Re: [HCP-Users] DTI on HCP data

[Glasser, Matthew]

It looks like you have the correct understanding of this.  One cannot easily 
apply the gradient nonlinearity effects on the diffusion gradients to the 
images, as really you need to apply them to the bvals and bvecs.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Szabolcs David 
mailto:davidszabolc...@gmail.com>>
Date: Thursday, August 10, 2017 at 7:03 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] DTI on HCP data

​Dear HCP Team,

I would like to use HCP diffusion data to do some diffusion tensor fitting and 
subsequently calculate maps of FA, MD, etc. For this I think it would be handy 
to use the followings:
$subject\T1w\Diffusion\bvals
$subject\T1w\Diffusion\bvecs
$subject\T1w\Diffusion\data.nii.gz

We can refer to these files as the result of the 'minimal processing pipeline' 
(Glasser 13 Neuroimage), as this diffusion data is already processed for motion 
and B0 inhomogeneities among many other artifacts. But since I would like to do 
some custom-made model estimation (aka. outside of FSL/dtifit/bedpostx), I need 
to implement a voxelwise bvecs rotation and bval calculation, because of the 
effect of the diffusion gradient nonlinearities. To do this the source is the 
$subject\T1w\Diffusion\grad_dev.nii.gz file.
A bit of matlab script is provided to calculate the proper bvec and bval per 
voxel. (this guy: 
http://www.humanconnectome.org/storage/app/media/documentation/data_release/Q1_Release_Appendix_II.pdf).

Generally: I am right with the above? In the mentioned paper this part is a bit 
confusing for me (highlighted some parts):

"The gradient nonlinearity correction warpfield is then calculated for the 
diffusion data to remove this spatial distortion (Jovicich et al., 2006), and 
the mean b0 image is distortion corrected. Additionally, the effects of 
gradient nonlinearity on the diffusion encoding magnitudes and directions are 
calculated (Bammer et al., 2003; Sotiropoulos it et al., 2013–this issue). The 
partial derivatives of the spatially-dependent magnetic field are used to 
calculate a gradient field tensor at each voxel, which maps “nominal” to actual 
gradient magnitudes and directions (Bammer et al., 2003). Using the gradient 
field tensor, the magnitude and direction of the diffusion-sensitizing 
gradients can be corrected at each brain voxel. This information is 
subsequently used for more accurate fiber orientation estimation."

In short: the diffusion weighted gradient nonlinearities are calculated, BUT 
not applied. That is why every time one wants to do model estimation diffusion 
gradient nonlinearities must be considered in a form to use different bvals and 
bvecs per voxel. In FSL for dtifit that would be calling the --gradnonlin 
option. In contrast, distortions from (regular) imaging gradients are 
corrected, after topup+eddy based correction for B0 inhomogeneities and eddy 
current distortion correction. This is stated right after the cited paragraph 
from the same paper:
"It is worth noting that the gradient nonlinearity correction is done at a much 
later stage in the diffusion pipeline than in the fMRIVolume pipeline. Ideally 
the gradient nonlinearity distortion correction would be done simultaneously 
with the B0 inhomogeneity distortion correction, as well as with the eddy 
current distortion correction and rigid-body motion correction, as all of these 
interact." -> but here the "gradient nonlinearity distortion correction" is 
about the imaging gradients, right? The correction of diffusion gradient 
nonlinearities are *still* stored in the grad_dev.nii.gz file and must be used 
during model estimation.

Apologies for the long email.

Best,
Szabolcs

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[HCP-Users] DTI on HCP data

[Szabolcs David]

​Dear HCP Team,

I would like to use HCP diffusion data to do some diffusion tensor fitting
and subsequently calculate maps of FA, MD, etc. For this I think it would
be handy to use the followings:
$subject\T1w\Diffusion\bvals
$subject\T1w\Diffusion\bvecs
$subject\T1w\Diffusion\data.nii.gz

We can refer to these files as the result of the 'minimal processing
pipeline' (Glasser 13 Neuroimage), as this diffusion data is already
processed for motion and B0 inhomogeneities among many other artifacts. But
since I would like to do some custom-made model estimation (aka. outside of
FSL/dtifit/bedpostx), I need to implement a voxelwise bvecs rotation and
bval calculation, because of the effect of the diffusion gradient
nonlinearities. To do this the source is the
$subject\T1w\Diffusion\grad_dev.nii.gz file.
A bit of matlab script is provided to calculate the proper bvec and bval
per voxel. (this guy:
http://www.humanconnectome.org/storage/app/media/documentation/data_release/Q1_Release_Appendix_II.pdf
).

