Re: [HCP-Users] gradient nonlinearity correction question

some plots of the T1 phantom data: >>>> >>>> T1_ND*.png - uncorrected images >>>> T1*.png    - scanner-corrected images >>>> T1_ND_gdc*.png - offline-corrected images >>>> >>>> Cheers, >>>> >>>> Kristian &

Re: [HCP-Users] gradient nonlinearity correction question

gt;> > Have you moved table? If you moved the table, you should manually >> > subtract it from qform, sform, and/or affine matrix in the nifty >> > header. >> > >> > Best, >> > Joo-won >> > >> &g

Re: [HCP-Users] gradient nonlinearity correction question

s successfully >>> cancelled. I apologize if you are receiving this twice now. >>> >>> >>> Quoting "Kim, Joo-won" <joo-won....@mssm.edu >>> <mailto:joo-won@mssm.edu>>: >>> >>>> Hi Kristian, >>>> >>&

Re: [HCP-Users] gradient nonlinearity correction question

Institute > > Icahn School of Medicine at Mount Sinai > > > > > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Keith > > Jamison <kjami...@umn.edu> > > Date: Monday, April 9, 2018 at 10:36 AM >

Re: [HCP-Users] gradient nonlinearity correction question

;>> Hi Kristian, >>> >>> Have you moved table? If you moved the table, you should manually >>> subtract it from qform, sform, and/or affine matrix in the nifty >>> header. >>> >>> Best, >>> Joo-won >>> >>>

Re: [HCP-Users] gradient nonlinearity correction question

t from qform, sform, and/or affine matrix in the nifty >> header. >> >> Best, >> Joo-won >> >> --- >> Joo-won Kim, Ph.D. >> Postdoctoral Fellow >> Translational and Molecular Imaging Institute >> Icahn School of Medicine at Mount Sinai >> >> >

Re: [HCP-Users] gradient nonlinearity correction question

> To: Kristian Loewe <k...@kristianloewe.com> > Cc: HCP Users <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] gradient nonlinearity correction question > > First make sure you're using the right coefficient file, copied > directly

Re: [HCP-Users] gradient nonlinearity correction question

umn.edu> > Date: Monday, April 9, 2018 at 10:36 AM > To: Kristian Loewe <k...@kristianloewe.com> > Cc: HCP Users <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] gradient nonlinearity correction question > > First make sure you're using the right coefficien

Re: [HCP-Users] gradient nonlinearity correction question

From: <hcp-users-boun...@humanconnectome.org> on behalf of Keith Jamison <kjami...@umn.edu> Date: Monday, April 9, 2018 at 10:36 AM To: Kristian Loewe <k...@kristianloewe.com> Cc: HCP Users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] gradient nonlinearity co

Re: [HCP-Users] gradient nonlinearity correction question

First make sure you're using the right coefficient file, copied directly from the scanner. The Prisma should have a file called coeff_AS82.grad, so the one you used in your *second* command above should be correct. Second is to be absolutely sure your input is the uncorrected volume (*_ND). If

Re: [HCP-Users] gradient nonlinearity correction question

Thanks Keith, Cropping is turned off by default in the version of dcm2niix that I'm using but I re-ran the conversion with "-x n" anyway. I also used fslreorient2std as per your suggestion. Unfortunately, the result is still the same. Do you have any other ideas? Cheers, Kristian

Re: [HCP-Users] gradient nonlinearity correction question

Some problems can arrise if the NIFTI files are unexpectedly manipulated prior gradient_unwarp. Two things to check: 1. dcm2nii and dcm2niix has options to perform additional processing like reorienting or cropping, some of which may be enabled by default. Make sure those are all DISABLED. (for

Re: [HCP-Users] gradient nonlinearity correction question

Hi, I would like to use gradunwarp for offline gradient nonlinearity correction of some data acquired on our local Siemens scanners. I used dcm2niix to convert the dicom data to nifti format. After applying gradunwarp to a T1 image in nifti format (the one that originally has the _ND

Re: [HCP-Users] gradient nonlinearity correction question

FYI, when available, you can enable it on the scanner in the "Resolution->Filter" tab with the "Distortion Correction" checkbox. It's often used for structural scans like MPRAGE, where you will see two DICOM folders in the output: and _ND. ND means "No Distortion [Correction]".. .A very

Re: [HCP-Users] gradient nonlinearity correction question

Some do for some sequences, but because it is not uniformly applied and because they are likely not to use optimal interpolation algorithms, we prefer to do offline correction. Peace, Matt. From: > on behalf