Re: [HCP-Users] A question about dtifit for the HCP data

[Saad Jbabdi]

Hi

The simplest thing to do is to fit the tensor model to the b1k shell. If you 
are interested in the mean kurtosis, you can use the flag in dtifit, but I 
would not trust the values you get for FA. That is because the model assumes 
that kurtosis is equal in all directions, which it isn’t. That slightly biases 
the tensor eigenvalues, which results in substantially higher FA values. You 
can also get the mean kurtosis by simply averaging the signal within each shell 
and fitting a quadratic to the log(data) [e.g. in matlab, python, or bash with 
fsl_glm].

Cheers
Saad


On 29 Jan 2019, at 23:13, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Dear HCP experts,

I saw some previous questions in the mailing list regarding dtifit, and some 
experts suggested that the simple tensor model is not appropriate at high 
b-values.  So I tried the two different options of either using "-kurt" flag or 
limiting the fitting to b=1000 shell, but the results from these two options 
were not nearly the same. Would you please suggest if there is any good way to 
evaluate the difference and choose one from these two options? Thank you.
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

[Saad Jbabdi]

Hi - that worked!  Thank you so much John.

Cheers
Saad



On 12 Apr 2018, at 17:00, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:


So it is a shape file.  Follow the same instructions as before except for the 
second step that has been updated to set the File Type to GIFTI Shape File.

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Shape File 
(*.shape.gii)
* Change the File Name so that it ends in “.shape.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.


Note that GIFTI func and shape are the same format and you can rename from 
.shape.gii to .func.gii.



Alternatively, if you can find the Caret Shape File in a terminal window, 
“wb_import”, included with the Workbench distribution, can be used to convert 
data files from Caret format to a Workbench compatible format.

wb_import -data-file
   CONVERT DATA FILE TO WORKBENCH FORMAT
  wb_import -data-file
 [-allow-overwrite]
 [-structure  structure-name]
 [-area-color-filearea-color-file-name]
 [-border-color-file  border-color-file-name]
 [-foci-color-filefoci-color-file-name]
 ]

On Apr 12, 2018, at 10:24 AM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

This one


On 12 Apr 2018, at 15:21, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:

Do you know the name and type of the file displayed as the primary overlay on 
the surface?  It should be selected in Primary Overlay on the Display Control’s 
Overlay/Underlay - Surface page.


On Apr 12, 2018, at 7:41 AM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi John

When I follow your steps it produces an empty func file:


http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;
  
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">
   
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
   
   




On 11 Apr 2018, at 19:24, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad



On 11 Apr 2018, at 16:36, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
Saad Jbabdi" 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad



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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

[Saad Jbabdi]

Hi John

When I follow your steps it produces an empty func file:


http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;
  
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">
   
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
   
   




On 11 Apr 2018, at 19:24, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad



On 11 Apr 2018, at 16:36, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
Saad Jbabdi" 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad



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Re: [HCP-Users] dtifit, bedpostx, voxel-wise correction of dMRI gradients

[Saad Jbabdi]

Or alternatively you could use the “—kurt” or “—kurtdir" flags which will add a 
“mean kurtosis” or “parallel/perpendicular kurtosis” parameters that can 
account for non-exponential decay.

Cheers
Saad



On 10 Oct 2017, at 03:53, Harms, Michael 
> wrote:


Also, if you fitting a simple tensor model via ‘dtifit’, you may want to 
consider limiting yourself to just the b=1000 shell (+ b=0’s), because the 
simple tensor model breaks down for high b-values.  There should be a post in 
the archive about this.

Cheers,
-MH

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

From: 
>
 on behalf of "Glasser, Matthew" >
Date: Monday, October 9, 2017 at 5:22 PM
To: Athanasia Metoki 
>, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] dtifit, bedpostx, voxel-wise correction of dMRI 
gradients

I believe both binaries will use the grad_dev to perform the correct described 
in the bvals and bvecs in a voxelwise manner.

Peace,

Matt.

From: 
>
 on behalf of Athanasia Metoki 
>
Date: Monday, October 9, 2017 at 3:29 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] dtifit, bedpostx, voxel-wise correction of dMRI gradients

Dear HCP experts,

I would like to analyze some HCP diffusion data. I am using the preprocessed 
HCP data from the 900 subjects release.

I would like to do dtifit and run bedpostx and then tractography (I know dtifit 
is unrelated to the latter bt I'm mentioning it because I would like to be 
consistent in my analysis).

