I would check what output you are getting without the structural image (and associated registration) first - run without the ' -s "/ASL_C003_T1.nii" - -regfrom "/ASL_C003/raw_asl.nii’ for now and check you get a perfusion image and reasonable values. You don’t need the --bat value here if you are using —wp (and a BAT as short as 0.7 isn’t likely for pcASL data, that value I would associate with pASL), Please make sure you have both --tis specified and --rpts for your data - given your previous explanation: oxford_asl needs to know what the timings of the individual volumes are and how many there are, and as noted before you need --ibf=rpt included in the command as well.

Michael


On 8 Apr 2020, at 23:01, Charlotte Sørensen <[log in to unmask]> wrote:

I still don't get any quantitative measurements.I have now changes the things in the commandline and have the following: 

oxford_asl -i "ASL_C003/pcASL_diffdata.nii.gz" -c "/ASL_C003/M0.nii" - -tis= 2,2.5,3,3.5,4 -o "/ASL_C003"  - -bolus=1.5 - -bat 0.7 - -t1 1.3 - -t1b 1.66 - -spatial - -wp - -mc - -casl -s "/ASL_C003_T1.nii" - -regfrom "/ASL_C003/raw_asl.nii"

There are several lines of error given in the terminal, but it seem to be about that the files from the analysis put in a folder "/tmp/fsl_* can not be found and thus several images cannot be read. 

Best/ 
Charlotte



Den ons. 8. apr. 2020 kl. 18.24 skrev Charlotte Sørensen <[log in to unmask]>:
Dear Flora

The --tis that I need to specify is kn the oxford_asl command right?

Best,
Charlotte 

ons. 8. apr. 2020 17.50 skrev Flora Kennedy McConnell <[log in to unmask]>:
Hello Charlotte,

One final thing to add to Martin and Michael's replies:

As well has having the "--ibf=" option to indicate the ordering of the PLDs in your data file and the "--rpts=2,2,2,3,3" to indicate the number of repeats at each PLD, you also need to specify the actual TIs using "--tis=". i.e. if you have a labelling duration of 1.5 and 5 PLDs of 0.2, 0.5, 0.8, 1.2, and 1.5 then you would include "--tis=1.7,2.0,2.3,2.7,3.0", where TI=LD+PLD.

All the best,
Flora

Flora Kennedy McConnell
------------------------------
Postdoctoral Research Associate

Department of Engineering Science
University of Oxford
Old Road Campus Research Building
Oxford, UK
OX3 7DQ
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Martin Craig <[log in to unmask]>
Sent: 08 April 2020 09:27
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] psASL data analysis
 
Hi Charlotte to use variable repeats you'd need to set the options as

--ibf=rpt --rpts=2,2,2,3,3

--ibf sets the block format which must be groups of repeats when using variable repeats. --rpts is used to specify the number of repeats at each ti. Currently you can't do this from the GUI but it's a planned addition.

Hope this helps
Martin
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Charlotte Sørensen <[log in to unmask]>
Sent: 08 April 2020 08:36
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] psASL data analysis
 
Thank you for your replay. 

I have still not gotten a trustworthy result, as I'm analyzing a healthy control subject and would expect normal perfusion. Thus, I'm now trying to run it though the command line instead, to keep more control of the processes during the way. 

stating different repeats for the PLD's I did the following in the asl_file command: --ntis=5 --ibf=2,2,2,3,3 
however, it gave an error saying something with this option not being supported. Have I noted it wrong? 

Best regards
Charlotte

Den man. 6. apr. 2020 kl. 18.28 skrev Michael Chappell <[log in to unmask]>:
Yes that also should be fine. It will slightly change the internal process - as where there are multiple repeats of the same PLD BASIL does a first analysis having averaged the data each each PLD and then does a subsequent analysis using the original data. This is aimed at achieving maximum robustness in the model inference. In practice it may well not make much difference, especially with the number of repeats in this case.

Michael

On 6 Apr 2020, at 15:07, Charlotte Sørensen <[log in to unmask]> wrote:

I just tried the following:
Info. I have 24 scans, 2 repeats of PLD 1,2 and 3 and 3 repeats of PLD 4 and 5.

I sat the PLD to 12 and then the number of repeats became 1. The the array of PLD was just sat to:
PLD1 PLD1 PLD2 PLD2 PLD3 PLD3 PLD4 PLD4 PLD4 PLD5 PLD5 PLD5. 

The analysis is running now. So you think this could be a solution?

Best, 
Charlotte 

man. 6. apr. 2020 15.59 skrev Michael Chappell <[log in to unmask]>:
If you have a variable number of repeats at each PLD you will need to use the oxfrod_asl command line tool rather than the GUI (which currently doesn’t support that case). Although you can set up the rest of the analysis in the GUI and then copy/modify the command line call it creates. You will need the ‘--rpts=‘ option and list the number of repeats at each PLD in the ‘--tis=‘ option.

Michael


On 6 Apr 2020, at 14:25, Charlotte Sørensen <[log in to unmask]> wrote:



---------- Forwarded message ---------
Fra: Charlotte Sørensen <[log in to unmask]>
Date: man. 6. apr. 2020 kl. 14.43
Subject: psASL data analysis
To: <[log in to unmask]>


Dear FSL Group

I have some questions relating pcASL data preprocessing and analysis with FSL

1) I don't have the same amount of repeats for each PLD, how can I specify that? Now when I input my 4D Nii input image and my number of PLD it says "invalid2 due to this.

2) I can not get the Output directory to work. I create a folder for where I want the output to be,but then it gives an error: "cannot create output directory"

Best regards
Charlotte Sørensen, Master student in Neuroscience and Neuroimaging

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