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		LISTSERV Archives
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		FSL January 2020
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Subject:
Re: CBF values too high using BASIL
From:
Iain Croall <[log in to unmask]>
Reply-To:
FSL - FMRIB's Software Library <[log in to unmask]>
Date:
Mon, 13 Jan 2020 13:13:21 +0000
Content-Type:
multipart/mixed
Parts/Attachments:
text/plain (22 lines) , BASIL_run_output.txt (1 lines)
Hi Flora,
Thanks very much for your email. I'll try and answer your questions as best as I can.

1. Yes I am using the GUI at the moment; I plan to switch to command line to process the rest of the participants once I've nailed the right set-up via the GUI! (I have done an initial check on all the different participant data and it is consistent in showing these large CBF values). I'll include an output in an accompanying text file.

2. I used N4 for the bias field correction; there was not necessarily evidence of a strong field that needed correcting, I tend to just do this as a matter of general pre-processing for T1 data. I have not touched the ASL or M0 images with this correction or anything else (the ones that go into BASIL are complete "raw" nifti's straight out of DICOM conversion with dcm2niix).

3. As I mentioned I'm inspecting the "perfusion_calib.nii.gz" file after each run, which I understand to be the major output from BASIL. To begin with, I would use a GM mask to calculate the average within all grey matter with fslstats (the mean coming out around 150). As I've turned to running multiple BASIL runs adjusting things here and there trying to better understand how it all fits together, I tend now to just visually look at the perfusion_calib image and select between various cortical GM pixels to check if anything seems different from before (these will consistently show values between 150-200). To my eye there may be more extremely "high" values which crop up superiorally in the brain, although it's not these pixels I look at to assess if the model has worked or not. So far I've always selected the "Partial Volume Correction" option in the BASIL analysis tab. 

As a general word the perfusion outputs do look overall reasonable as CBF / subtraction images.

The attached output is from a BASIL run where I did my usual visual inspection which showed these high values, and also ran "fslstats perfusion_calib.nii.gz -k gm_mask.nii.gz -m -s" which gave "152.821940 105.780550". A visual inspection showed the GM mask was sensible.

Thanks again,
Iain

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/usr/local/fsl/bin/imcp "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/Pre_Processing/N4_T1_Oriented.nii.gz" "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/structural_head"



Return code: 0



/usr/local/fsl/bin/imcp "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/Pre_Processing/Stripped_T1.nii.gz" "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/structural_brain"



Return code: 0



/usr/local/fsl/bin/oxford_asl  -i "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/DICOM_SOURCE_-_pCASL_v5.4_20180927093747_302.nii" --ibf=rpt --iaf=ct --tis 3.60 --bolus 1.80 --casl --slicedt 0.02800 -s "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/structural_head" --sbrain "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/structural_brain" -c "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/DICOM_M0_V5.4_20180927093747_401.nii" --tr 10.00 --cgain 1.00 --cmethod voxel --t1 1.30 --bat 1.30 --t1b 1.65 --alpha 0.85 --fixbolus --spatial --mc --pvcorr --artoff -o "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp"

OXFORD_ASL - running

Version: v4.0.6-dirty Thu Jul 11 15:08:11 2019

Saving results in natve (ASL aquisition) space to /mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/native_space

Saving results in structural space to /mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/struct_space

Pre-processing

Motion Correction

Number of voxels is:108800

Number of repeats in data is:30

Outputting ASL data mean at each TI

Done.

Number of inversion times: 1

Number of timepoints in data: 		30

Number of repeats in data: 30

3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60 3.60

Performing registration

ASL_REG

Input file is: /tmp/fsl_iRf86F_ox_asl/meanasl_brain

Registration MAIN stage (FLIRT)

Tidying up

ASL_REG - Done.

Segmenting the structural image

Creating mask

Setting up BASIL

Instructing BASIL to use automated spatial smoothing

Calling BASIL on data - conventional perusion image

Creating output directory: /tmp/fsl_iRf86F_ox_asl/init/basil

here

STEP 1: VB - Tissue

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/init/basil/step1/logfile

 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/init/basil/step1/logfile

STEP 2: Spatial VB Tissue - init with STEP 1

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/init/basil/step2/logfile

 0%5%10%15%20%25%30%35%40%45%50%55%60%65%70%75%80%85%90%95%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/init/basil/step2/logfile

End.