Generally: I am right with the above? In the mentioned paper this part is a
bit confusing for me (highlighted some parts):

"The gradient nonlinearity correction warpfield is then calculated for the
diffusion data to remove this spatial distortion (Jovicich et al., 2006),
and the mean b0 image is distortion corrected. *Additionally, the effects
of gradient nonlinearity on the diffusion encoding magnitudes and
directions are calculated (Bammer et al., 2003; Sotiropoulos it et al.,
2013–this issue).* The partial derivatives of the spatially-dependent
magnetic field are used to calculate a gradient field tensor at each voxel,
which maps “nominal” to actual gradient magnitudes and directions (Bammer
et al., 2003). *Using the gradient field tensor, the magnitude and
direction of the diffusion-sensitizing gradients can be corrected at each
brain voxel.* This information is subsequently used for more accurate fiber
orientation estimation."

In short: the diffusion weighted gradient nonlinearities are calculated,
BUT not applied. That is why every time one wants to do model estimation
diffusion gradient nonlinearities must be considered in a form to use
different bvals and bvecs per voxel. In FSL for dtifit that would be
calling the --gradnonlin option. In contrast, distortions from (regular)
imaging gradients are corrected, after topup+eddy based correction for B0
inhomogeneities and eddy current distortion correction. This is stated
right after the cited paragraph from the same paper:
"It is worth noting that the gradient nonlinearity correction is done at a
much later stage in the diffusion pipeline than in the fMRIVolume pipeline.*
Ideally the gradient nonlinearity distortion correction would be done
simultaneously with the B0 inhomogeneity distortion correction, as well as
with the eddy current distortion correction and rigid-body motion
correction, as all of these interact*." -> but here the "gradient
nonlinearity distortion correction" is about the imaging gradients, right?
The correction of diffusion gradient nonlinearities are *still* stored in
the grad_dev.nii.gz file and must be used during model estimation.

Apologies for the long email.

Best,
Szabolcs

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Re: [HCP-Users] The best set of annotations for any MRI scan?

[Glasser, Matthew]

I’m not aware of a public dataset like this, but perhaps someone else on the 
list is.

Peace,

Matt.

From: anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 1:35 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] The best set of annotations for any MRI scan?

My colleagues are trying to create algorithms to auto-label volumes of brain 
images.
They will need a set of human made annotations to serve as a template for 
learning.
Are you aware of anyone that has this type of data?

On Thu, Aug 10, 2017 at 11:27 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Like I said, I would really need to know more about what you are trying to do.

Peace,

Matt.

From: anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 12:48 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] The best set of annotations for any MRI scan?

Hi Matt,
Thanks for your response, I mean a set of human added labels that are 
associated with specific locations of the scan.
Best,
anita

On Thu, Aug 10, 2017 at 9:52 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I don’t know what you mean by annotations or what scan you are referring to?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 11:33 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] The best set of annotations for any MRI scan?

Hi,
I am looking for the most complete set of annotations for a scan, which file 
should I pull?
Thank you in advance,
anita

--
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243


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--
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orcid.org/-0002-5497-0243




--
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243


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Re: [HCP-Users] aspera dowload trouble

[Elam, Jennifer]

Hi Michael,

You can access the data via REST calls-- take a look at: 
https://wiki.humanconnectome.org/display/PublicData/How+To+Access+Subject+Data+via+REST

You can also access the data on AWS-- more info on that here: 
https://wiki.humanconnectome.org/display/PublicData/How+To+Connect+to+Connectome+Data+via+AWS


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: Michael Stauffer 
Sent: Thursday, August 10, 2017 2:11:56 PM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org; Hileman, Michael
Subject: Re: [HCP-Users] aspera dowload trouble

Elam, thanks very much for the info.

I haven't had time to try this, and the user looking for the data has indeed 
downloaded it in the meantime while on another network. But I'll keep this info 
for next time.

Is there an scp/sftp/rsync route to the data sets? I have a machine on a 
different network that should not be firewalled, but it's shell-only (no gui).

-M

On Mon, Aug 7, 2017 at 11:34 AM, Elam, Jennifer 
mailto:e...@wustl.edu>> wrote:

Hi Michael,

Have you tried following the instructions on 
https://wiki.humanconnectome.org/display/PublicData/Aspera+Plugin%3A+Help+and+FAQ?