Two questions:

a) I found this dtifit command in the HCP mail list archives:
dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz -o >>> 
$OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz

But also I found this code for voxel-wise correction of dMRI gradients:
https://www.humanconnectome.org/storage/app/media/documentation/data_release/Q1_Release_Appendix_II.pdf

When I run the dtifit command above do I use the new_bvals and new_bvecs?

Hence do I run:
dtifit -k data.nii.gz -r new_bvecs -b new_bvals -m nodif_brain_mask.nii.gz -o 
>>> $OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz

or does the "--gradnonlin=grad_dev.nii.gz" in the command does the same job as 
the code I found in the Q1_Release_Appendix_II.pdf?

b) When I run bedpostx_gpu do I need to use the new_bvals in a script like this:
bedpostx_gpu T1w/Diffusion -n 3 -b 3000 -model 3 -g —rician

Thank you.

Best,
Athanasia Metoki
Psychology Doctoral Student - Brain and Cognitive Sciences Program
Cognitive Neuroscience Laboratory
Temple University
Department of Psychology
1701 N 13th St.
Philadelphia, PA 19122
Email: athanasia.met...@temple.edu

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[HCP-Users] Announcing UK-dHCP first data release

[Saad Jbabdi]

Hi All,

On behalf of the UK Developing Human Connectome Project consortium:

We would like to announce the first preliminary release of data as part of the 
Developing Human Connectome Project (dHCP) – an ERC-funded collaboration 
between King’s College London, Imperial College London and Oxford University.

This is the project’s first open access data release which consist of images of 
40 representative term neonatal subjects. The imaging data includes structural 
imaging, structural connectivity data (diffusion MRI) and functional 
connectivity data (resting-state fMRI). This preliminary data release comes 
with minimal accompanying meta data: gender, age at birth and age at scan. More 
specific information about the available data can be found in the accompanying 
data release notes. To access the data please follow this 
link<https://data.developingconnectome.org/> (**). You will be required to 
agree to a simple data sharing agreement.

We invite colleagues in the field to explore and feedback on the value and 
characteristics of the image dataset. The image data are processed using 
analysis pipelines that are subject to further development.

The project to date has successfully completed 584 neonatal scans and further 
data is still being collected, including fetal imaging (imaging babies before 
birth). Future data releases will consist of comprehensive image data with 
accompanying clinical, neurodevelopmental and genetics information.


Best wishes

Saad Jbabdi


(**) https://data.developingconnectome.org/app/template/Login.vm



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Re: [HCP-Users] How I can use grad_dev file for tensor fitting using FSL dtifit?

[Saad Jbabdi]

Hi
Yes you can, but not for calculating FA. We use the ball and stick model to 
calculate orientations that we then use for tractography.

Cheers
Saad

On 18 Oct 2014, at 14:56, 임솔 cogsci...@gmail.commailto:cogsci...@gmail.com 
wrote:

Hi Saad,
Thank you very much for your help! I've got better understanding of this issue 
thanks to your papers. Can I use the ball and stick model using a gamma 
distribution of diffusivities with FSL?

Best regards,
Sol

On 18 October 2014 14:05, Saad Jbabdi 
saad.jba...@ndcn.ox.ac.ukmailto:saad.jba...@ndcn.ox.ac.uk wrote:
Hi Sol
I would recommend that you use the b=1000 shell and run dtifit.
You can extract the b=1000 shell from the data using fslsplit and fslmerge. We 
will soon release a tool (fslselectvols) which should make this more 
straightforward.

Cheers
Saad.



On 17 Oct 2014, at 15:34, 임솔 cogsci...@gmail.commailto:cogsci...@gmail.com 
wrote:

Thank you so much for your helpful replies!

While waiting for comments from Oxford, what do you recommend for tensor 
fitting?

Many thanks,
Sol

On 16 October 2014 18:19, Harms, Michael 
mha...@wustl.edumailto:mha...@wustl.edu wrote:

Note though that you'll want to consider whether to use all the shells if 
computing a standard tensor fit because the assumption of Gaussian diffusion 
and mono exponential decay starts to break down for b1500 or so.

Perhaps someone from Oxford will chime in with more detailed thoughts on that 
issue.

cheers,
-MH

--
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: 314-747-6173tel:314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edumailto:mha...@wustl.edu

From: House, Matthew House hou...@mir.wustl.edumailto:hou...@mir.wustl.edu
Date: Thursday, October 16, 2014 12:11 PM
To: 임솔 cogsci...@gmail.commailto:cogsci...@gmail.com, 
HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org 
HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] How I can use grad_dev file for tensor fitting using 
FSL dtifit?

