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Thanks and I will consider attending it! Thank you a lot, Carlotta. Il Mer 20 Giu 2018, 17:57 Matthew Webster <[log in to unmask]> ha scritto: > 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. > > Il Mar 19 Giu 2018, 19:05 Rachelle Ho <[log in to unmask]> ha scritto: > >> 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. >>> >>> >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Mail >>> priva di virus. www.avast.com >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> >>> >>> 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 >>>> <http://www.fmrib.ox.ac.uk/primers/intro_primer/ExBox19/IntroBox19.html>. >>>> 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. >>>>> >>>>> >>>>> ######################################################################## >>>>> >>>>> To unsubscribe from the FSL list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1