Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

t's native space to the list. I'm going to
>>>> check that. Meanwhile, I asked our local MR team to acquire an
>>>> additional data set using a phantom. The difference between the
>>>> scanner-corrected image and the offline-corrected image is not as
>>>> striking in this case but it's visible. Based on the phantom data, I
>>>> am inclined to say that both corrections work reasonably well, even
>>>> though they are not exactly the same. I also tried the
>>>> offline-correction on some phantom EPI data and it seems to work well
>>>> as it (together with EPI distortion correction) restores the original
>>>> shape of the phantom pretty nicely.
>>>>
>>>> The differences between the correction variants applied to the
>>>> subject's data are actually rather small inside the brain but become
>>>> larger towards the neck, which is to be expected as the distance to
>>>> the magnetic isocenter becomes greater in that direction.
>>>> Nevertheless, I orginally thought that the differences between
>>>> scanner- and offline-corrected images would be smaller than that.
>>>>
>>>> Find attached 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
>>>>
>>>>
>>>> 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 apologize if you are receiving this twice now.
>>>>
>>>>
>>>> Quoting "Kim, Joo-won" <joo-won@mssm.edu
>>>> <mailto:joo-won@mssm.edu>>:
>>>>
>>>>> 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
>>>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Keith
>>>>> Jamison <kjami...@umn.edu <mailto:kjami...@umn.edu>>
>>>>> Date: Monday, April 9, 2018 at 10:36 AM
>>>>> To: Kristian Loewe <k...@kristianloewe.com 
>>>>> <mailto:k...@kristianloewe.com>>
>>>>> Cc: HCP Users <hcp-users@humanconnectome.org
>>>>> <mailto: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><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><mailto

Re: [HCP-Users] gradient nonlinearity correction question

[Glasser, Matthew]

That code uses trilinear interpolation by default, but you can output a
warpfield and use splines which should be much crisper.

Peace,

Matt.

On 4/11/18, 11:59 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Kristian Loewe" <hcp-users-boun...@humanconnectome.org on behalf of
k...@kristianloewe.com> wrote:

>Hi Joo-won,
>
>I am not sure, which one looks more anatomically reasonable. The
>scanner-corrected one looks a little bit more crisp compared to the
>offline-corrected, which appears a little more smooth by comparison.
>Perhaps this could have something to do with the interpolation algorithm
>used?
>
>Thanks for the information regarding the table position! That's good to
>know. It reports as 0\0\0, though.
>
>Cheers,
>
>Kristian
>
>
>On 11.04.2018 16:19, Kim, Joo-won wrote:
>> Hi Kristian,
>> 
>> Which one looks more reasonable, online or offline correction for
>>subject data?
>> 
>> On my data, dicom header (0019, 1014) contains table position.
>> 
>> Best,
>> Joo-won
>> 
>> On 4/11/18, 9:31 AM, "Kristian Loewe" <k...@kristianloewe.com> wrote:
>> 
>>  Hi Joo-won and Keith,
>>  
>>  I don't think that the table has been moved. Is there any
>>information
>>  somewhere in the dicom header to double-check this?
>>  
>>  I am using the coeff_AS82.grad file for the Prisma data (the second
>>  command). The first command was what I used for the Verio data.
>>Also,
>>  I double-checked that I am using the uncorrected volume as input.
>>  
>>  I am not sure if I am supposed/allowed to send screenshots of the
>>  actual data in the subject's native space to the list. I'm going to
>>  check that. Meanwhile, I asked our local MR team to acquire an
>>  additional data set using a phantom. The difference between the
>>  scanner-corrected image and the offline-corrected image is not as
>>  striking in this case but it's visible. Based on the phantom data,
>>I
>>  am inclined to say that both corrections work reasonably well, even
>>  though they are not exactly the same. I also tried the
>>  offline-correction on some phantom EPI data and it seems to work
>>well
>>  as it (together with EPI distortion correction) restores the
>>original
>>  shape of the phantom pretty nicely.
>>  
>>  The differences between the correction variants applied to the
>>  subject's data are actually rather small inside the brain but
>>become
>>  larger towards the neck, which is to be expected as the distance to
>>  the magnetic isocenter becomes greater in that direction.
>>  Nevertheless, I orginally thought that the differences between
>>  scanner- and offline-corrected images would be smaller than that.
>>  
>>  Find attached 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
>>  
>>  
>>  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 apologize if you are receiving this twice now.
>>  
>>  
>>  Quoting "Kim, Joo-won" <joo-won@mssm.edu>:
>>  
>>  > 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
>> 

Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

 uncorrected images
>>> T1*.png    - scanner-corrected images
>>> T1_ND_gdc*.png - offline-corrected images
>>>
>>> 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 apologize if you are receiving this twice now.
>>>
>>>
>>> Quoting "Kim, Joo-won" <joo-won....@mssm.edu 
>>> <mailto:joo-won@mssm.edu>>:
>>>
>>>> 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 
>>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Keith
>>>> Jamison <kjami...@umn.edu <mailto:kjami...@umn.edu>>
>>>> Date: Monday, April 9, 2018 at 10:36 AM
>>>> To: Kristian Loewe <k...@kristianloewe.com <mailto:k...@kristianloewe.com>>
>>>> Cc: HCP Users <hcp-users@humanconnectome.org 
>>>> <mailto: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><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><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  _new and then
>>>> gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py=DwQFaQ=shNJtf5dKgNcPZ6Yh64b-A=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE=>
>>>>  
>>>> on
>>>> _new
>>>>
>>>> -Keith
>>>>
>>>>
>>>> On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe
>>>> <k...@kristianloewe.com 
>>>> <mailto: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 

Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

Hi Joo-won,

I am not sure, which one looks more anatomically reasonable. The 
scanner-corrected one looks a little bit more crisp compared to the 
offline-corrected, which appears a little more smooth by comparison. 
Perhaps this could have something to do with the interpolation algorithm 
used?

Thanks for the information regarding the table position! That's good to 
know. It reports as 0\0\0, though.

Cheers,

Kristian


On 11.04.2018 16:19, Kim, Joo-won wrote:
> Hi Kristian,
> 
> Which one looks more reasonable, online or offline correction for subject 
> data?
> 
> On my data, dicom header (0019, 1014) contains table position.
> 
> Best,
> Joo-won
> 
> On 4/11/18, 9:31 AM, "Kristian Loewe" <k...@kristianloewe.com> wrote:
> 
>  Hi Joo-won and Keith,
>  
>  I don't think that the table has been moved. Is there any information
>  somewhere in the dicom header to double-check this?
>  
>  I am using the coeff_AS82.grad file for the Prisma data (the second
>  command). The first command was what I used for the Verio data. Also,
>  I double-checked that I am using the uncorrected volume as input.
>  
>  I am not sure if I am supposed/allowed to send screenshots of the
>  actual data in the subject's native space to the list. I'm going to
>  check that. Meanwhile, I asked our local MR team to acquire an
>  additional data set using a phantom. The difference between the
>  scanner-corrected image and the offline-corrected image is not as
>  striking in this case but it's visible. Based on the phantom data, I
>  am inclined to say that both corrections work reasonably well, even
>  though they are not exactly the same. I also tried the
>  offline-correction on some phantom EPI data and it seems to work well
>  as it (together with EPI distortion correction) restores the original
>  shape of the phantom pretty nicely.
>  
>  The differences between the correction variants applied to the
>  subject's data are actually rather small inside the brain but become
>  larger towards the neck, which is to be expected as the distance to
>  the magnetic isocenter becomes greater in that direction.
>  Nevertheless, I orginally thought that the differences between
>  scanner- and offline-corrected images would be smaller than that.
>  
>  Find attached 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
>  
>  
>  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 apologize if you are receiving this twice now.
>  
>  
>  Quoting "Kim, Joo-won" <joo-won@mssm.edu>:
>  
>  > 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
>  &

Re: [HCP-Users] gradient nonlinearity correction question

[Stephen Smith]

Hi - no, in my experience running the post-hoc correction should look virtually 
identical to the on-scanner correction.

Note that this will not be the case for 2D (eg EPI) data because on-scanner can 
only be done 2D - so that won't match post-hoc 3D correction.

Cheers.




