Problem with ASL CBF maps

[Abir Toudi]

Dear HCP Users,

I'm working on ASL CBF extraction maps, so I followed all the steps of the quantification, and I don't undrestand why I  having this king of results. Very much dark in the middle of the CBF map.

Could you help me to fix the problem. I'm blocked at this stage!

Thank you very much.

Abir.

.

[Glasser, Matt]

Is this using HCP data or the HCP ASL pipeline?

Matt.

.

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[Abir Toudi]

I have used the HCP data and then I tried with another healthy subject. Same results !!

Abir.

[Glasser, Matt]

Using the HCP’s ASL pipeline?

Matt.

 

From: Abir Toudi <abirtro...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, May 12, 2022 at 9:36 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matt" <glas...@wustl.edu>
Subject: Re: [hcp-users] Problem with ASL CBF maps

 

 

I have used the HCP data and then I tried with another healthy subject. Same results !!

 

Abir.

Le jeudi 12 mai 2022 à 16:03:24 UTC+2, glas...@wustl.edu a écrit :

Is this using HCP data or the HCP ASL pipeline?

Matt.

 

From: Abir Toudi <abirtro...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, May 12, 2022 at 8:46 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Problem with ASL CBF maps

 

 

Dear HCP Users,

 

I'm working on ASL CBF extraction maps, so I followed all the steps of the quantification, and I don't undrestand why I  having this king of results. Very much dark in the middle of the CBF map.

 

Could you help me to fix the problem. I'm blocked at this stage!

 

Thank you very much.

Abir.

 

.

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[Abir Toudi]

Thank you mathew for your response.

No, I didn't use the HCP pipelines.

I want to try the HCP pipeline but I found some difficult in the installation of FSL software on windows.

Best,

Abir.

[Harms, Michael]

 

Hi Abir,

One of the QuNex developers told me that he was able to pull the docker image from the QuNex GitLab and run some sample commands.

 

So maybe the QuNex container (which includes the HCPpipelines) is a path forward for you.

https://qunex.yale.edu/

 

There is a lot of documentation available at the above link.  If you run into problems or have questions there is a QuNex Forum available as well.

 

Cheers,

-MH

 

-- 

Michael Harms, Ph.D.

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

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: Abir Toudi <abirtro...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Friday, May 13, 2022 at 1:27 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matt" <glas...@wustl.edu>
Subject: Re: [hcp-users] Problem with ASL CBF maps

 

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[Abir Toudi]

Dear Matt, 

thank you very much for your response, I'm gonna try it. 

Is it possible to execute the ASL to quantify CBF maps without M0 volume?

Because M0 is missing on my data!!

Thank you again.

Abir.

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[Harms, Michael]

Perhaps an ASL processing expert can chime in, but my simple understanding is that the M0 volumes are important for being able to compute estimates of CBF in real physical units.

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANJ5V0h7z0gGepE0Sd%3DYLhPHG3LG4d5HM580SBWVLAa_XV_9gQ%40mail.gmail.com.

[Abir Toudi]

Dear Matt,

Thank you very much for the information.

Your help is well appreciated.

Abir.

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[Flora Kennedy McConnell]

Hi Abir,

 

It is potentially possible to use the control images (those without labelling) from the ASL data time series to produce estimates of CBF in physical units if the M0 data is not available. However, this is only possible if the ASL data were acquired without background suppression (fortunately this is the case for the HCP data). Generally the M0 images are better suited to quantification because they have a much longer TR.

 

If you don’t have the M0 images then it might be worth extracting the ASL control images from the longest PLD and attempting to use those in place of an M0 image (ideally accounting for the short TR of the ASL data), to see if you get sensible CBF numbers out. However, if you can get access to the M0 image, then that would be the preferred route for quantification.

 

All the best,

Flora

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[Abir Toudi]

Dear Flora,

Thank you for your reply,

Unfortunately, the ASL data were acquired with background suppression.

I will try extracting the ASL control images from the longest PLD and attempting to use those in place of an M0 image.

Best,

Abir.

[Flora Kennedy McConnell]

Hi Abir,

 

I think the HCP Lifespan data were acquired without background suppression – is that the data you are using?

 

If the data you have were acquired with background suppression then it will not be possible to use the control images for quantification and so it is not even worth trying it.

[Abir Toudi]

Hello Flora,

The data I'm working on is personal data, but still I tried to use the control images but the results were not.

The problem is that I didn't acquire the M0 volume, and I need to generate CBF maps. Really I don't know how. 

Do you have any idea if perfusion maps could help me to have quantitative information about selected ROI?

Your help is always appreciated. Thanks a lot.

Best?

Abir.

[Flora Kennedy McConnell]

Hi Abir,

 

If your ASL data is background suppressed and you do not have M0 images then you cannot produce CBF maps in absolute units of ml/100g/min, and so you can only produce relative CBF maps.

 

Relative CBF maps can still be useful e.g. if you normalise the relative CBF map for each individual by dividing the voxelwise values by that individual’s mean relative CBF value for grey matter, then comparisons can be made between ROIs, and voxelwise group analyses can still be performed using this normalised relative CBF, rather than using the more typical absolute quantitative CBF, to which you don’t have access.

[Abir Toudi]

Dear Flora,

Thank you very much for the help, 

Could you tell me how I can generate these relative CBF maps? I'm a little lost.

Your help is always appreciated.

Abir.