Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

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Mutsaerts, H.J.M.M. (Henk Jan)

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Nov 22, 2020, 5:15:22 AM11/22/20

to McIntosh, Roger Christopher, Dillon, Kaitlyn Emily, Clement Patricia, Petr, Jan, ExploreASL

Hi Roger,

Thanks, great to hear! Would be best if you can join our weekly clinical/user meeting, in which everybody gives a short presentation about their project, and we go through image quality control and other image analysis interpretation issues that come up.

Patricia (CC) manages this meeting and has set up a very nice form to fill in if you decide to join. Everyone is free to join, also to get some ideas from other projects and ASL data!

Henk

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent/UCL/Mutsaerts Research

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

From: McIntosh, Roger Christopher <r.mci...@miami.edu>
Date: Wednesday, 18 November 2020 at 19:35
To: Mutsaerts, H.J.M.M. (Henk Jan) <h.j.mu...@amsterdamumc.nl>
Cc: Dillon, Kaitlyn Emily <kxd...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hello Henk,

I hope that all use well. I am pleased to inform you that we were able to run the pipeline and quantify the ASL! Most of the data looks wonderful and we were even able to run some ROI analyses with your atlases. Thank you.

There were, however, some images that did not pass quality control. There are some with clear ringing that probably cannot be salvaged, and others that seem to have an issue with the skull-stripping. We are not sure any of those can be salvaged. If you wouldn't mind to take a quick look, it would be greatly appreciated.

Thanks very much.

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Mutsaerts, H.J.M.M. (Henk Jan) <h.j.mu...@amsterdamumc.nl>
Sent: Sunday, October 11, 2020 6:12 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Cc: Dillon, Kaitlyn Emily <kxd...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hi Roger,

Yes, this is a known bug that I introduced by introducing new functionality in creating population-based templates, this should have been resolved in the newer version.

Which version did you use? We’re testing version 1.3.0 now and will soon release this.

Best, Henk

On 5 Oct 2020, at 23:50, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Henk:

I hope all is well.

Thanks for your input. That last change worked. We were successful in creating M0 files and ExporeASl made it up to Population module before the job was terminated.

I was hoping you could advise us regarding the attached error log? All the other error logs completed without error, so perhaps it's internal.

Thanks very much. Looking forward to hearing from you.

Regards.

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Mutsaerts, H.J.M.M. (Henk Jan) <h.j.mu...@amsterdamumc.nl>
Sent: Friday, September 11, 2020 2:12 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

This should probably be:

imPar = ExploreASL_ImportConfig('/deep/mcintosh/work/ExploreASL3/NameOfYourStudy);

and if you work in Windows it should be e.g.:

imPar = ExploreASL_ImportConfig('c:\deep\mcintosh\work\ExploreASL3\NameOfYourStudy);

HERE you can find a video tutorial about the import. Meanwhile, I will ask if you can try out our new GUI demo, while it is not tested fully yet, this is much easier to setup!

Best, Henk

--

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent/UCL/Mutsaerts Research

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

From: "McIntosh, Roger Christopher" <r.mci...@miami.edu>
Date: Thursday, 10 September 2020 at 22:48
To: "Mutsaerts, H.J.M.M. (Henk Jan)" <h.j.mu...@amsterdamumc.nl>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hi Henk,

Does anything seem to be out of sorts in this import_config file:

function imPar = ExploreASL_ImportConfig('/deep/mcintosh/work/ExploreASL3/Sub-020/raw');

I've tried different combinations, but it always returns a MATLAB error of unexpected expression pointing to the (') at the beginning of the path.  I read in the ExploreASL_Import help that "the setup uses the SPM form of regular expressions, which can be daunting at first.....".

Really sorry for all the hiccups along the way. We are determined to get this pipeline going!

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Mutsaerts, H.J.M.M. (Henk Jan) <h.j.mu...@amsterdamumc.nl>
Sent: Friday, September 4, 2020 3:10 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Cc: Clement Patricia <Patricia...@uzgent.be>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Sounds good!

In the ExploreASL_import, you can just treat the ASL dicom series as single ASL scan, which will indeed result in ASL4D.nii with two images, a deltaM and M0.

With these DataPar settings, the extraction of the second image as separate M0.nii should then be done by ExploreASL automatically.

Hope this helps, let me know if it worked!

