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:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Antonin Skoch mailto:a...@ikem.cz>>
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 confusin
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 suffi
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 dc
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
Quoting
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 y
From: on behalf of Keith Jamison
Date: Monday, April 9, 2018 at 10:36 AM
To: Kristian Loewe
Cc: HCP Users
Subject: 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 h
low
> Translational and Molecular Imaging Institute
> Icahn School of Medicine at Mount Sinai
>
>
> From: on behalf of Keith
> Jamison
> Date: Monday, April 9, 2018 at 10:36 AM
> To: Kristian Loewe
> Cc: HCP Users
> Subject: Re: [HCP-Users] gradient nonlinearity corr
tional and Molecular Imaging Institute
> Icahn School of Medicine at Mount Sinai
>
>
> From: on behalf of Keith
> Jamison
> Date: Monday, April 9, 2018 at 10:36 AM
> To: Kristian Loewe
> Cc: HCP Users
> Subject: Re: [HCP-Users] gradie
>> Best,
>> Joo-won
>>
>> ---
>> Joo-won Kim, Ph.D.
>> Postdoctoral Fellow
>> Translational and Molecular Imaging Institute
>> Icahn School of Medicine at Mount Sinai
>>
>>
>> From: on behalf of Keith
>> Jamison
>> Dat
> was too large). I am not sure if the first email was successfully
>> cancelled. I apologize if you are receiving this twice now.
>>
>>
>> Quoting "Kim, Joo-won" :
>>
>>> Hi Kristian,
>>>
>>> Have you moved table? If you moved the
and/or affine matrix in the nifty
> > header.
> >
> > Best,
> > Joo-won
> >
> > ---
> > Joo-won Kim, Ph.D.
> > Postdoctoral Fellow
> > Translational and Molecular Imaging Institute
> > Icahn
ges
>>>
>>> Cheers,
>>>
>>> Kristian
>>>
>>>
>>> PS:
>>> I am sending this email for the second time (apparently the attachment
>>> was too large). I am not sure if the first email was successfully
>>> cancelled. I apo
apologize if you are receiving this twice now.
>>
>>
>> Quoting "Kim, Joo-won" :
>>
>> > Hi Kristian,
>> >
>> > Have you moved table? If you moved the table, you should manually
>> > subtract
a:
>>>>
>>>> T1_ND*.png - uncorrected images
>>>> T1*.png - scanner-corrected images
>>>> T1_ND_gdc*.png - offline-corrected images
>>>>
>>>> Cheers,
>>>>
>>>> Kristian
>>>>
>>>>
&
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