Fabber variance calculator

Working in /tmp/fsl_iRf86F_ox_asl/init/basil/step2

Calculating variance for: ftiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/init/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=10

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/init/basil/step2/finalMVN mean value=1.41032e+06

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/init/basil/step2/var_ftiss

Calculating variance for: delttiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/init/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=10

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/init/basil/step2/finalMVN mean value=1.41032e+06

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/init/basil/step2/var_delttiss

Done.

Creating output directory: /tmp/fsl_iRf86F_ox_asl/basil

here

STEP 1: VB - Tissue - init with STEP 0

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/basil/step1/logfile

 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/basil/step1/logfile

STEP 2: Spatial VB Tissue - init with STEP 1

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/basil/step2/logfile

 0%5%10%15%20%25%30%35%40%45%50%55%60%65%70%75%80%85%90%95%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/basil/step2/logfile

End.

Fabber variance calculator

Working in /tmp/fsl_iRf86F_ox_asl/basil/step2

Calculating variance for: ftiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=10

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/basil/step2/finalMVN mean value=8.34421

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/basil/step2/var_ftiss

Calculating variance for: delttiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=10

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/basil/step2/finalMVN mean value=8.34421

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/basil/step2/var_delttiss

Done.

Performing final registration

Performing registration

ASL_REG

Input file is: /tmp/fsl_iRf86F_ox_asl/ftiss

Registration FINAL stage (BBR)

'/tmp/fsl_iRf86F_ox_asl/mask.nii.gz' and '/tmp/fsl_iRf86F_ox_asl/mask.nii.gz' are the same file

Running BBR

Applying POWELL correction

finit, fend, fextrap = 0.430218 , 0.428844 , 0.42865

fval = 0.428686

Applying POWELL correction

finit, fend, fextrap = 0.428686 , 0.425773 , 0.424231

fval = 0.424133

0.423095 0.999573 0.008776 -0.027860 0.000000 -0.010549 0.997884 -0.064156 0.000000 0.027238 0.064423 0.997551 0.000000 -2.613947 -7.865969 16.773292 1.000000 

BBR end

Saving FINAL output

'/tmp/fsl_iRf86F_ox_asl/tissseg.nii.gz' and '/tmp/fsl_iRf86F_ox_asl/tissseg.nii.gz' are the same file

Tidying up

ASL_REG - Done.

Number of voxels is:19922

Number of repeats in data is:1

Start extrapolation!

Done.

/usr/local/fsl/bin/oxford_asl: line 2197: [: argument expected

Could not find a supported file with prefix "/mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/native_space/sensitivity"

Creating output directory: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil

here

STEP 1: VB - Tissue

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step1/logfile

 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step1/logfile

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp mean value=4.13306

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp_ftiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp mean value=4.13306

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/gmcbf_init'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: valim=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/gmcbf_init mean value=57.2851

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp mean value=1.71934

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/wmcbf_init'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: valim=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/wmcbf_init mean value=22.914

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/temp

STEP 2: Spatial VB Tissue PVE - init with STEP 1

----------------------

Welcome to FABBER v4.0.5-dirty

----------------------

Last commit: Thu Jul 11 14:55:43 2019

Logfile started: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/logfile

 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%100%



Final logfile: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/logfile

End.

Fabber variance calculator

Working in /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2

Calculating variance for: ftiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_ftiss

Calculating variance for: fwm

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_fwm

Calculating variance for: delttiss

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_delttiss

Calculating variance for: deltwm

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_deltwm

Calculating variance for: pvgm

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_pvgm

Calculating variance for: pvwm

FABBER: MVNtool

FabberRunDataNewimage::Loading mask data from '/tmp/fsl_iRf86F_ox_asl/mask'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=1

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=1 sec

FabberRunDataNewimage::Intents: 0, 0, 0, 0

FabberRunDataNewimage::Setting coordinates from extent

FabberRunDataNewimage::Loading data from '/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN'

FabberRunDataNewimage::Dimensions: x=80, y=80, z=17, vols=36

FabberRunDataNewimage::Voxel size: x=3mm, y=3mm, z=8mm, TR=4.55 sec

FabberRunDataNewimage::Intents: 1005, 0, 0, 0

FabberRunDataNewimage::Applying mask to data...

FabberRunData::GetVoxelData: input=/tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/finalMVN mean value=13.9355

FabberRunDataNewimage::Saving to nifti: /tmp/fsl_iRf86F_ox_asl/pvcorr/basil/step2/var_pvwm

Done.

Output is /mnt/hgfs/SHARED_FILES/NCGS_Pilot/Study_Data/BASIL_CBF_Calculating/NCGS01A/dcm2niix_IMAGES/temp/

OXFORD_ASL - done.



Return code: 0



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