Cheers

--

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent/UCL/Mutsaerts Research

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

From: "McIntosh, Roger Christopher" <r.mci...@miami.edu>
Date: Thursday, 3 September 2020 at 23:35
To: "Mutsaerts, H.J.M.M. (Henk Jan)" <h.j.mu...@amsterdamumc.nl>
Cc: Clement Patricia <Patricia...@uzgent.be>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hello Henk,

Thanks very much for your response. It seems like ExploreASL is really coming along. We would be very much interested in joining these meetings; hopefully share some results at that time. Kindly forward me the information for the meeting.

Regarding the NKI dataset. Thanks for the suggestion. I've contacted the PIs, but they have no clue. I also reached out to Siemens to see if they have some default settings for the Siemens MAGNETOM Trio-Tim. It seems like they are currently not scanning so it may be tough to track down the MR-tech, however I will keep trying. Such a rich dataset, would yield some good research studies.

Regarding the HIV-Miami dataset. Thanks for sending me the script. Indeed, the data has background suppression. I made a few attempts with the revised parm file (attached). I was holding off until the new version drops, but maybe it is not applicable here. Would you recommend estracting the second dicom image from the ASL image and converting it to .nii so that we can identify that as the M0 file for ExploreASl?

Very best regards.

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Mutsaerts, H.J.M.M. (Henk Jan) <h.j.mu...@amsterdamumc.nl>
Sent: Sunday, August 30, 2020 4:11 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Cc: Clement Patricia <Patricia...@uzgent.be>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hi Roger,

Good to hear from you! ExploreASL is actually moving forwards quite nicely. We are creating a graphical user interface, and ASL-BIDS is nearly ready. So many problems will become much easier in the near future! I would encourage you to join our weekly ExploreASL user meeting, where we discuss image analysis from a clinical/physiological perspective, and each user will provide feedback but also share visual QC that we can discuss.

Patricia is our “user expert”, she is managing the meetings. It will be early on the Friday morning for you, around 09h00-ish depending on the time zone.

Specifically:

It shouldn’t take that long to get info about the PLD? I would actually suggest to see if you can call those that control the scanner, during their waiting for whatever patient scan, they should easily be able to pull up a protocol and export it to XML/PDF. Was this the Siemens or GE sequence (GE is easier, it has only 3 options for PLD, 1025, 1525, 2025, for kids, adults, elderly, respectively.
You are providing conflicting information, as using the control image as M0 is usually something you would only do if there is no background suppression applied in the ASL sequence. In your case, you have correctly set the number of background suppression pulses to 5. You should have a separate M0 image, which is probably the second image in your GE sequence. Even though, the program probably tries to extract the control image, which GE doesn’t output as it does the control-label subtraction directly on the scanner. So you need to change the parameters into:

x.M0 = 'separate_scan';

x.M0PositionInASL4D = 2;

x.Q.BackGrSupprPulses = 5;

x.Q.SliceReadoutTime = 0; % you have a 3D readout, so no slice readout difference, but this parameter should be ignored whatsoever in your case

When you redo the import, and start ExploreASL, it should now correctly identify that the second ASL image is the M0 scan, and separate this for correct processing & analysis.

Let me know if this works! We are working on some bugs in release 1.2.0, r1.2.1 will probably come out tomorrow.

--

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent/UCL/Mutsaerts Research

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

From: "McIntosh, Roger Christopher" <r.mci...@miami.edu>
Date: Thursday, 27 August 2020 at 21:16
To: "henkjanm...@gmail.com" <henkjanm...@gmail.com>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Hi Henk!

I hope all is well with you and your family.

We are still awaiting to hear from the NKI group regarding the PLD for the dataset from neuropsych-hypertension manuscript draft I sent last year.

For now we are moving ahead with the HIV+ data. I know that you are busy, I am hoping you could take a quick look at this error log to see why the program is not recognizing the M0 images from our HIV dataset, even though it was specified in the parms file to extract it from the control image.

Thanks so much.

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Sunday, February 2, 2020 4:08 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

This is the population module, best to check the ASL module where the error seems to occur.

How about a Skype on either (Miami time):

Feb 11 - between 08h00 & 11h00

Feb 12 - between 08h00 & 09h30, 10h30 & 11h30

Are you attending the AAIC in Amsterdam? Alternatively I can visit your lab, we can exchange some presentations and brainstorm on the project. There seems to be an interesting overlap between our work, I’m just now writing a grant for the development of ASL as “cerebrovascular aging” biomarker of cognitive decline, which could be very important in the investigation of the effects of hypertension!

