include IVIM code from Dr. Amita Shukla-Dave Lab at MSKCC #52
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| Copyright (c) 2014, Jimmy Shen | |||
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Should this be included? It seems to be a separate toolbox. https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
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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
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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 Center<https://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.txt<https://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$>:
@@ -0,0 +1,24 @@
+Copyright (c) 2014, Jimmy Shen
Hey! Thanks for this great submit!
Some questions:
It seems like the toolbox includes some generic toolboxes like the NIFTI toolbox. Do we need that to be part of the package, or could we take it as a requirement?
Also, what does the code do? Is it just fitting, or does it do more processing?
Thanks!
Oliver and Eric
—
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AID5QMAL2XXJ57CQFLJFKBTYW47GNAVCNFSM6AAAAABEF7KHU2VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTSMRQGIZTANZZGE__;!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCMN5yy_8$>.
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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 Center<https://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.txt<https://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 GitHub<https://urldefense.com/v3/__https:/github.com/OSIPI/TF2.4_IVIM-MRI_CodeCollection/pull/52*discussion_r1514784620__;Iw!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCIGShdOg$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AID5QMAL2XXJ57CQFLJFKBTYW47GNAVCNFSM6AAAAABEF7KHU2VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTSMRQGIZTANZZGE__;!!KVWo1iE!SMb7JOGD6xXObPLSfLIkvbFVOfkf4pGmz3lKKF1U9pLihSeHCRtNUd9jtx45w9Coa1hWbs53beshAisCMN5yy_8$>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
=====================================================================
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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
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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? |
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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! |
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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: |
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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? |
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Apologies for the late responses on my part, I have not been receiving the notifications for this thread. I'll work on addressing the ASV and demo scripts now, sending update when they are complete. |
@locastre, Any updates :)? |
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 ([email protected]), Dr. Ramesh Paudyal ([email protected]), Dr. Amita Shukla-Dave ([email protected])
Institution: Memorial Sloan Kettering Cancer Center
Department: Medical Physics
Address: 321 E 61st St, New York, NY 10022