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

---
Joo-won Kim, Ph.D.
Postdoctoral Fellow
Translational and Molecular Imaging 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
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 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 you include some matched screenshots of the uncorrected, offline-corrected, 
and scanner-corrected volumes, we can maybe help evaluate the difference.


On Mon, Apr 9, 2018 at 4:09 AM, Kristian Loewe 
<k...@kristianloewe.com<mailto:k...@kristianloewe.com>> wrote:
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 Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>>:
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 dcm2niix add "-x n" and for dcm2nii you can
add "-x N -r N"
2. We also usually use "fslreorient2std <origT1> <origT1>_new and then
gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=>
 on <origT1>_new

-Keith


On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe 
<k...@kristianloewe.com<mailto:k...@kristianloewe.com>>
wrote:
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 suffix), I proceeded to compare the result with the
Siemens-corrected T1 image. I expected that they would look very
similar but in fact they look quite different. I am wondering if this
is to be expected to some degree because of differences in the
correction algorithms or what else might be the reason for this. Could
it be the case, for example, that the wrong center is being used for
some reason?

I have tried this for a T1 image acquired on a Verio and another one
from a Prisma using

   
gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=>
 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad
-n

and

   
gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=>
 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS82.grad -n

respectively.

I would really appreciate any help or advice you can provide.

Cheers,

Kristian


Quoting Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>>:

> 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: <scanname> and <scanname>_ND.  ND means "No
> Distortion [Correction]".. .A very confusing choice of acronym.  You can
> then compare the online corrected (not _ND) and offline using gradunwarp.
>
> -Keith
>
>
> On Wed, Oct 19, 2016 at 4:44 PM, Glasser, Matthew 
> <glass...@wustl.edu<mailto:glass...@wustl.edu>>
> wrote:
>
>> 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: 
>> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
>>  on behalf of Antonin
Skoch <
>> a...@ikem.cz<mailto:a...@ikem.cz>>
>> Date: Wednesday, October 19, 2016 at 4:27 PM
>> To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
>> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] gradient nonlinearity correction question
>>
>> Dear experts,
>>
>> during the set-up of gradunwarp scripts, it came to my mind, why scanner
>> vendors standardly do not perform gradient nonlinearity correction
directly
>> on the scanner as part of on-line image reconstruction system (i.e. ICE
in
>> Siemens)?
>>
>> Regards,
>>
>> Antonin Skoch
>>
>>
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