Hello Carlotta,This question is very general: The standard FEAT pre-processing does use a number of the parameters you list as they are part of the NIFTI header. B0 unwarping is advised, but a moot point if fieldmaps are not available. If you are unfamiliar with FEAT and FSL you might want to consider attending the San Diego FSL course in late October this year, which will be a great introduction to FSL and image analysis.
Hope this helps,Kind Regards,Matthew
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 20 Jun 2018, at 09:10, Carlotta Fabris <[log in to unmask]> wrote:
Thanks for your answer Rachelle!
The parameters I talk about are tge acquisition parameters like, TR, TE, voxel size, etc.
My colleges are worried that the steps of the FSL preprocessing are not tge best option because we don't put as input those parameters.
I hope it is more clear now!Thank you a lot,Carlotta.
Hi Carlotta,
I'm not the most experienced with this, so I'm not sure which parameters you're referring to. Can you give me an example of which parameters you're wondering about?
The preprocessing step will include blurring, motion corrections, B0 corrections, etc. (items related to correcting your images before you analyze them). After you complete these steps (or chose to skip them), you can analyze your data based on your design (i.e. you can specify the number of groups or conditions you have).
Best wishes,Rachelle
On Mon, Jun 18, 2018 at 4:32 AM, Carlotta Fabris <[log in to unmask]> wrote:
Hi Rachelle!
Thank you for the clear answer, but I still have some doubts regarding the preprocessing pipeline.
I am not sure that the pipeline I did (standard pipeline for task-based fmri data) reflects the parameters I have. Are the parameters in the preprocessing or it is not necessary to insert them in the preprocessing?
I hope my question is clear,Carlotta.
2018-06-14 19:21 GMT+02:00 Rachelle Ho <[log in to unmask]>:
Hi Carlotta,
Fieldmap unwarping is helpful but not necessary. If you have B0 scans, you'll be able to create a fieldmap with FSL. The fieldmap corrections help fix any distortions you see in your functional scans. If you register your functional images to an anatomical and find that the functional image looks odd / warped / doesn't match the boundaries of the anatomical, fieldmap corrections can help correct and improve the quality of your data before you analyze it.
Functional / EPI data is susceptible to distortions in the magnetic field, which causes some of the distortions to the shape of your images. That's why we collect information about the fieldmap when the data is acquired.
Hope this helps answer your questions.
Best wishes,Rachelle
On Thu, Jun 14, 2018 at 5:48 AM, Carlotta Fabris <[log in to unmask]> wrote:
Hi Matthew, sorry to bother you again, but I was wondering if the B0 unwarping is a necessary step in a preprocessing pipeline.
I am asking you this, because I never did it and I don't have a field map to put as input, but should I perform this step or is it required only in certain conditions?
The information I have on my data are these: Data were acquired on a 3 Tesla Siemens Vereo MRI scanner with a 32-channel birdcage radio frequency headcoil (neckcoil was not used, leaving 28 channels). For the functional scans, a 28 slice axial prescription (5 mm thickness) gave whole brain coverage. For each imaging run, a series of 190 gradient echo echoplanar volumes were acquired over each: TE = 35 ms, TR = 2000 ms, Flip Angle =75O, NEX = 1, BW = 100.0, FOV = 24mm, matrix =128 x 128 (in-plane resolution of 1.875mm2).
Thank you,
Carlotta.
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