Combining multiple b0
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Farzan
Jan 26, 2016, 2:54:29 PM1/26/16
to Diffusion-imaging
Dear all,
Since acquiring of multiple b0 image is recommended, I want to try it. As I checked on Siemens 3T Trio, acquisition of multi b0 images simultaneity is impossible. I mean that for 5 b0 image I should run the DWI protocol (with 1 b-value) 5 times. Would you please let me know if I am wrong or there is another way to do it?
My second question is related to the first one. If I acquired 5 b0 image separately, how could I combine them with other DW images?As in DTI software packages, one Nifti file should be uploaded which is containing all DWIs, what should I do with 5 different b0 images and 1 DWI (in N gradient direction)?
I would greatly appreciate any help you can give me.
Thank you in advance
Since acquiring of multiple b0 image is recommended, I want to try it. As I checked on Siemens 3T Trio, acquisition of multi b0 images simultaneity is impossible. I mean that for 5 b0 image I should run the DWI protocol (with 1 b-value) 5 times. Would you please let me know if I am wrong or there is another way to do it?
My second question is related to the first one. If I acquired 5 b0 image separately, how could I combine them with other DW images?As in DTI software packages, one Nifti file should be uploaded which is containing all DWIs, what should I do with 5 different b0 images and 1 DWI (in N gradient direction)?
I would greatly appreciate any help you can give me.
Thank you in advance
Do Tromp
Jan 26, 2016, 5:48:48 PM1/26/16
to Farzan, Diffusion-imaging
Hi,
I am aware of this issue with Siemens scanners, and as far as I know your option is a good way of dealing with it (although anyone with Siemens experience please interject if there are better options).
If you want to merge different nifti files you can use the FSL toolbox, specifically fslmerge will do the trick.
Example code:
flsmerge -t merged_output b0_1.nii b0_2.nii b0_n.nii dwi.nii
Best of luck,
~Do
Farzan
Jan 27, 2016, 1:16:45 AM1/27/16
to Diffusion-imaging
Dear Do,
Thank you very much. I thought fslmerge is just can be used to concatenate multiple 3D files and create a single 4D image file or in multiple b0 images with different phase encode direction.
Now, I'll try it. Thanks
Best Regards
Best Regards
Thank you very much. I thought fslmerge is just can be used to concatenate multiple 3D files and create a single 4D image file or in multiple b0 images with different phase encode direction.
Now, I'll try it. Thanks
Best Regards
Best Regards
Samuel A. Hurley
Feb 13, 2016, 5:42:06 PM2/13/16
to Farzan, Diffusion-imaging
Hi Farzan,
If it is not too late, I would suggest modifying the DiffusionVectors.txt (or DiffusionVectors.dvs) file located in C:\MedCom\MrCustomer\seq with a custom set of diffusion encoding directions. If you let me know the number of directions and number of b=0 images you want, I can generate an optimal point set for you to use in future studies.
For a study that has already started and is still ongoing, I would suggested that you do NOT change the parameteres midway through.
Best,
-Sam
---
Samuel A. Hurley, PhD
MRI Physics Support Scientist
FMRIB Centre, University of Oxford
Telephone: +44 (0) 1865 222733
Farzan
Feb 14, 2016, 1:20:19 AM2/14/16
to Diffusion-imaging, f.keyv...@gmail.com
Dear Samuel,
Thank you very much.
I'm going to acquire images in 64 direction with b=3000 (HARDI) and three b0 images. This coming Tuesday, my new study is started. Would you please give me more information about your suggestion? I don't understand how it's possible.
And as an another question, would you please let me know if these parameters are suitable for HARDI? Considering SNR, what is optimal b value, 2500 or 3000?
Best Regards
Thank you very much.
I'm going to acquire images in 64 direction with b=3000 (HARDI) and three b0 images. This coming Tuesday, my new study is started. Would you please give me more information about your suggestion? I don't understand how it's possible.
And as an another question, would you please let me know if these parameters are suitable for HARDI? Considering SNR, what is optimal b value, 2500 or 3000?
Best Regards
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