On 31 Jan 2020, at 05:42, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Thursday, January 30, 2020 12:00 PM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Yes, which one have you used?

Can you send me a single ASL_module_log.txt file for the ones from which you don’t have a CBF.nii or qCBF*.nii?

On 30 Jan 2020, at 17:40, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Ok, got it.

Is ExploreASL-0.9.9.1.zip the version we should be using?

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Thursday, January 30, 2020 11:34 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Yes, your CBF images seem to be missing, so something went wrong in generating them. You cannot use the mean control images for that.

For GM volume you should use the mrc1T1 images. Are you using the latest version of the pipeline (i.e. the version from the public GitHub?)

On 30 Jan 2020, at 17:31, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Sure. Just let me know when you are free. I don't have much going on over the next few weeks.

For now, since my RA is in today, we are going to move forward with manually extracting the GMV. Kindly verify that we can use PV_pGM_Sub**.nii file for this.

This is the only error message that came up for qCBF:

070_GetROIstatistics was performed

Warning: Couldnt find spatial CoV information! File missing, skipping...

> In xASL_qc_SortBySpatialCoV (line 53)

In xASL_module_Population (line 215)

In xASL_Iteration>runIteration (line 356)

In xASL_Iteration (line 95)

In ExploreASL_Master (line 136)

In run (line 86)

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Thursday, January 30, 2020 11:25 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

No that’s a different file. Let’s look through the results together over Skype. Can we plan something after next week (grant deadline)?

Thanks! Henk

On 30 Jan 2020, at 16:41, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Hi Henk,

We do not have any files named CBF.nii or qCBF.nii. There is a mean_control*_ASL_1.nii file in the population folder. I presume we can use this file for ROI analysis?

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Thursday, January 30, 2020 2:11 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Yes, sorry that is confusing indeed. Vascular crushing is an ASL acquisition parameter that allows to “crush” all spins that flow faster than a certain speed, usually this is used to remove the macrovascular ASL signal. This is usually not applied, since it was advised against in the 2014 Alsop MRM ASL consensus paper, because of the SNR penalty.

So indeed your ASL scans are without crushing. You should have CBF.nii in the native space folders (ASL_1) and qCBF*.nii in the Population folder (standard space). Both are the quantified CBF maps. Then you can obtain ROI-values for the spatial CoV and mean/median CBF with or without partial volume correction with some ExploreASL code, this is explained HERE, at the end, it says “Quantitative analysis: ROI analysis”. This shows where you can find it or get new ROI-values based on different atlases.

You’re welcome! Let me know if you need more help.

BW, Henk

On 30 Jan 2020, at 05:26, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Hello Henk,

I hope all is well. I was able to reprocess all of the data in exploreASL. Per your recommendation I plan to use the gray matter volume generated from the exploreASL pipeline to extract the ROIs. With regards to spatial CoV, you state in your 2017 paper in JCBFM "The spatial CoV was obtained from the non-crushed ASL scans, which represent the current recommended ASL sequence without direct ATT information."

I presume that all the ASL_1 files are non-crushed. Could you please tell me which of the output files I should be using for spatial Cov versus CBF? I attached a snapshot of the population folder.

Thanks a bunch! Looking forward to the results.

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Monday, January 13, 2020 1:48 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

On 12 Jan 2020, at 18:07, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Thanks, Henk.

I did the import myself, but will retry with the import parameters you provided me.

Good, should not be too difficult. Its only important to get the ASL4D.json sidecar.

Taking a look at the spatial Cov parameter is a great idea. From what I understand it is similar to the resting state connectivity approach, i.e., the spatial covariance associated with spontaneous neural activity at rest, but instead using the perfusion signal.

No, its different. Its not a covariance, it is the SD/mean. It provides an estimate of how much label has arrived in the tissue or still resides in the proximal vessels, which works as a global proxy for cerebrovascular health.

Will the program produce a report or an actual dataset (.nii) that can be used to extract ROI-based values?

Both! Check out this tutorial

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Sunday, January 12, 2020 10:45 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Thanks, the bug you showed is fixed in a newer version. The version I gave you was still a beta version, the final version can be downloaded at www.github.com/ExploreASL/ExploreASL.git or www.ExploreASL.org.

Also, the ASL4D.nii file lacks it sidecar, which the ExploreASL_Import.m either generates as ASL4D.json (per ASL-BIDS) or ASL4D_parms.mat (legacy). Did you do the import yourself? You can either use the ExploreASL_Import parameters (which I think I gave you?) or dcm2niiX, it provides the .json sidecar that is needed.

