Pre-processing features

[JoeNYC1]

Can you please elaborate how or which pre-processing tools best suits qMRLab. I am interested in longitudinal studies and would like to know if there is registration, template/atlas matching features available.

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[agahkarakuzu]

Hi @JoeNYC1 we have some workflow modules that incorporate ANTS for alignment. I assume that you'd like to use atlases? It is possible to incorporate any software/process to the mix. Which qMRI model would you like to use?

[JoeNYC1]

Thank you very much for your reply. I am actually planning to use qMRI framework to perform longitudinal studies of tumor metastasis in the pelvic bone (I am sorry if this seems outside of the more standard use of the software but the many modules make it an attractive choice). Given the variability within the population, each person serves as their own reference – so volumes would be co-registered to the initial scan. The primary models are relaxation and diffusion, with the possibility of MTR. The workflow you use for ANTS relies on what type of registration? Thank you From: Agah ***@***.***> Sent: Friday, April 23, 2021 11:08 AM To: qMRLab/qMRLab ***@***.***> Cc: Mazaheri Tehrani, Yousef/Medical Physics ***@***.***>; Mention ***@***.***> Subject: [EXTERNAL] Re: [qMRLab/qMRLab] Pre-processing features (#444) Hi @JoeNYC1<https://github.com/JoeNYC1> we have some workflow modules that incorporate ANTS <https://www.nitrc.org/projects/ants> for alignment. I assume that you'd like to use atlases? It is possible to incorporate any software/process to the mix. Which qMRI model would you like to use? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#444 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATZ2TJOEH5YDYNVNQ54QI4LTKGEMVANCNFSM43OWMJYQ>. *** Only open attachments or links from trusted senders. Report phishing to ***@***.******@***.***> *** ===================================================================== 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.

[agahkarakuzu]

I am sorry if this seems outside of the more standard use of the software but the many modules make it an attractive choice

qMRI for pelvic bone imaging sounds cool, nothing to be sorry about :)

OK, in your case, I think, you'd like to perform some volume alignment between qMRI input pairs (e.g. multiple flip angle images). Given the anatomy, I don't have much experience. How much your input pairs suffer from respiratory motion would be a good factor to consider. But if you have a preferred tool, we can bring it in.

I would suggest organizing your inputs in BIDS format (the name of the standard implies brain imaging, but that's OK :) ). This is the format our workflows recognize.

Bottomline, I would lean towards leaving registration software/method choice to your discretion. You may want to use ANTs, Elastix, FSL ... many options out there. Have you tried any so far?

[JoeNYC1]

Thank you very much for your help.

>I would suggest organizing your inputs in BIDS<https://bids-specification.readthedocs.io/en/latest/> format.

What might be the best way to learn how qMRI interfaces with BIDS. I am not familiar with BIDS.

>Bottomline, I would lean towards leaving registration software/method choice to your discretion.

Elastix is the software which would be most helpful. A matlab wrapper is available so I can stay within the matlab environment. My plan is to merge features of qMRI with sc toolbox: for longitudinal analysis, I would like to use the features provided by sc toolbox (segmentation, registration to template, motion correction) with qMRI (quantification). I am not sure if this has been looked into previously? I am interested in metastatic cancer, which are typically located in the spine, or pelvis bone. Thank you From: Agah ***@***.***> Sent: Friday, April 23, 2021 11:32 AM To: qMRLab/qMRLab ***@***.***> Cc: Mazaheri Tehrani, Yousef/Medical Physics ***@***.***>; Mention ***@***.***> Subject: [EXTERNAL] Re: [qMRLab/qMRLab] Pre-processing features (#444) I am sorry if this seems outside of the more standard use of the software but the many modules make it an attractive choice qMRI for pelvic bone imaging sounds cool, nothing to be sorry about :) OK, in your case, I think, you'd like to perform some volume alignment between qMRI input pairs (e.g. multiple flip angle images). Given the anatomy, I don't have much experience. How much your input pairs suffer from respiratory motion would be a good factor to consider. But if you have a preferred tool, we can bring it in. I would suggest organizing your inputs in BIDS<https://bids-specification.readthedocs.io/en/latest/> format (the name of the standard implies brain imaging, but that's OK :) ). This is the format our workflows recognize. Bottomline, I would lean towards leaving registration software/method choice to your discretion. You may want to use ANTs, Elastix, FSL ... many options out there. Have you tried any so far? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#444 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATZ2TJJSJURLJ6F3P73S3TTTKGHGHANCNFSM43OWMJYQ>. *** Only open attachments or links from trusted senders. Report phishing to ***@***.******@***.***> *** ===================================================================== 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.

