Load T1 in Tarquin

[Lotfi Kesraoui]

Hi my dears, 

I am trying to load a T1 image on Tarquin 4.3.10 after having processed the MRS data but it's not working. I am clicking on the « Load MRI » button but nothing happens. Did one of you had already this problem ? 

Thank you ! 

Lotfi 

[Martin Wilson]

Hi Lotfi,

Does this only happen with a particular MRS data file?

Martin

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[Lotfi Kesraoui]

Hi Martin , 

Our MRS data are in the format .SDAT and .SPAR from a Philips scanner. 

For the  « Load MRI » button , I see it on the GUI but when I click on it there is no window opening. It’s as if the button is deactivated. We tried on a MAC and a PC but in the two cases it was not working. 

Thank you for your help ! 

Lotfi Kesraoui,

Le jeudi 16 mars 2017 04:56:24 UTC-4, Martin Wilson a écrit :

Hi Lotfi,

Does this only happen with a particular MRS data file?

Martin

On 13 March 2017 at 14:40, Lotfi Kesraoui <lotfik...@gmail.com> wrote:
> Hi my dears,
>
> I am trying to load a T1 image on Tarquin 4.3.10 after having processed the
> MRS data but it's not working. I am clicking on the « Load MRI » button but
> nothing happens. Did one of you had already this problem ?
>
> Thank you !
>
>
> Lotfi
>
>
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[Lotfi Kesraoui]

Dear Martin, 

Is possible that the problem is related to the particular version I am using (4.3.10) ? I didn't try to load our SDAT/SPAR data in other versions of Tarquin. 

Thank you  ! 

Lotfi 

Le jeudi 16 mars 2017 04:56:24 UTC-4, Martin Wilson a écrit :

Hi Lotfi,

Does this only happen with a particular MRS data file?

Martin

On 13 March 2017 at 14:40, Lotfi Kesraoui <lotfik...@gmail.com> wrote:
> Hi my dears,
>
> I am trying to load a T1 image on Tarquin 4.3.10 after having processed the
> MRS data but it's not working. I am clicking on the « Load MRI » button but
> nothing happens. Did one of you had already this problem ?
>
> Thank you !
>
>
> Lotfi
>
>
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[Martin Wilson]

Hi Lofti,

I doubt that the version makes a difference. Do you have the same
problem with the example data provided with TARQUIN?

Martin

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[Lotfi Kesraoui]

Hi Martin, 

Yes I tried also with the example data and it's the same problem. 

Thank you ! 

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[Martin Wilson]

Ahh, I think you must be using the quick fit dialogue to load the
data. Use the advanced fit one instead...



Martin

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[Lotfi Kesraoui]

Dear Martin, 

Yes that's true when I do the advanced fit, I can then click on the « Load MRI » button and I can select the T1 image. But when I choose the T1 in DICOM format, an error message appears : « Problem loading MRI. ». 

I tried also to load the T1 image in Nifti format, but it's not working. Our T1 is a 3D image, does it have to be in 2D ? 

Or maybe it should not be in DICOM or Nifti format ? 

Thanks again, 

Lotfi Kesraoui 

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[Martin Wilson]

Hi Lotfi,

Try having only the DICOM files that correspond to the T1 image in
that directory. I think TARQUIN automatically tries to read all the
files in that particular folder, if you have T2s etc you'll probably
get an error.

Martin

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[Lotfi Kesraoui]

Dear Martin, 

Finally it was not working because my DICOM T1 was in 3D and not in 2D. So I used Slicer to do the conversion with the module CreateaDicomSeries (https://www.slicer.org/wiki/Modules:CreateaDicomSeries-Documentation-3.6). 

And as you advised me I kept only DICOM files that correspond to the T1 image in the directory. 

It works , thank you!  

Lotfi 

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[Lotfi Kesraoui]

Dear Martin, 

Finally it was not working because my DICOM T1 was in 3D and not in 2D. So I used Slicer to do the conversion with the module CreateaDicomSeries (https://www.slicer.org/wiki/Modules:CreateaDicomSeries-Documentation-3.6). 

And as you advised me I kept only DICOM files that correspond to the T1 image in the directory. 

It works , thank you!  

Lotfi 

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[Martin Wilson]

Thanks for the update. Nice to see persistence paying off!

Martin

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[Lotfi Kesraoui]

You welcome. Yes that's true! 

Actually, I have a quick question : is it possible to see the T1 image in Axial view ? For now, it's in Sagittal view (picture attached). 

Thank you ! 

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[Andreas Bartsch]

Hi Lotfi,

can you make the original DICOMs and the MRS (anonymized) available for download?

Is it Siemens?

Cheers,

Andreas

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[Lotfi Kesraoui]

Dear Andreas, 

Yes, you can download the data from this link : https://drive.google.com/open?id=0B6G8tmqC40L1TUpFLUZOYndVVEU

It's in Philips format. I think the problem is related to the conversion of the T1 from DICOM 3D to DICOM 2D when I use Slicer (CreateaDicomSeries module). The slices generated are in Sagittal view. I didn't find how to generate slices in Axial view. Do you have an idea ? 

Thank you for you help ! 

Lotfi 

[Andreas Bartsch]

Hi,

I have no experience with Philips but can you reslice on the scanner and use this?

Cheers,

Andreas

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[Lotfi Kesraoui]

Hi, 

No I cannot reslice on the scanner. I have to use a software to do that. I found Slicer doing a good job to generate slices in Sagittal view , but I didn't find how to generate slices in Axial view. 

Thank you! 

Lotfi 

[samira raminfard]

Hi,

I have got another problem by loading MRI. The MRS grid not registered correctly on T1 image. 

This happen just for Data which acquired from GE scanner.

I have attached a screenshot from the position of grid on T1.

Regards

Samira

[Martin Wilson]

Hi Samira,

Yes, I'm afraid I didn't get round to extracting the geometry
information from GE p files. This might be helpful:

https://sourceforge.net/projects/sivic/

Martin

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[samira raminfard]

Hi Martin,

Thank you very much for your suggestion. 

Yes, I will use it.

Bests

Samira

[Neda Naderi]

Dear Martin,

Hi

I got the same problem as Samira's (unable to register MRSI grid on MR image) in tarquin 11(linux). the data is pfile from GE scanner. How can we tackle this problem in tarquin 11???

I would appreciate your reply

Regards,

Neda