For your dataset I would be very interested to see the results for our new parameter “spatial CoV”!

Did you read the papers about this? It is a good whole-brain (or per vascular circulation) summary parameter of the cerebrovascular health, and correlates nicely with cognition and cardiovascular parameters.

It would be interesting to look how this correlates in your study. Then you can differentiate the more “cerebrovascular” and “metabolic/functional” effects by looking at what is explained by spatial CoV and CBF, respectively.

BW, Henk

On 12 Jan 2020, at 16:03, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

McIntosh, Roger Christopher has shared OneDrive for Business files with you. To view them, click the links below.

population.tar.gz

sub.tar(1).gz

Attached.

Thanks,

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402



From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Saturday, January 11, 2020 3:41 PM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Thanks, but can you send a full single dataset, i.e. the full subject folder with contents?

Best, Henk

On 11 Jan 2020, at 18:16, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

I have a few conflicts this week but I may check out MCI afterwards.

Best,

-RM

Roger McIntosh, Ph.D.
Assistant Professor
University of Miami
Department of Psychology
Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047
Fax: 305-284-3402



From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Friday, January 10, 2020 4:01:12 PM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Thanks, I will take a look. Ze I know well, his toolbox was the first around! Are you attending the HAI in Miami this week? My colleagues are going there

On Fri, Jan 10, 2020, 19:01 McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Thanks, Henk.

I have attached the dataset and log from the failed analysis. From what I can tell these are the scan parameters we shared back on 5/22. I don't think I actually got confirmation they were okay so perhaps I made a mistake with the DataPar file. Please let me know if you recreate the error on your end.

My apologies, I was referring to Ze Wang's ASL toolbox https://www.cfn.upenn.edu/~zewang/ASLtbx.php

ASL Data Processing Toolbox - cfn.upenn.edu

The Center for Functional Neuroimaging at the University of Pennsylvania provides unification for currently distributed medical center efforts in physiological and clinical brain imaging and advance the general interests of the brain imaging community through targeted methods development, symposia and colloquia, handling of regulatory issues, and fund-raising efforts.

www.cfn.upenn.edu

Thanks again,

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402



From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Thursday, January 9, 2020 2:48 PM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Sure, I will have a look, easiest if you can send me the log files, or even better, a single complete dataset that went wrong.

Is the DataPar the one that I provided you, from the Siemens sequence that I tested? Then at least we know that the parameters should be correct ;)

I have never heard of ASLstudio, could you provide me with a link? We are also creating an overview of existing ASL pipelines within ISMRM OSIPI, so it would be good to add this one as well.

Finally, the pipeline will get a minor important update next week or so, it would be best to use this one, as a stable release. We shifted everything to a new public GitHub (GitHub.com/ExploreASL/ExploreASL.git)

BW, Henk

On 8 Jan 2020, at 22:01, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Hello Henk,

Thanks for taking a look at this. Sorry for the delay. I was digging up the data that my RA was working on an came to find: (1) ROI analysis was actually done outside of ExploreASL and (2) the mean_control subtraction image was used and not spatial covariance, and (3) - here's the kicker- he actually used a different program (ASLstudio) to derive the subtraction image data used in the analysis!

I am in the processing of re-analyzing the data with the intent of running the ROI analysis in ExploreASL and seemed to have hit a snag at the quantification of ASL module.

I am not able to see the tsv results in the population/stats folder.

Here is the error:

xASL_Move: overwriting /deep/mcintosh/work/exploreASL/practice/Population/PV_pGM_Sub-002.nii

xASL_Move: overwriting /deep/mcintosh/work/exploreASL/practice/Population/PV_pWM_Sub-002.nii

M0 image processing skipped, because no M0 available

Quantifying ASL

Loading PWI & M0 images

M0 scan used

ERROR: Job iteration terminated!

ans =

'Error using xASL_nifti (line 24)

/deep/mcintosh/work/exploreASL/practice/Population/M0_Sub-002_ASL_1.nii does not exist as .nii or as .nii.gz

Error in xASL_nifti2IM (line 13)

IM = xASL_nifti(NIfTIfile);

Error in xASL_wrp_Quantify (line 110)

M0_im = xASL_nifti2IM(M0Path);

Error in xASL_module_ASL (line 323)

xASL_wrp_Quantify( x );

