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Hi Carlotta, The preprocessing steps that were applied by FEAT are summarised in the report file (your_analysis.feat/report.html). However, for the most part, it is your responsibility to keep track of both the image acquisition parameters, and the preprocessing/analysis steps that you have chosen to apply to the data. Cheers, Paul On 25 June 2018 at 09:15, Carlotta Fabris <[log in to unmask]> wrote: > Hi Matthew, sorry to bother you again, but I have another question. > > My colleges would like to know how they could retrieve the parameters and > the steps I did for the preprocessing, once I give them the files produced > by FEAT. What can I tell them? > > Thanks, > 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> > <#m_1017025069472575252_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > 2018-06-20 17:57 GMT+02:00 Matthew Webster <[log in to unmask]> > : > >> 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 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1