> On 11 Apr 2018, at 17:51, Kristian Loewe <k...@kristianloewe.com> wrote:
> 
> Hi Michael,
> 
> Thanks for the suggestion! By default, we are using the 3D correction on 
> the scanner. But I applied the 2D correction to the ND data set 
> separately to see what it looks like. The result is different from both 
> the 3D-scanner-correction and the offline-correction but looks 
> reasonable too.
> 
> Is it the case that for HCP data the scanner-corrected images look 
> almost exactly the same as the offline-corrected images or is it 
> ok/normal for them to differ a bit, especially further away from the 
> isocenter?
> 
> Cheers,
> 
> Kristian
> 
> 
> On 11.04.2018 15:42, Harms, Michael wrote:
>> 
>> One thought: Are you sure you are using the “3D” (and not the “2D”) 
>> correction on the scanner?
>> 
>> --
>> Michael Harms, Ph.D.
>> 
>> ---
>> 
>> Associate Professor of Psychiatry
>> 
>> Washington University School of Medicine
>> 
>> Department of Psychiatry, Box 8134
>> 
>> 660 South Euclid Ave.Tel: 314-747-6173
>> 
>> St. Louis, MO  63110  Email: mha...@wustl.edu
>> 
>> On 4/11/18, 8:31 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
>> Kristian Loewe" <hcp-users-boun...@humanconnectome.org on behalf of 
>> k...@kristianloewe.com> wrote:
>> 
>> Hi Joo-won and Keith,
>> 
>> I don't think that the table has been moved. Is there any information
>> somewhere in the dicom header to double-check this?
>> 
>> I am using the coeff_AS82.grad file for the Prisma data (the second
>> command). The first command was what I used for the Verio data. Also,
>> I double-checked that I am using the uncorrected volume as input.
>> 
>> I am not sure if I am supposed/allowed to send screenshots of the
>> actual data in the subject's native space to the list. I'm going to
>> check that. Meanwhile, I asked our local MR team to acquire an
>> additional data set using a phantom. The difference between the
>> scanner-corrected image and the offline-corrected image is not as
>> striking in this case but it's visible. Based on the phantom data, I
>> am inclined to say that both corrections work reasonably well, even
>> though they are not exactly the same. I also tried the
>> offline-correction on some phantom EPI data and it seems to work well
>> as it (together with EPI distortion correction) restores the original
>> shape of the phantom pretty nicely.
>> 
>> The differences between the correction variants applied to the
>> subject's data are actually rather small inside the brain but become
>> larger towards the neck, which is to be expected as the distance to
>> the magnetic isocenter becomes greater in that direction.
>> Nevertheless, I orginally thought that the differences between
>> scanner- and offline-corrected images would be smaller than that.
>> 
>> Find attached 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
>> 
>> 
>> 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 apologize if you are receiving this twice now.
>> 
>> 
>> Quoting "Kim, Joo-won" <joo-won@mssm.edu>:
>> 
>>> 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@humanco

Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

Hi Michael,

Thanks for the suggestion! By default, we are using the 3D correction on 
the scanner. But I applied the 2D correction to the ND data set 
separately to see what it looks like. The result is different from both 
the 3D-scanner-correction and the offline-correction but looks 
reasonable too.

Is it the case that for HCP data the scanner-corrected images look 
almost exactly the same as the offline-corrected images or is it 
ok/normal for them to differ a bit, especially further away from the 
isocenter?

Cheers,

Kristian


On 11.04.2018 15:42, Harms, Michael wrote:
> 
> One thought: Are you sure you are using the “3D” (and not the “2D”) 
> correction on the scanner?
> 
> --
> Michael Harms, Ph.D.
> 
> ---
> 
> Associate Professor of Psychiatry
> 
> Washington University School of Medicine
> 
> Department of Psychiatry, Box 8134
> 
> 660 South Euclid Ave.Tel: 314-747-6173
> 
> St. Louis, MO  63110  Email: mha...@wustl.edu
> 
> On 4/11/18, 8:31 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Kristian Loewe" <hcp-users-boun...@humanconnectome.org on behalf of 
> k...@kristianloewe.com> wrote:
> 
> Hi Joo-won and Keith,
> 
> I don't think that the table has been moved. Is there any information
> somewhere in the dicom header to double-check this?
> 
> I am using the coeff_AS82.grad file for the Prisma data (the second
> command). The first command was what I used for the Verio data. Also,
> I double-checked that I am using the uncorrected volume as input.
> 
> I am not sure if I am supposed/allowed to send screenshots of the
> actual data in the subject's native space to the list. I'm going to
> check that. Meanwhile, I asked our local MR team to acquire an
> additional data set using a phantom. The difference between the
> scanner-corrected image and the offline-corrected image is not as
> striking in this case but it's visible. Based on the phantom data, I
> am inclined to say that both corrections work reasonably well, even
> though they are not exactly the same. I also tried the
> offline-correction on some phantom EPI data and it seems to work well
> as it (together with EPI distortion correction) restores the original
> shape of the phantom pretty nicely.
> 
> The differences between the correction variants applied to the
> subject's data are actually rather small inside the brain but become
> larger towards the neck, which is to be expected as the distance to
> the magnetic isocenter becomes greater in that direction.
> Nevertheless, I orginally thought that the differences between
> scanner- and offline-corrected images would be smaller than that.
> 
> Find attached 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
> 
> 
> 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 apologize if you are receiving this twice now.
> 
> 
> Quoting "Kim, Joo-won" <joo-won@mssm.edu>:
> 
>> 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 t

