Data dimension mismatch (reading from .cpx file)

[rsumesh]

Hi,
I am relatively new to Gpilab. I am trying to read in a cpx file. I know that it contains 3D information and also know the expected 3d matrix size. However, when I load the .cpx file through philips data reader node, I get information from only one slice, and not the entire volume. The info pane also confirms that what is read in is just a single slice and not a volume. I have tried to switch on and off a lot of options, but the end results in the same. Is this a known issue? If so, is there a work around to fix this?

With Regards,
Umesh

[jplij]

Hi, I am relatively new to Gpilab. I am trying to read in a cpx file. I know that it contains 3D information and also know the expected 3d matrix size. However, when I load the .cpx file through philips data reader node, I get information from only one slice, and not the entire volume. The info pane also confirms that what is read in is just a single slice and not a volume. I have tried to switch on and off a lot of options, but the end results in the same. Is this a known issue? If so, is there a work around to fix this?

With Regards, Umesh

Hey Umesh,
I have a similar situation as you. May I ask how did it work out in the end? Thank you in advance.

[rsumesh]

Hi, I did not manage to solve this directly. As far as I remember, I reacquired the data and wrote the data to par/rec or xml/rec and took it from there. Sorry, I won't be able to help you with this. With Regards, Umesh

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On Wed, 17 Nov 2021 at 18:16, JP ***@***.***> wrote: Hi, I am relatively new to Gpilab. I am trying to read in a cpx file. I know that it contains 3D information and also know the expected 3d matrix size. However, when I load the .cpx file through philips data reader node, I get information from only one slice, and not the entire volume. The info pane also confirms that what is read in is just a single slice and not a volume. I have tried to switch on and off a lot of options, but the end results in the same. Is this a known issue? If so, is there a work around to fix this? [image: gpilab_issue] <https://user-images.githubusercontent.com/13951606/68527246-e5e88a80-030a-11ea-9749-d9ac2d7ef102.png> With Regards, Umesh Hey Umesh, I have a similar situation as you. May I ask how did it work out in the end? Thank you in advance. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKOE5XIVGO25QVX632ZQDLUMOP3TANCNFSM4JLFPDZQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[sandeepganji]

You are trying to read a prescan. The GPI Philips read node is not very well optimized for the B0-Prescan.
Is there a specific reason for reading the B0 Prescan?

[jplij]

You are trying to read a prescan. The GPI Philips read node is not very well optimized for the B0-Prescan. Is there a specific reason for reading the B0 Prescan?

s not very well optimized for the B0-Prescan.
Is there a specific reason for reading the B0 Prescan?

Hi, thank you for your reply. I am actually reading the SenseRefScan.cpx to get the k-space data for coil sensitivity estimation. Umesh's way works but with a magnitude image. Gyrotools might be an alternative, but not open source.

[sandeepganji]

Reading the coil sensitivity estimation from the SenseRefScan.cpx is a bit tricky, as the default SenseRefScan.cpx is a 700x700x560 mm3 FOV scan with very low resolution, multiple stacks and you have to do MPR & location adjustment based on your actual scan FOV. I would recommend for initial testing, perform your own coil ref scan using a FFE scan, matched to your actual scan FOV.