.0225385,
-0.0349477,
0.0171238,
0.988817,
-0.148149 ],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20181125 GCC4.8.2"
-------------------------------------
Scanner Setup Info
Nucleus = "H1";
SmartSelect = "yes";
Coil 1 (exclude) = "None";
Uniformity = "CLEAR";
FOV RL (mm) = 240;
AP (mm) = 240;
FH (mm) = 135;
ACQ voxel size RL (mm) = 3;
AP (mm) = 3;
Slice thickness (mm) = 7;
Recon voxel size RL (mm) = 3;
AP (mm) = 3;
Fold-over suppression = "no";
Reconstruction matrix = 80;
SENSE = "yes";
P reduction (AP) = 2.29999995;
k-t BLAST = "no";
Stacks = 1;
type = "parallel";
slices = 17;
slice gap = "user defined";
gap (mm) = 1;
slice orientation = "transverse";
fold-over direction = "AP";
fat shift direction = "P";
Stack Offc. AP (P=+mm) = 0;
RL (L=+mm) = 0;
FH (H=+mm) = 0;
Ang. AP (deg) = 0;
RL (deg) = -0;
FH (deg) = -0;
Free rotatable = "no";
Minimum number of packages = 1;
Slice scan order = "FH";
Large table movement = "no";
PlanAlign = "no";
REST slabs = 0;
Interactive positioning = "no";
Patient position = "head first";
Patient body position = "head first";
Patient orientation = "supine";
Patient body orientation = "supine";
Scan type = "Imaging";
Scan mode = "MS";
technique = "FFE";
Contrast enhancement = "no";
Acquisition mode = "cartesian";
Fast Imaging mode = "EPI";
shot mode = "single-shot";
Echoes = 1;
partial echo = "no";
shifted echo = "no";
TE = "shortest";
Flip angle (deg) = 90;
TR = "user defined";
(ms) = 10000;
Halfscan = "no";
Water-fat shift = "maximum";
RF Shims = "fixed";
Shim = "auto";
mDIXON = "no";
Fat suppression = "SPIR";
strength = "strong";
frequency offset = "default";
Water suppression = "no";
MTC = "no";
Research prepulse = "no";
Diffusion mode = "no";
T1 mapping = "no";
SAR mode = "high";
B1 mode = "default";
SAR allow first level = "yes";
PNS mode = "high";
Gradient mode = "maximum";
SofTone mode = "no";
Cardiac synchronization = "no";
Heart rate > 250 bpm = "no";
Respiratory compensation = "no";
Navigator respiratory comp = "no";
Flow compensation = "no";
Temporal slice spacing = "default";
fMRI echo stabilisation = "no";
NSA = 1;
Angio / Contrast enh. = "no";
Quantitative flow = "no";
Manual start = "no";
Dynamic study = "no";
Arterial Spin labeling = "no";
Preparation phases = "auto";
Interactive F0 = "no";
B0 field map = "no";
MIP/MPR = "no";
Images = "M", (3) "no";
Autoview image = "M";
Calculated images = (4) "no";
Reference tissue = "Grey matter";
Recon compression = "No";
Preset window contrast = "soft";
Reconstruction mode = "immediate";
Save raw data = "no";
Hardcopy protocol = "no";
Image filter = "system default";
Uniformity correction = "no";
Geometry correction = "default";
IF_info_seperator = 1634755923;
Total scan duration = "00:20.0";
Rel. SNR = 1;
Act. TR/TE (ms) = "10000 / 12";
ACQ matrix M x P = "80 x 80";
ACQ voxel MPS (mm) = "3.00 / 3.00 / 7.00";
REC voxel MPS (mm) = "3.00 / 3.00 / 7.00";
Scan percentage (%) = 100;
Packages = 1;
Min. slice gap (mm) = -0;
EPI factor = 35;
Act. WFS (pix) / BW (Hz) = "9.456 / 45.9";
BW in EPI freq. dir. (Hz) = "2056.7";
Min. WFS (pix) / Max. BW (Hz) = "7.328 / 59.3";
Min. TR/TE (ms) = "581 / 12";
Head SAR = "< 3 %";
Whole body SAR / level = "0.0 W/kg / normal";
SED = " 0.0 kJ/kg";
Coil Power = "3 %";
Max B1+rms = "0.41 uT";
PNS / level = "82 % / 1st level";
dB/dt = "124.8 T/s";
Sound Pressure Level (dB) = 13.0079298;
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JSON info
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.738,
"Manufacturer": "Philips",
"ManufacturersModelName": "Ingenia",
"InstitutionName": "Sheffield_University",
"InstitutionalDepartmentName": "MRI",
"DeviceSerialNumber": "42223",
"StationName": "PHILIPS-EO688RT",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "NCGS_VISIT_1",
"SoftwareVersions": "5.4.1_5.4.1.0",
"MRAcquisitionType": "2D",
"SeriesDescription": "SOURCE_-_pCASL_v5.4",
"ProtocolName": "SOURCE_-_pCASL_v5.4",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"],
"SeriesNumber": 302,
"AcquisitionTime": "09:47:7.070000",
"AcquisitionNumber": 3,
"PhilipsRWVSlope": 1.42882,
"PhilipsRWVIntercept": 0,
"PhilipsRescaleSlope": 1.42882,
"PhilipsRescaleIntercept": 0,
"PhilipsScaleSlope": 0.0148321,
"UsePhilipsFloatNotDisplayScaling": 1,
"SliceThickness": 7,
"SpacingBetweenSlices": 8,
"SAR": 0.281032,