Re: [HCP-Users] gradient nonlinearity correction question

[Kim, Joo-won]

Hi Kristian,

Which one looks more reasonable, online or offline correction for subject data?

On my data, dicom header (0019, 1014) contains table position.

Best,
Joo-won

On 4/11/18, 9:31 AM, "Kristian Loewe" <k...@kristianloewe.com> wrote:

Hi Joo-won and Keith,

I don't think that the table has been moved. Is there any information  
somewhere in the dicom header to double-check this?

I am using the coeff_AS82.grad file for the Prisma data (the second  
command). The first command was what I used for the Verio data. Also,  
I double-checked that I am using the uncorrected volume as input.

I am not sure if I am supposed/allowed to send screenshots of the  
actual data in the subject's native space to the list. I'm going to  
check that. Meanwhile, I asked our local MR team to acquire an  
additional data set using a phantom. The difference between the  
scanner-corrected image and the offline-corrected image is not as  
striking in this case but it's visible. Based on the phantom data, I  
am inclined to say that both corrections work reasonably well, even  
though they are not exactly the same. I also tried the  
offline-correction on some phantom EPI data and it seems to work well  
as it (together with EPI distortion correction) restores the original  
shape of the phantom pretty nicely.

The differences between the correction variants applied to the  
subject's data are actually rather small inside the brain but become  
larger towards the neck, which is to be expected as the distance to  
the magnetic isocenter becomes greater in that direction.  
Nevertheless, I orginally thought that the differences between  
scanner- and offline-corrected images would be smaller than that.

Find attached 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


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 apologize if you are receiving this twice now.


Quoting "Kim, Joo-won" <joo-won@mssm.edu>:

> 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  _new and then
> 
https://urldefense.proofpoint.com/v2/url?u=http

Re: [HCP-Users] gradient nonlinearity correction question

[Harms, Michael]

One thought: Are you sure you are using the “3D” (and not the “2D”) correction 
on the scanner?

--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu

On 4/11/18, 8:31 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
Kristian Loewe" <hcp-users-boun...@humanconnectome.org on behalf of 
k...@kristianloewe.com> wrote:

Hi Joo-won and Keith,

I don't think that the table has been moved. Is there any information
somewhere in the dicom header to double-check this?

I am using the coeff_AS82.grad file for the Prisma data (the second
command). The first command was what I used for the Verio data. Also,
I double-checked that I am using the uncorrected volume as input.

I am not sure if I am supposed/allowed to send screenshots of the
actual data in the subject's native space to the list. I'm going to
check that. Meanwhile, I asked our local MR team to acquire an
additional data set using a phantom. The difference between the
scanner-corrected image and the offline-corrected image is not as
striking in this case but it's visible. Based on the phantom data, I
am inclined to say that both corrections work reasonably well, even
though they are not exactly the same. I also tried the
offline-correction on some phantom EPI data and it seems to work well
as it (together with EPI distortion correction) restores the original
shape of the phantom pretty nicely.

The differences between the correction variants applied to the
subject's data are actually rather small inside the brain but become
larger towards the neck, which is to be expected as the distance to
the magnetic isocenter becomes greater in that direction.
Nevertheless, I orginally thought that the differences between
scanner- and offline-corrected images would be smaller than that.

Find attached 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


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 apologize if you are receiving this twice now.


