That all make sense -- thanks a lot, Matt. We will use the applywarp
output. Concatenation of tarnsforms is also something we do.

Sandy

On Mon, Aug 7, 2017 at 6:11 PM Glasser, Matthew <glass...@wustl.edu> wrote:

> Hi Sandhitsu,
>
>    1. You could take a difference between the two images to see if
>    anything beyond the extreme slice is affected much
>    2. We do really try to avoid trilinear interpolation because of its
>    blurring effect.  For offline correction we output the warpfield which
>    allows us to use applywarp from FSL to do a less blurring spline
>    interpolation.  Additionally we try to concatenate warpfields/affine
>    matrices so that only a single resampling occurs.
>
> Best,
>
> Matt.
>
> From: Sandhitsu Das <su...@seas.upenn.edu>
> Date: Monday, August 7, 2017 at 3:39 PM
> To: "Harms, Michael" <mha...@wustl.edu>, Matt Glasser <glass...@wustl.edu>,
> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] Offline vs. online gradient nonlinearity
> correction
>
> Thank you both for responding, guys! Followup questions:
>
> 1) When you say "probably" for 3), whatever is going on, can we assume
> this will be limited to the last one slice only ?
> 2) I see your point about interpolation, but I thought you mentioned when
> you were here that the trilinear is something that you do as well (I see
> the output files named that way also, or should we be using the "warped"
> file ?).
>
> On Fri, Aug 4, 2017 at 2:34 PM Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>>
>> FYI: We are switching over to using ‘dcm2niix’, which is Chris Rorden’s
>> newer, actively maintained conversion tool.
>>
>>
>>
>> --
>>
>> Michael Harms, Ph.D.
>>
>> -----------------------------------------------------------
>>
>> Conte Center for the Neuroscience of Mental Disorders
>>
>> Washington University School of Medicine
>>
>> Department of Psychiatry, Box 8134
>>
>> 660 South Euclid Ave.                        Tel: 314-747-6173
>> <(314)%20747-6173>
>>
>> St. Louis, MO  63110                                          Email:
>> mha...@wustl.edu
>>
>>
>>
>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of "Glasser,
>> Matthew" <glass...@wustl.edu>
>> *Date: *Friday, August 4, 2017 at 1:21 PM
>> *To: *Sandhitsu Das <su...@seas.upenn.edu>, "
>> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> *Subject: *Re: [HCP-Users] Offline vs. online gradient nonlinearity
>> correction
>>
>>
>>
>>    1. Yes
>>    2. We use dcm2nii.
>>    3. Probably
>>
>> I would use offline so you are sure that all of your images are being
>> corrected the same way and have control over how the resampling is being
>> done (i.e. not adding blurring from trilinear interpolation).
>>
>>
>>
>> Peace,
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Sandhitsu
>> Das <su...@seas.upenn.edu>
>> *Date: *Friday, August 4, 2017 at 12:06 PM
>> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> *Subject: *[HCP-Users] Offline vs. online gradient nonlinearity
>> correction
>>
>>
>>
>> This is following up on a thread here
>>
>>
>>
>> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03502.html
>>
>>
>>
>> We are evaluating online vs. offline correction on our 3T Simens Prisma
>> system using a phantom. I have three questions:
>>
>>
>>
>> 1) Looks like the gradunwarp script is agnostic to the sequence type.
>> Does this mean that we should use it the same way for any sequence
>> (including structural or functional) as a first preprocesing step ?
>>
>>
>>
>> 2) The gradunwarp script takes nifti input. My understanding is that the
>> coefficient file defines the known nonlinearity profile using scanner
>> coordinates. Does this mean the output may be different when using nifti
>> files produced by different dicom converters which can potentially change
>> the coordinate system in some way ?
>>
>>
>>
>> 3) Please see the two attached screenshots that compare online vs.
>> offline corrections. The two images show a middle coronal slice and and a
>> terminal one respectively. Bottom shows original, top left shows online
>> corrected, top right shows offline corrected. While in the middle slice it
>> looks like offline and online produces pretty much the same output
>> (although we didn't quantitatively evaluate yet), there is something funny
>> going on at the terminal slices. Artifact of boundary condition assumptions
>> ?
>>
>>
>>
>> Any help is much appreciated. We can't move on with our studies until we
>> figure out the right way to do this as this is (presumably) the very first
>> pre-processing step.
>>
>>
>>
>> Thanks,
>>
>> Sandy
>>
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