search

nighres / nighres

Processing tools for high-resolution neuroimaging
http://nighres.readthedocs.io/en/latest/
Apache License 2.0
62 stars 41 forks source link

finding QSM #196

Open shaharEd opened 1 year ago

shaharEd commented 1 year ago

Hi, we try to make some volumetry with nighres. the database looks like that image the nighres command requests T1, T2* and QSM - which I believe are here, but I can't find them. could you help us? Thx Shahar

piloubazin commented 1 year ago

It looks like you have all the ingredients: the mp2rage gives you T1 directly, the t2star multiecho can be used to get T2* (flash_t2s_fitting in nighres) and QSM (using your favorite QSM package, I use tgv-qsm but only because the others are in matlab). Check the latest testing example (v1.5) for some qmri recobstruction code, too.

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: shaharEd @.> Sent: Tuesday, July 11, 2023 5:48:48 PM To: nighres/nighres @.> Cc: Subscribed @.***> Subject: [nighres/nighres] finding QSM (Issue #196)

Hi, we try to make some volumetry with nighres. the database looks like that [image]https://user-images.githubusercontent.com/104447628/252719305-899a3ef3-934a-42b1-b90f-26bdb316eea6.png the nighres command requests T1, T2* and QSM - which I believe are here, but I can't find them. could you help us? Thx Shahar

— Reply to this email directly, view it on GitHubhttps://github.com/nighres/nighres/issues/196, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AESNPWQETO2NDFV3COM5ASDXPVYWBANCNFSM6AAAAAA2GGX4H4. You are receiving this because you are subscribed to this thread.Message ID: @.***>

shaharEd commented 1 year ago

Just to make sure - which of the files I have to use in order to create the QSM?

piloubazin commented 1 year ago

the t2star_multiecho is likely a flash-type sequence: you can get the T2* from fitting the magnitude, and the QSM from processing the phase (often both magnitude and phase, depending on the method you use)