Hi, Sol.  There is a hidden option of ‘--gradnonlin’ in the dtifit command to 
enable this function.  Below is an example command that I used in a script to 
loop over the HCP DTI data.

dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz -o 
$OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz

~Matt

From: 
hcp-users-boun...@humanconnectome.orgmailto:hcp-users-boun...@humanconnectome.org
 [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of ??
Sent: Thursday, October 16, 2014 12:06 PM
To: HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org
Subject: [HCP-Users] How I can use grad_dev file for tensor fitting using FSL 
dtifit?

Dear all,

I'm trying to fit the diffusion tensor model using FSL dtifit but I do not know 
how to include gradient correction using grad_dev file. There is an option flag 
'-gradadj' in Camino to do it. What would be the equivalent argument for FSL 
dtifit? Many thanks.

Best,
Sol

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--
Saad Jbabdi, PhD
MRC Career Development Fellow 
University Research Lecturer

FMRIB Centre, University of Oxford,
John Radcliffe Hospital, Oxford, OX3 9DU, UK.
tel (+44)1865-222466tel:%28%2B44%291865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad

Re: [HCP-Users] How I can use grad_dev file for tensor fitting using FSL dtifit?

[Saad Jbabdi]

Hi Sol
I would recommend that you use the b=1000 shell and run dtifit.
You can extract the b=1000 shell from the data using fslsplit and fslmerge. We 
will soon release a tool (fslselectvols) which should make this more 
straightforward.

Cheers
Saad.



On 17 Oct 2014, at 15:34, 임솔 cogsci...@gmail.commailto:cogsci...@gmail.com 
wrote:

Thank you so much for your helpful replies!

While waiting for comments from Oxford, what do you recommend for tensor 
fitting?

Many thanks,
Sol

On 16 October 2014 18:19, Harms, Michael 
mha...@wustl.edumailto:mha...@wustl.edu wrote:

Note though that you'll want to consider whether to use all the shells if 
computing a standard tensor fit because the assumption of Gaussian diffusion 
and mono exponential decay starts to break down for b1500 or so.

Perhaps someone from Oxford will chime in with more detailed thoughts on that 
issue.

cheers,
-MH

--
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: 314-747-6173tel:314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edumailto:mha...@wustl.edu

From: House, Matthew House hou...@mir.wustl.edumailto:hou...@mir.wustl.edu
Date: Thursday, October 16, 2014 12:11 PM
To: 임솔 cogsci...@gmail.commailto:cogsci...@gmail.com, 
HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org 
HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] How I can use grad_dev file for tensor fitting using 
FSL dtifit?

Hi, Sol.  There is a hidden option of ‘--gradnonlin’ in the dtifit command to 
enable this function.  Below is an example command that I used in a script to 
loop over the HCP DTI data.

dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz -o 
$OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz

~Matt

From: 
hcp-users-boun...@humanconnectome.orgmailto:hcp-users-boun...@humanconnectome.org
 [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of ??
Sent: Thursday, October 16, 2014 12:06 PM
To: HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org
Subject: [HCP-Users] How I can use grad_dev file for tensor fitting using FSL 
dtifit?

Dear all,

I'm trying to fit the diffusion tensor model using FSL dtifit but I do not know 
how to include gradient correction using grad_dev file. There is an option flag 
'-gradadj' in Camino to do it. What would be the equivalent argument for FSL 
dtifit? Many thanks.

Best,
Sol

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--
Saad Jbabdi, PhD
MRC Career Development Fellow 
University Research Lecturer

FMRIB Centre, University of Oxford,
John Radcliffe Hospital, Oxford, OX3 9DU, UK.
tel (+44)1865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdihttp://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi




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Re: [HCP-Users] gifti labels to volume

[Saad Jbabdi]

 prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdihttp://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi


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[HCP-Users] Missing values in movement regressor files - Q3 tfMRI 200 subjects

[Saad Jbabdi]

Hi All

I am not sure if this has already been flagged, but there are missing values in 
the files:

156233/MNINonLinear/Results/tfMRI_GAMBLING_RL/Movement_Regressors.txt
156233/MNINonLinear/Results/tfMRI_SOCIAL_LR/Movement_Regressors.txt
366446/MNINonLinear/Results/tfMRI_WM_RL/Movement_Regressors.txt


Are there fixes readily available? (couldn't find any on the wiki).

Cheers,
Saad.



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