Quoting "Kim, Joo-won" <joo-won@mssm.edu>:

> 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  _new and then
> gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py=DwQFaQ=shNJtf5dKgNcPZ6Yh64b-A=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJ

Re: [HCP-Users] gradient nonlinearity correction question

[Kim, Joo-won]

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  _new and then
gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py=DwQFaQ=shNJtf5dKgNcPZ6Yh64b-A=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE=>
 on _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=DwQFaQ=shNJtf5dKgNcPZ6Yh64b-A=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE=>
 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=DwQFaQ=shNJtf5dKgNcPZ6Yh64b-A=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE=>
 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:  and _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

Re: [HCP-Users] gradient nonlinearity correction question

[Keith Jamison]

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  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 :
>
> 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  _new and then
>> gradient_unwarp.py on _new
>>
>> -Keith
>>
>>
>> On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe 
>> 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 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad
>>> -n
>>>
>>> and
>>>
>>>gradient_unwarp.py 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 :
>>>
>>> > 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 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 
>>> > 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:  on behalf of Antonin
>>> Skoch <
>>> >> a...@ikem.cz>
>>> >> Date: Wednesday, October 19, 2016 at 4:27 PM
>>> >> To: "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
>>> >>
>>> >>
>>> >> ___
>>> >> HCP-Users mailing list
>>> >> HCP-Users@humanconnectome.org
>>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >> The materials in this message are private and may contain Protected
>>> >> Healthcare Information or other information of a sensitive nature. If
>>> you
>>> >> are not the intended recipient, be advised that any unauthorized use,
>>> >> disclosure, copying or the taking of any action in reliance on the
>>> contents
>>> >> of this information is strictly prohibited. If you have received this
>>> email
>>> >> in error, please immediately notify the sender via telephone or return
>>> mail.
>>> >>
>>> >> ___

Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

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 :

> 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  _new and then
> gradient_unwarp.py on _new
>
> -Keith
>
>
> On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe 
> 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 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad
>> -n
>>
>> and
>>
>>gradient_unwarp.py 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 :
>>
>> > 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 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 
>> > 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:  on behalf of Antonin
>> Skoch <
>> >> a...@ikem.cz>
>> >> Date: Wednesday, October 19, 2016 at 4:27 PM
>> >> To: "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
>> >>
>> >>
>> >> ___
>> >> HCP-Users mailing list
>> >> HCP-Users@humanconnectome.org
>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >>
>> >>
>> >> --
>> >>
>> >> The materials in this message are private and may contain Protected
>> >> Healthcare Information or other information of a sensitive nature. If
>> you
>> >> are not the intended recipient, be advised that any unauthorized use,
>> >> disclosure, copying or the taking of any action in reliance on the
>> contents
>> >> of this information is strictly prohibited. If you have received this
>> email
>> >> in error, please immediately notify the sender via telephone or return
>> mail.
>> >>
>> >> ___
>> >> HCP-Users mailing list
>> >> HCP-Users@humanconnectome.org
>> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >>
>> >
>> > ___
>> > HCP-Users mailing list
>> > HCP-Users@humanconnectome.org
>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] gradient nonlinearity correction question

[Keith Jamison]

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  _new and then
gradient_unwarp.py on _new

-Keith


On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe 
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 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad
> -n
>
> and
>
>gradient_unwarp.py 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 :
>
> > 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 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 
> > 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:  on behalf of Antonin
> Skoch <
> >> a...@ikem.cz>
> >> Date: Wednesday, October 19, 2016 at 4:27 PM
> >> To: "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
> >>
> >>
> >> ___
> >> HCP-Users mailing list
> >> HCP-Users@humanconnectome.org
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >>
> >> --
> >>
> >> The materials in this message are private and may contain Protected
> >> Healthcare Information or other information of a sensitive nature. If
> you
> >> are not the intended recipient, be advised that any unauthorized use,
> >> disclosure, copying or the taking of any action in reliance on the
> contents
> >> of this information is strictly prohibited. If you have received this
> email
> >> in error, please immediately notify the sender via telephone or return
> mail.
> >>
> >> ___
> >> HCP-Users mailing list
> >> HCP-Users@humanconnectome.org
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
> ___
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>

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Re: [HCP-Users] gradient nonlinearity correction question

[Kristian Loewe]

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 T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS097.grad -n

and

   gradient_unwarp.py 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 :

> 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 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 
> 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:  on behalf of Antonin Skoch <
>> a...@ikem.cz>
>> Date: Wednesday, October 19, 2016 at 4:27 PM
>> To: "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
>>
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users



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Re: [HCP-Users] gradient nonlinearity correction question

[Keith Jamison]

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 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 
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:  on behalf of Antonin Skoch <
> a...@ikem.cz>
> Date: Wednesday, October 19, 2016 at 4:27 PM
> To: "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
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] gradient nonlinearity correction question

[Glasser, Matthew]

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 of Antonin Skoch >
Date: Wednesday, October 19, 2016 at 4:27 PM
To: "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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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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