Our Aspera server is configured to use TCP and UDP Port 33001 for file 
transfers instead of a common port such as Port 22. If you are downloading from 
behind an institutional firewall, please speak with your IT people to ensure 
that Port 33001 is open to both TCP and UDP traffic.


You also might try downloading from home and see if that works to test if it is 
an institutional firewall issue.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: 
hcp-users-boun...@humanconnectome.org
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Michael Stauffer mailto:mgsta...@gmail.com>>
Sent: Friday, August 4, 2017 5:32:04 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] aspera dowload trouble

Hi,

I'm trying to use the aspera plug-in to download some data but it keeps 
stalling. It's not my server's firewall because disabling that doesn't help. It 
might be my institution's firewall. In any case, do I go here for help with 
that or to Aspera directly? I can see a connection error in the 
aspera-scp-transfer.log file, e.g.:

2017-08-04 18:07:13 [3027-4aff6700] ERR [ascp] Failed to connect to 
asperax...@asp-connect1.wustl.edu
2017-08-04 18:07:13 [3027-4aff6700] ERR [ascp] TCP connect failed, err=111

Thanks

-M

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Re: [HCP-Users] aspera dowload trouble

[Michael Stauffer]

Elam, thanks very much for the info.

I haven't had time to try this, and the user looking for the data has
indeed downloaded it in the meantime while on another network. But I'll
keep this info for next time.

Is there an scp/sftp/rsync route to the data sets? I have a machine on a
different network that should not be firewalled, but it's shell-only (no
gui).

-M

On Mon, Aug 7, 2017 at 11:34 AM, Elam, Jennifer  wrote:

> Hi Michael,
>
> Have you tried following the instructions on https://wiki.humanconnectome.
> org/display/PublicData/Aspera+Plugin%3A+Help+and+FAQ?
> Our Aspera server is configured to use *TCP and UDP Port 33001* for file
> transfers instead of a common port such as Port 22. If you are downloading
> from behind an institutional firewall, please speak with your IT people to
> ensure that Port 33001 is open to both TCP and UDP traffic.
>
>
> You also might try downloading from home and see if that works to test if
> it is an institutional firewall issue.
>
>
> Best,
>
> Jenn
>
>
> Jennifer Elam, Ph.D.
> Scientific Outreach, Human Connectome Project
> Washington University School of Medicine
> Department of Neuroscience, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> e...@wustl.edu
> www.humanconnectome.org
>
> --
> *From:* hcp-users-boun...@humanconnectome.org  humanconnectome.org> on behalf of Michael Stauffer 
> *Sent:* Friday, August 4, 2017 5:32:04 PM
> *To:* hcp-users@humanconnectome.org
> *Subject:* [HCP-Users] aspera dowload trouble
>
> Hi,
>
> I'm trying to use the aspera plug-in to download some data but it keeps
> stalling. It's not my server's firewall because disabling that doesn't
> help. It might be my institution's firewall. In any case, do I go here for
> help with that or to Aspera directly? I can see a connection error in the
> aspera-scp-transfer.log file, e.g.:
>
> 2017-08-04 18:07:13 [3027-4aff6700] ERR [ascp] Failed to connect to
> asperax...@asp-connect1.wustl.edu
> 2017-08-04 18:07:13 [3027-4aff6700] ERR [ascp] TCP connect failed, err=111
>
> Thanks
>
> -M
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] The best set of annotations for any MRI scan?

[Glasser, Matthew]

Like I said, I would really need to know more about what you are trying to do.

Peace,

Matt.

From: anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 12:48 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] The best set of annotations for any MRI scan?

Hi Matt,
Thanks for your response, I mean a set of human added labels that are 
associated with specific locations of the scan.
Best,
anita

On Thu, Aug 10, 2017 at 9:52 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I don’t know what you mean by annotations or what scan you are referring to?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 11:33 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] The best set of annotations for any MRI scan?

Hi,
I am looking for the most complete set of annotations for a scan, which file 
should I pull?
Thank you in advance,
anita

--
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243


___
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--
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243


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Re: [HCP-Users] The best set of annotations for any MRI scan?

[Glasser, Matthew]

I don’t know what you mean by annotations or what scan you are referring to?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of anita bandrowski mailto:band...@gmail.com>>
Date: Thursday, August 10, 2017 at 11:33 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] The best set of annotations for any MRI scan?