"EchoTime": 0.014379,
"RepetitionTime": 4.55,
"FlipAngle": 90,
"CoilString": "MULTI_COIL",
"PartialFourier": 0.4375,
"PercentPhaseFOV": 100,
"EchoTrainLength": 35,
"PhaseEncodingSteps": 80,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 80,
"PixelBandwidth": 2055,
"PhaseEncodingAxis": "j",
"ImageOrientationPatientDICOM": [
0.999135,
-0.0225385,
-0.0349477,
0.0171238,
0.988817,
-0.148149 ],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20181125 GCC4.8.2"
------------------------------------
Scanner Setup Info
Nucleus = "H1";
SmartSelect = "yes";
Coil 1 (exclude) = "None";
Uniformity = "CLEAR";
FOV RL (mm) = 240;
AP (mm) = 240;
FH (mm) = 135;
ACQ voxel size RL (mm) = 3;
AP (mm) = 3;
Slice thickness (mm) = 7;
Recon voxel size RL (mm) = 3;
AP (mm) = 3;
Fold-over suppression = "no";
Reconstruction matrix = 80;
SENSE = "yes";
P reduction (AP) = 2.29999995;
k-t BLAST = "no";
Stacks = 1;
type = "parallel";
slices = 17;
slice gap = "user defined";
gap (mm) = 1;
slice orientation = "transverse";
fold-over direction = "AP";
fat shift direction = "P";
Stack Offc. AP (P=+mm) = 0;
RL (L=+mm) = 0;
FH (H=+mm) = 0;
Ang. AP (deg) = 0;
RL (deg) = -0;
FH (deg) = -0;
Free rotatable = "no";
Minimum number of packages = 1;
Slice scan order = "FH";
Large table movement = "no";
PlanAlign = "no";
REST slabs = 0;
Interactive positioning = "no";
Patient position = "head first";
Patient body position = "head first";
Patient orientation = "supine";
Patient body orientation = "supine";
Scan type = "Imaging";
Scan mode = "MS";
technique = "FFE";
Contrast enhancement = "no";
Acquisition mode = "cartesian";
Fast Imaging mode = "EPI";
shot mode = "single-shot";
Echoes = 1;
partial echo = "no";
shifted echo = "no";
TE = "shortest";
Flip angle (deg) = 90;
TR = "user defined";
(ms) = 4550;
Halfscan = "no";
Water-fat shift = "maximum";
RF Shims = "fixed";
Shim = "auto";
mDIXON = "no";
Fat suppression = "SPIR";
strength = "strong";
frequency offset = "default";
Water suppression = "no";
MTC = "no";
Research prepulse = "no";
Diffusion mode = "no";
T1 mapping = "no";
SAR mode = "high";
B1 mode = "default";
SAR allow first level = "yes";
PNS mode = "high";
Gradient mode = "maximum";
SofTone mode = "no";
Cardiac synchronization = "no";
Heart rate > 250 bpm = "no";
Respiratory compensation = "no";
Navigator respiratory comp = "no";
Flow compensation = "no";
Temporal slice spacing = "default";
fMRI echo stabilisation = "no";
NSA = 1;
Angio / Contrast enh. = "no";
Quantitative flow = "no";
Manual start = "no";
Dynamic study = "individual";
dyn scans = 30;
dyn scan times = "shortest";
fov time mode = "default";
dummy scans = 0;
immediate subtraction = "no";
fast next scan = "no";
synch. ext. device = "no";
dyn stabilization = "no";
prospect. motion corr. = "no";
Keyhole = "no";
Arterial Spin labeling = "pCASL";
label type = "parallel slab";
label distance (mm) = 96.8600006;
label location = "F";
label duration = 1800;
post label delay (ms) = 1800;
vascular crushing = "no";
back. supp. = "auto 2 pulse";
phases = 1;
Preparation phases = "auto";
Interactive F0 = "no";
B0 field map = "no";
MIP/MPR = "no";
ASL source images = "All";
Images = "M", (3) "no";
Autoview image = "M";
Calculated images = (4) "no";
Reference tissue = "Grey matter";
Recon compression = "No";
Preset window contrast = "soft";
Reconstruction mode = "immediate";
Save raw data = "no";
Hardcopy protocol = "no";
Image filter = "system default";
Uniformity correction = "no";
Geometry correction = "default";
IF_info_seperator = 1634755923;
Total scan duration = "04:42.1";
Rel. SNR = 1;
Act. TR/TE (ms) = "4550 / 13";
Dyn. scan time = "00:09.1";
Time to k0 = "00:04.6";
ACQ matrix M x P = "80 x 80";
ACQ voxel MPS (mm) = "3.00 / 3.00 / 7.00";
REC voxel MPS (mm) = "3.00 / 3.00 / 7.00";
Scan percentage (%) = 100;
Packages = 1;
Min. slice gap (mm) = -0;
EPI factor = 35;
Act. WFS (pix) / BW (Hz) = "8.677 / 50.1";
BW in EPI freq. dir. (Hz) = "2291.3";
Min. WFS (pix) / Max. BW (Hz) = "7.935 / 54.7";
Min. TR/TE (ms) = "4254 / 13";
Head SAR = "< 76 %";
Whole body SAR / level = "< 0.3 W/kg / normal";
SED = "< 0.1 kJ/kg";
Coil Power = "76 %";
Max B1+rms = "2.05 uT";
PNS / level = "75 % / normal";
dB/dt = "112.3 T/s";
Sound Pressure Level (dB) = 23.1009483;
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