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fmriprep performs a field-map-less susceptibility correction ( http://fmriprep.readthedocs.io/en/latest/sdc.html), but I've never tried it. They do note that its experimental. -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX On Thu, Jun 14, 2018 at 12:32 PM, Carlotta Fabris <[log in to unmask]> wrote: > Very helpful thank you Rachelle! > > > Il Gio 14 Giu 2018, 19:22 Rachelle Ho <[log in to unmask]> ha scritto: > >> Hi Carlotta, >> >> Fieldmap unwarping is helpful but not necessary. If you have B0 scans, >> you'll be able to create a fieldmap with FSL >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fmrib.ox.ac.uk_primers_intro-5Fprimer_ExBox19_IntroBox19.html&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=O4Jiro7Q6tC1OYs1VodfEfe2xFNTbFezUhM5yk7rEAs&s=al4pKx66WdWBg3UtQD-9NFx3wblxUptAR_8tAMU2Yt4&e=>. >> 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 >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DFSL-26A-3D1&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=O4Jiro7Q6tC1OYs1VodfEfe2xFNTbFezUhM5yk7rEAs&s=qozWMh4802A9UC5nEVGXdwCPVbWPlsq4u8VWU6nmAGo&e=> >>> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DFSL-26A-3D1&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=O4Jiro7Q6tC1OYs1VodfEfe2xFNTbFezUhM5yk7rEAs&s=qozWMh4802A9UC5nEVGXdwCPVbWPlsq4u8VWU6nmAGo&e=> >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DFSL-26A-3D1&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=O4Jiro7Q6tC1OYs1VodfEfe2xFNTbFezUhM5yk7rEAs&s=qozWMh4802A9UC5nEVGXdwCPVbWPlsq4u8VWU6nmAGo&e=> > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1