include IVIM code from Dr. Amita Shukla-Dave Lab at MSKCC

[locastre]

We have contributed our codebase for intravoxel incoherent motion (IVIM) code from the MRI-QAMPER MATLAB package, developed by Dr. Amita Shukla-Dave's lab at Memorial Sloan Kettering Cancer Center.

Authors: Eve LoCastro (locastre@mskcc.org), Dr. Ramesh Paudyal (paudyalr@mskcc.org), Dr. Amita Shukla-Dave (davea@mskcc.org) Institution: Memorial Sloan Kettering Cancer Center Department: Medical Physics Address: 321 E 61st St, New York, NY 10022

[locastre]

Hi Oliver and Eric,

Sure, it is fine to list nifti_toolbox as a requirement. The code does some optional image smoothing for preprocessing and accounting for SNR. It also checks that the bvalue images are in the correct (increasing b-value) order. It outputs the ROI parameter maps for D, D*, and f, and also outputs ROI-average values into a CSV file. I can add more of this information into the script comments as documentation.

Cheers, Eve

Eve LoCastro, M.S. Advanced Software Developer Medical Physics, Service for Predictive Informatics

Memorial Sloan Kettering Cancer Centerhttps://mskcc.org/ 321 E 61st St, Rm. 207C New York, NY 10022

Mobile: +1 (718) 406-4248 @.**@.>

From: Oliver Gurney-Champion @.> Sent: Wednesday, March 6, 2024 11:23 AM To: OSIPI/TF2.4_IVIM-MRI_CodeCollection @.> Cc: LoCastro, Eve @.>; Author @.> Subject: [EXTERNAL] Re: [OSIPI/TF2.4_IVIM-MRI_CodeCollection] include IVIM code from Dr. Amita Shukla-Dave Lab at MSKCC (PR #52)

@oliverchampion commented on this pull request. In src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/utils/nifti_toolbox/license. txt: > @@ -0,0 +1,24 @@ +Copyright (c) 2014, Jimmy Shen Hey! Thanks for this great submit! Some questions: 

@oliverchampion commented on this pull request.

---

In src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/utils/nifti_toolbox/license.txthttps://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$:

@@ -0,0 +1,24 @@

+Copyright (c) 2014, Jimmy Shen

Hey! Thanks for this great submit! Some questions: It seems like the toolbox includes some generic toolboxes like the NIFTI toolbox. Do we need that to be part of the package, or could we take it as a requirement? Also, what does the code do? Is it just fitting, or does it do more processing?

Thanks!

Oliver and Eric

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AID5QMAL2XXJ57CQFLJFKBTYW47GNAVCNFSM6AAAAABEF7KHU2VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTSMRQGIZTANZZGE__;!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCMN5yy_8$. You are receiving this because you authored the thread.Message ID: @.**@.>>

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[locastre]

Thanks so much, Eve Amita

Amita Shukla-Dave, Ph. D., FISMRM Vice Chairman Radiology-Medical Physics Outreach Deputy Service Chief Predictive Informatics Director Quantitative Imaging Attending Physicist (Professor), Member Departments of Medical Physics and Radiology Memorial Sloan-Kettering Cancer Center New York, NY 10065 phone:212-639-3184 @.*** http://www.mskcc.org/research/lab/amita-dave

From: LoCastro, Eve @.> Sent: Wednesday, March 06, 2024 11:28 AM To: OSIPI/TF2.4_IVIM-MRI_CodeCollection @.>; OSIPI/TF2.4_IVIM-MRI_CodeCollection @.> Cc: Dave, Amita @.> Subject: RE: [EXTERNAL] Re: [OSIPI/TF2.4_IVIM-MRI_CodeCollection] include IVIM code from Dr. Amita Shukla-Dave Lab at MSKCC (PR #52)

Hi Oliver and Eric,

Sure, it is fine to list nifti_toolbox as a requirement. The code does some optional image smoothing for preprocessing and accounting for SNR. It also checks that the bvalue images are in the correct (increasing b-value) order. It outputs the ROI parameter maps for D, D*, and f, and also outputs ROI-average values into a CSV file. I can add more of this information into the script comments as documentation.

Cheers, Eve

Eve LoCastro, M.S. Advanced Software Developer Medical Physics, Service for Predictive Informatics

Memorial Sloan Kettering Cancer Centerhttps://mskcc.org/ 321 E 61st St, Rm. 207C New York, NY 10022

Mobile: +1 (718) 406-4248 @.**@.>

From: Oliver Gurney-Champion @.**@.>> Sent: Wednesday, March 6, 2024 11:23 AM To: OSIPI/TF2.4_IVIM-MRI_CodeCollection @.**@.>> Cc: LoCastro, Eve @.**@.>>; Author @.**@.>> Subject: [EXTERNAL] Re: [OSIPI/TF2.4_IVIM-MRI_CodeCollection] include IVIM code from Dr. Amita Shukla-Dave Lab at MSKCC (PR #52)

@oliverchampion commented on this pull request. In src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/utils/nifti_toolbox/license. txt: > @@ -0,0 +1,24 @@ +Copyright (c) 2014, Jimmy Shen Hey! Thanks for this great submit! Some questions: 

@oliverchampion commented on this pull request.

---

In src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/utils/nifti_toolbox/license.txthttps://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$:

@@ -0,0 +1,24 @@

+Copyright (c) 2014, Jimmy Shen

Hey! Thanks for this great submit! Some questions: It seems like the toolbox includes some generic toolboxes like the NIFTI toolbox. Do we need that to be part of the package, or could we take it as a requirement? Also, what does the code do? Is it just fitting, or does it do more processing?

Thanks!

Oliver and Eric

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AID5QMAL2XXJ57CQFLJFKBTYW47GNAVCNFSM6AAAAABEF7KHU2VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTSMRQGIZTANZZGE__;!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCMN5yy_8$. You are receiving this because you authored the thread.Message ID: @.**@.>>

=====================================================================

Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

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[etpeterson]

Just checking in on this because it's been a while. Were you planning on cleaning it or were you expecting someone to take this over?

[oliverchampion]

Hey! Way too late, but I am reviewing the code. You code is way more extensive then all the other commits, so this may take some more effort/time. But we will get there! For now there are some things to address.

[oliverchampion]

You have a demo as "demo_QAMPER_IVIM.m", which is very useful. But as Git gets clogged up fast with files, we do not want nii files in Git. I see you have removed the test data (good!) but obviously the demo now fails.

Luckily, our Git comes with some test data that is stored on Zenodo: https://zenodo.org/records/10696605. This data is automatically downloaded whenever needed, as we coded the git such that it runs utilities/data_simulation/Download_data.py and stores it in "download\Data". I am now running your code with the abdomen.nii.gz data, and this works! However, it required me to (1) download the data manually and (2) make a mask.

So my questions are: 1: can we make sure the data is downloaded automatically whenever we need it for you demo (maybe this is not possible... Then you can refer to the location in the file) 2: is it required to add a mask.nii.gz or can it run without a mask/an automated mask?

[oliverchampion]

I think there are several files in here that are not needed, such as the .asv files. Could you remove the asv files, and add .asv to the .gitignore?