qi ssfp_ellipse

[atl404]

Would it be possible to post an example JSON file for qi ssfp_ellipse?

Thanks.

[spinicist]

Hello,

Apologies, this was missing from the docs. I've added it in this [commit] (https://github.com/spinicist/QUIT/commit/d39b5394b7afd68e3b98836604fbdbb916e90b23#diff-b1a9cca87b23c0eac392fdc91661ed4d).

Is this clear? Let me know if it works!

[atl404]

Thanks, the program ran without problem but I think I probably messed something up as images are either noisy (g) or just noise (the rest). I think I need to check if I correctly converted the phase steps to frequency offsets (as this is what is entered at the scanner). One other question, in your experience are 3 pairs sufficient or is it worthwhile to acquire more images?

Thanks.

From: Tobias Wood notifications@github.com Sent: Wednesday, March 25, 2020 4:07 PM To: spinicist/QUIT QUIT@noreply.github.com Cc: Jones, Richard richard.jones@choa.org; Author author@noreply.github.com Subject: Re: [spinicist/QUIT] qi ssfp_ellipse (#25)

External sender. Use caution with links and attachments.

Hello,

Apologies, this was missing from the docs. I've added ithttps://quit.readthedocs.io/en/latest/Docs/Relaxometry.html#qi-ssfp-ellipse in this [commit] (d39b539#diff-b1a9cca87b23c0eac392fdc91661ed4dhttps://github.com/spinicist/QUIT/commit/d39b5394b7afd68e3b98836604fbdbb916e90b23#diff-b1a9cca87b23c0eac392fdc91661ed4d).

Is this clear? Let me know if it works!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/spinicist/QUIT/issues/25#issuecomment-604058232, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO5Y45XGOKTLTRLL3JXWDX3RJJP5TANCNFSM4LS7RNMA.

[spinicist]

Hello,

3 pairs spaced equally (so 60 degrees between each increment) were sufficient for my paper. However, the original PLANET authors used 5 pairs (10 data points).

If you can put the images on a service I can download them from, I'm happy to take a quick look.

[atl404]

Hi there,

Richard Jones (coeurdelion2@protonmail.com) invited you to view the file " Transfer.zip " on Dropbox.

Richard said: "PLANET data (see e-mail for details). Thanks, Richard"

View file1

Enjoy! The Dropbox team Richard and others will be able to see when you view this file. Other files shared with you through Dropbox may also show this info. Learn more2 in our help center.

[atl404]

Thanks for the offer, which I’m happy to take advantage of. I’ll put the data on dropbox shortly, the rest of the relevant information is :-

Data acquired on a 3T Philips Ingenia scanner, TR=5msec. Phase offsets implemented using frequency offsets in the standard user interface, phase offsets of -2•••• -•••• •• •••• 2•••• •, which corresponded to frequency offsets of -66.67, -33.33, 0, 33.33, 66.67 and 100.0 Hz respectively. Magnitude and phase data saved on the scanner, converted from DICOM to NIFIT using dcm2nii, the resulting magnitude and phase NIFTI files were converted to complex NIFTI using your qicomplex routine, these were then concatenated into a single file. I’ve also included the magnitude and phase data for one offset and the complex data for this offset created using both quit & fslcomplex and the result of subtracting the two complex data sets (which wasn’t zero). The magnitude images were summed and bet was used to create a brain mask from the summed data set. Let me know if I’ve forgotten anything.

Thanks in advance,

Richard

From: Tobias Wood notifications@github.com Sent: Saturday, March 28, 2020 9:20 AM To: spinicist/QUIT QUIT@noreply.github.com Cc: Jones, Richard richard.jones@choa.org; Author author@noreply.github.com Subject: Re: [spinicist/QUIT] qi ssfp_ellipse (#25)

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Hello,

3 pairs spaced equally (so 60 degrees between each increment) were sufficient for my paperhttps://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.28149. However, the original PLANET authors used 5 pairs (10 data points).

If you can put the images on a service I can download them from, I'm happy to take a quick look.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/spinicist/QUIT/issues/25#issuecomment-605446601, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO5Y45XARBH3TK6C37OQAULRJX2QVANCNFSM4LS7RNMA.

[atl404]

Hi there,

In case you missed it, Richard Jones (coeurdelion2@protonmail.com) shared "Transfer.zip" with you on Dropbox.

Richard said: "PLANET data (see e-mail for details). Thanks, Richard"

View on Dropbox1

Thanks!

• The Dropbox Team

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[spinicist]

Posting here for posterity as the problem was solved via e-mail: The input phase images (from a Philips scanner) had a scaling factor of 1000 (i.e. range was roughly -3141 to +3141). They needed to be divided by 1000 to get a range of -pi to +pi before conversion to complex and processing.