Hi Flora,

 thank you, this is tremendously helpful.

Re your point #2, great, that is similar to what I did (except for the fact I have fewer volumes). I will try to pull the info out of the JSON image (though, after emailing the list it occurred to me that I might be able to infer it from the dicom header values too perhaps..).

At present, then, my uncertainty is about how many PLD there are. Just as you said, the PDF from the console when I look in Sequence - special reports:
PCASL Options:        mdPCASL
Labeling Duration:  1500000 us.
Postlabeling delay: 184628 us.
LabelPlaneOffset:   95 mm.

However, when I set the first option (mdPCASL) at the console, the "pop up help text" says that this setting is for multi-PLD (the other two options I think were single PLD mdPCASL and a third one I cannot recall [I'll be at the scanner later today or tomorrow, so will verify]); however, I cannot find any trace of the other PLDs.

I will report (and print a PDF) later today or tomorrow.

 Thank you so much for the input already!

 best

 Martin

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Flora Kennedy McConnell <[log in to unmask]>
Sent: 02 October 2019 10:09
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] Oxford ASL and MB-pCASL
 
Hi Martin,

I have some experience of working with the multiband ASL data from the HCP Aging/Development studes. I should be able to help with the analysis.
  1. The data I have from HCP are multi PLD pcASL. I am not familiar with the scanner console setup, as I haven't been involved in the acquisition. However, it is very common for me to receive Siemens datasets with a scan parameter PDF that describes a single PLD PASL sequence in the 'Contrast - ASL'  field, and then includes a 'Sequence - special' field which describes the multi PLD pcASL sequence I am expecting. I wonder if the more specialised research-focused multi PLD squences are included on the scanners as modifications to the existing single PLD product sequence.
  2. There are some differences between our datasets: the HCP ASL data have 90 volumes (86 label-control pairs + 2 noise images + 2 calibration images). My initial analysis steps have been to:
    1. use fslroi to separate off the label-control pairs (volumes 0 to 85 in my case).
    2. use fslroi to separate off the calibration images (volumes 88 and 89 in my case)
    3. so far, I've not come across a way to use the noise images.
    4. then feed the label-control pairs into oxford_asl as the input data (-i option), and the two calibration images into oxford_asl using the -c option.
  3. The HCP datasets that I am using are also multibands with 6 bands. I was able to calculate the time per slice from the .json file that I was given with the data. If that is something that you have access to, then it is the difference between the times in the "SliceTiming" field.
I hope that helps. Get back in touch if you have more questions. I am happy to help.

All the best,
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 M <[log in to unmask]>
Sent: 01 October 2019 22:48
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] Oxford ASL and MB-pCASL
 
Hi All,

I'm "bumping" this post again in case, one year later, there is someone on the mailing list who can help.

The question is for anyone who has used the UMinn mb-PCASL sequence (part of the HCP project sequences I believe). Unfortunately there is just very little documentation which makes it hard (for me!) to "translate" the parameters from the scanner's console to the FSL ASL tools.

Here are some questions for anyone who uses the sequence:

1. The sequence seems to me to be single PLD [but in the siemens sequence screen under the “Sequence>Special” tab it seems to say it is a multi PLD acquisition? I can only see one PLD specified however..]
2. The sequences has 70 (tag-control) measurements, but the last 4 are radically different. The v1.0 documentation says that "The  implemented MB-EPI  PCASL  sequence  acquires  two  M0  images after label/control images series. The mean image of these two M0 images can be used for CBF quantification" but what are the 3rd-/4th-to-last scans (which I assume I have to remove?)
3. This is multiband with 6 bands, but how to find the acquisition time per slice?

Cheers

 Martin
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of SUBSCRIBE FSL Erik <[log in to unmask]>
Sent: 30 June 2018 20:22
To: [log in to unmask] <[log in to unmask]>
Subject: [FSL] Oxford ASL and MB-pCASL
 
Hi everyone
Does anyone have experience with using the UMinn multiband pCASL sequence and processing in FSL? There isn't much documentation, but as far as I can gather, 4 additional images are acquired at the end of the sequence, the last two I think are the M0 calibration images and the two preceding are maybe thermal noise? Is there a way to use these in FSL or should I just remove these from the asl nifti?

Also, I presume these are tag-control pairs, but not sure how to tell for certain.

I would appreciate any guidance on using this sequence in FSL if anyone has used this. Thanks in advance!

Erik

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1


To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1


To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1