Hi,
I am looking for the most complete set of annotations for a scan, which file 
should I pull?
Thank you in advance,
anita

--
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243


___
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[HCP-Users] The best set of annotations for any MRI scan?

[anita bandrowski]

Hi,
I am looking for the most complete set of annotations for a scan, which
file should I pull?
Thank you in advance,
anita

-- 
All key biological entities deserve an #RRID!
orcid.org/-0002-5497-0243

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Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

[Xavier Guell Paradis]

Dear Tim and Matt,
Thank you very much for your help, now it works! I had my clusters registered 
to the S900_Average_T1w_restore.nii file, but they had to be registered to the 
MNI152_T1_2mm.nii.gz file.
Thank you very much,
Xavier.

From: Timothy Coalson [tsc...@mst.edu]
Sent: Wednesday, August 09, 2017 6:55 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

If your "mycluster.nii" is in a different volume space than 222 MNI RPI space, 
then it may not let you use it that way.  Compare the nifti header against this 
file in the HCP pipelines, using fslhd or wb_command -nifti-information 
-print-header:

global/templates/MNI152_T1_2mm.nii.gz

If it is different, then you will need to resample your label volume.

Tim


On Wed, Aug 9, 2017 at 4:38 PM, Xavier Guell Paradis 
mailto:xavie...@mit.edu>> wrote:
Dear Tim,
Thank you for your reply
I have made sure that I have the group .dconn file opened, and I can see that 
it is correctly opened because I can see connectivity when I click on any 
structure.
However, I still have the same problem: I do not see the option of "Show Cifti 
Connectivity" when I right-click the cluster of the dlabel file I have created 
(however, I can see the dlabel file in the "Labels" list of the "Features 
Toolbox").

These are the steps I followed to create the dlabel file; I imagine I did 
something wrong in these steps but I cannot figure out what:
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label 
mycluster_labelStep2.dlabel.nii -volume 
mycluster_label.nii mycluster_label.nii
The resulting dlabel file is "mycluster_labelStep2.dlabel.nii"

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu]
Sent: Wednesday, August 09, 2017 4:57 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; 
hcp-users@humanconnectome.org

Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

You need to have a dtseries (or dconn) file open before you can see any kind of 
connectivity.  If you only have the labels/rois open, how do you expect it to 
figure out connectivity information?

Note that we only have options for averaging things inside a label, the ROI 
file will not be useful in the GUI for this purpose.

Tim


On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis 
mailto:xavie...@mit.edu>> wrote:
Dear Matt,
Thank you for your reply. I have realized that a very curious thing happens:
- If I open the dlabel file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dscalar file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dlabel file AND the dscalar file and right-click the cluster in 
wb_view (note that the cluster is now present twice: in the dlabel file and in 
the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show 
Cifti Connectivity" option.

I opened wb_view multiple times to make sure that this is true: I only see the 
"Show Data/Time Series Graph" once I have opened both files; but I still do not 
see the "Show Cifti Connectivity" option.

This is a strange pattern, but perhaps it is a clue to find out what I am doing 
wrong.

An extra piece of information that might be useful: when I open the dlabel 
file, I can see it listed in the "Labels" list of the "Features ToolBox".

Thank you very much,
Xavier.

From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, August 09, 2017 2:13 PM
To: Xavier Guell Paradis; NEUROSCIENCE tim

Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

It should work if you skip the last step and use the dlabel file.

Peace,

Matt.

From: Xavier Guell Paradis mailto:xavie...@mit.edu>>
Date: Wednesday, August 9, 2017 at 9:43 AM
To: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser 
mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
-cifti-all-labels-to-rois.
After this, when I right-click the cluster in wb_view, I see the option "Show 
Data/Time Series Graph For Parcel [my cluster]" but I do not see the opti

Re: [HCP-Users] Offline vs. online gradient nonlinearity correction

[Sandhitsu Das]

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  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 
> Date: Monday, August 7, 2017 at 3:39 PM
> To: "Harms, Michael" , Matt Glasser ,
> "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  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: * on behalf of "Glasser,
>> Matthew" 
>> *Date: *Friday, August 4, 2017 at 1:21 PM
>> *To: *Sandhitsu Das , "
>> 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: * on behalf of Sandhitsu
>> Das 
>> *Date: *Friday, August 4, 2017 at 12:06 PM
>> *To: *"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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>> di