Error in xASL_Iteration>runIteration (line 353)

[result, x] = jobfn(job_ex, x);

Error in xASL_Iteration (line 92)

[bAborted, xOut] = runIteration(dbSettings);

Error in ExploreASL_Master (line 85)

[~, x] = xASL_Iteration(x,'xASL_module_ASL');

Error in run (line 86)

evalin('caller', [script ';']);'

-----

Here is the DATA_PAR.m input file.

function x = DATA_PAR( x )

%DATA_PAR Part of ExploreASL, loading basic study settings

% HJMM Mutsaerts 2018

% Define study

x.name   = 'NKI';

x.subject_regexp = '^Sub-\d{3}$';

% list parameters here

x.M0 = 'no_background_suppression'; % Dennis obtained in PET-MRI study, rescale Ingenia-Intera later

x.Q.BackGrSupprPulses = 2;

x.readout_dim = '2D'; % 2D or 3D

x.Quality = 1; % 1 = normal, 0 = low for fast try-out

x.DELETETEMP = true;

x.Vendor = 'Siemens'; % Options: 'GE_product' 'GE_WIP' 'Philips' 'Siemens', for applying vendor-specific scale factors

x.Q.LabelingType = 'CASL'; % Options: 'PASL' (pulsed Q2-TIPS) or 'CASL' (CASL/PCASL)

% NB: pulsed without Q2TIPS cannot be reliably quantified because the bolus width cannot be identified

% CASL & PCASL are both continuous ASL methods, identical quantification

x.Q.Initial_PLD = 1000; % Philips Utrecht == instellingen origineel van Thijs (v\ufffd\ufffdr white paper)

x.Q.LabelingDuration = 1000; %?

x.Q.SliceReadoutTime = 150; % (minTR-PLD-labdur)/n_slices = (3800-1000-1000)/24 =

x.bReproTesting = false;

end

Could you please advise?

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

From: Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Friday, December 27, 2019 6:37 AM
To: McIntosh, Roger Christopher <r.mci...@miami.edu>
Cc: Lobo, Judith Diane <jl...@miami.edu>; Paparozzi, Jeremy Mathew <jmp...@miami.edu>; jeremy Paparozzi <jpapar...@gmail.com>
Subject: Re: Multimodal Imaging Analysis of Cognitive Flexibility in Hypertension

Thanks, this looks good! I added some initial thoughts.

Do you want me to have a better look now or in a later stage?

For the ASL & T1w image processing, can you indicate which parts you used from ExploreASL and which parts you did yourself/with different techniques? Then I can fill in the missing steps. The exact details of ExploreASL are in the ExploreASL paper, so we can always refer to this, and repeat some short parts. Also, I would try to keep the processing similar for the different sequences (T1w/ASL/fMRI). Did you have FLAIRs, as these participants may have WMH that can be taken into account in image processing?

Which co-author position did you want to give me (I’m fine with anything of course)? I inserted my affiliations.

Do we specifically focus on the executive performance only in this paper, is it known that hypertension mainly affects the executive functions, and that other cognitive functions remain relatively intact?

The CBF group differences are interesting, did you also test the spatial CoV? Because I would presume the differences to be more of a vascular than 'neuromuscular coupling’ kind.

Thanks, happy holidays to you too!

Best wishes from Amsterdam,

Henk

Best wishes/hartelijke groet,
Henk(-Jan) Mutsaerts, MD PhD
Amsterdam UMC/ UZ Ghent
Phone: +31 6 4390 8284; Skype: hj.mutsaerts

On 26 Dec 2019, at 16:17, McIntosh, Roger Christopher <r.mci...@miami.edu> wrote:

Hello Henk,

Happy Holidays.

I have attached a very rough draft of the paper so that you can take add your methods for the ASL pre-processing pipeline and any comments or revisions you may have for the overall study. We still need to reconcile Table 2 so that the sample sizes coincide for each imaging modality and add a connectivity map showing the magnitude of z-scores for executive control network in each group.

As of now the target journal is Brain and Cognition.

Thanks again for your all your help with the ASL pipeline.

Best regards,

-RM

Roger McIntosh, Ph.D.

Assistant Professor

University of Miami

Department of Psychology

Divisions of Health, Cognitive and Behavioral Neuroscience

Director BREATH Lab

Phone: 305-243-2047

Fax: 305-284-3402

<HTN_NTN_CBF_n46_RM4_JP.docx>

<lock.tar.gz>

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