[JoeNYC1]

Can I just follow up on one question? Is there a way to connect qMRI capabilities with spinal cord toolbox? Would this need to be done with the python implementation of sc toolbox or with the older matlab version? Thank you very much. From: Mazaheri Tehrani, Yousef/Medical Physics Sent: Monday, April 26, 2021 1:43 PM To: qMRLab/qMRLab ***@***.***> Subject: RE: [EXTERNAL] Re: [qMRLab/qMRLab] Pre-processing features (#444) Thank you very much for your help.

>I would suggest organizing your inputs in BIDS<https://bids-specification.readthedocs.io/en/latest/> format.

What might be the best way to learn how qMRI interfaces with BIDS. I am not familiar with BIDS.

>Bottomline, I would lean towards leaving registration software/method choice to your discretion.

Elastix is the software which would be most helpful. A matlab wrapper is available so I can stay within the matlab environment. My plan is to merge features of qMRI with sc toolbox: for longitudinal analysis, I would like to use the features provided by sc toolbox (segmentation, registration to template, motion correction) with qMRI (quantification). I am not sure if this has been looked into previously? I am interested in metastatic cancer, which are typically located in the spine, or pelvis bone. Thank you From: Agah ***@***.******@***.***>> Sent: Friday, April 23, 2021 11:32 AM To: qMRLab/qMRLab ***@***.******@***.***>> Cc: Mazaheri Tehrani, Yousef/Medical Physics ***@***.******@***.***>>; Mention ***@***.******@***.***>> Subject: [EXTERNAL] Re: [qMRLab/qMRLab] Pre-processing features (#444) I am sorry if this seems outside of the more standard use of the software but the many modules make it an attractive choice qMRI for pelvic bone imaging sounds cool, nothing to be sorry about :) OK, in your case, I think, you'd like to perform some volume alignment between qMRI input pairs (e.g. multiple flip angle images). Given the anatomy, I don't have much experience. How much your input pairs suffer from respiratory motion would be a good factor to consider. But if you have a preferred tool, we can bring it in. I would suggest organizing your inputs in BIDS<https://bids-specification.readthedocs.io/en/latest/> format (the name of the standard implies brain imaging, but that's OK :) ). This is the format our workflows recognize. Bottomline, I would lean towards leaving registration software/method choice to your discretion. You may want to use ANTs, Elastix, FSL ... many options out there. Have you tried any so far? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#444 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATZ2TJJSJURLJ6F3P73S3TTTKGHGHANCNFSM43OWMJYQ>. *** Only open attachments or links from trusted senders. Report phishing to ***@***.******@***.***> *** ===================================================================== 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.

[agahkarakuzu]

@JoeNYC1 can you give a specific example? Using each software in its own environment with the latest stable versions would make a much better practice.

You can take take outputs from one software and use it as an input for the other one. Usually combining software at this level works well. Do you need something more involved?

[agahkarakuzu]

That'd be also helpful if you can respond from GitHub instead of email :)

[JoeNYC1]

Ok. thank you very much.

[jcohenadad]

Is there a way to connect qMRI capabilities with spinal cord toolbox? Would this need to be done with the python implementation of sc toolbox or with the older matlab version?

You can call SCT as a UNIX command from Matlab using the unix() function. Here is a tip if you are using a mac, and here is a conversation from a user who wrapped SCT commands within Matlab. In any case, I strongly recommend you always use the latest version of SCT.

[JoeNYC1]

Thank you - I will follow up on your links. I apologize for not using the github platform to raise my questions. From: Julien Cohen-Adad ***@***.***> Sent: Thursday, April 29, 2021 12:08 PM To: qMRLab/qMRLab ***@***.***> Cc: Mazaheri Tehrani, Yousef/Medical Physics ***@***.***>; Mention ***@***.***> Subject: [EXTERNAL] Re: [qMRLab/qMRLab] Pre-processing features (#444) Is there a way to connect qMRI capabilities with spinal cord toolbox? Would this need to be done with the python implementation of sc toolbox or with the older matlab version? You can call SCT as a UNIX command from Matlab using the unix() function. Here<https://spinalcordtoolbox.com/en/latest/user_section/installation.html#matlab-integration-on-mac> is a tip if you are using a mac, and here<spinalcordtoolbox/spinalcordtoolbox#405> is a conversation from a user who wrapped SCT commands within Matlab. In any case, I strongly recommend you always use the latest version of SCT. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#444 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATZ2TJOG3N36KOE4Z4STIULTLF74FANCNFSM43OWMJYQ>. *** Only open attachments or links from trusted senders. Report phishing to ***@***.******@***.***> *** ===================================================================== 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.