export from convertor failed

Question

export from convertor failed

Closed this issue 3 years ago · 12 comments

I am experiencing some problems with importing several of the scans. Most of the scans are correctly converted from Bruker files to Nifti+JSON files, but for our T2 TurboRARE high resolution files, I get a message that the export failed with an error such as this:

java.lang.NumberFormatException: For input string: "@15*(1)"

I am working in Windows 10, using Matlab R2020b and MRI Files Manager 20.2.2a.

Answer 1 · 2021-04-20T16:28:08.000Z

Hi,

Thank you for your feedback.
We will try to solve your problem asap.
Could you send us at least a single dataset via a dropbox link (or other)?

thank you,
Benjamin

Answer 2 · 2021-04-21T13:01:02.000Z

Hi,
thank you for the dataset.
I have the same issue on my side. I also observed an error in the conversion of perfusion_FAIR_EPI sequence (there is a mix of images between the 5 dimensions).
I will ask the developer of this import software to work on it.

@montigno could you please have a look to this data. There are 2 conversions problems

for the T2 TurboRARE high resolution (no conversion at all)
for the perfusion_FAIR_EPI (there is one conversion but images are mixed).
you will be able to find the data here: https://filesender.renater.fr/?s=download&token=b46ace1b-0833-4889-839e-ec4bb59de15d

We will get back to you asap.

best,

Answer 3 · 2021-04-22T06:18:38.000Z

Thank you!

Answer 4 · 2021-04-26T08:51:57.000Z

Hi,

mri_conv is compatible with Paravision 5 and 6, not with Paravision 360 but i am modifying the code to make it compatible, i think it will not take much time.

I'll keep you informed

best,

Olivier M.

Answer 5 · 2021-04-29T15:18:55.000Z

Hi Olivier,

Great, thank you!

Best,
Elsa

Answer 6 · 2021-05-04T12:57:19.000Z

Hi,

I put a new version of mri_conv in the 'dev' branch, it is compatible with Paravision360 but other bugs may appear.
I let Benjamin put the software in the master branch.

Best,

Olivier

Answer 7 · 2021-05-04T13:10:59.000Z

Hi,

we have to test this code before to merge it to the master.
But @eckuijper, you can download the branch 'dev' here: https://github.com/nifm-gin/MP3/tree/dev

Let us know if it works.

best,
Benjamin

Answer 8 · 2021-05-13T17:40:12.000Z

Dear Benjamin and Oliver,

Thank you very much! The conversion of the raw data works now, the issue with the T2 TurboRARE high resolution and perfusion_FAIR_EPI scans is solved.
However, we experience a problem with the conversion of the parameter maps of the T2star MGE scans, these are now not correctly loaded (example image attached). Have you seen this problem before?

Kind regards,
Elsa

Answer 9 · 2021-05-17T06:50:15.000Z

Dear Elsa,

I solved the problem but I have to see with Benjamin for the intensity of the image, it seems high to me but it is perhaps normal.
We keep you informed.

Best regards,

Olivier

Answer 10 · 2021-05-18T12:19:36.000Z

Dear Elsa,

I put a new version of mri_conv (21.6.1a) in the 'dev' branch (I solved the intensity problem).
You can download it here: https://github.com/nifm-gin/MP3/tree/dev.

Best,

Olivier

Answer 11 · 2021-05-18T14:33:53.000Z

Dear Olivier,

Great, thank you! I will download and try it!

Best,
Elsa

Answer 12 · 2021-05-19T09:37:57.000Z

Dear Olivier,

I just checked the upload of the T2star parameter maps and the problem is indeed solved :) Thank you!

Best,
Elsa