Re: [HCP-Users] Simple GLM for cordial thickness and myelin maps in workbench?

[Harms, Michael]

Hi,
Not in wb_command at the current time.  You could of course load the data into 
Matlab and run a regression there, if all you care about is the effect size of 
the relationship.  What PALM nicely gives you is the ability to control for 
multiple comparisons in a statistically rigorous manner using permutation 
testing.

Cheers,
-MH

--
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

From:  on behalf of "Linnman, 
Clas,Ph.D." 
Date: Saturday, March 17, 2018 at 8:30 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Simple GLM for cordial thickness and myelin maps in 
workbench?

Hi,

I would like to do a linear regression between a variable and cortical 
thickness in a subset of participants from the HCP1200, controlling for a 
couple of factors.
Is PALM the (only) way to do that, or are there any basic statistical commands 
that can be used in wb_command?

Best
Clas


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Re: [HCP-Users] Fw:

[HERACLES PANAGIOTIDES]

Tim,

Thank you very much for taking the time to reply.  I am hoping to be able to 
resolve this issue with FSL.  I have no experience with the Workbench platform. 
 I can look in that direction if I run out of FSL options.  Do you know if 
there is anyone who might be able to help with this?

Thanks again,
-hp

From: Timothy Coalson 
Sent: Friday, March 16, 2018 2:15 PM
To: Glasser, Matthew 
Cc: HERACLES PANAGIOTIDES ; hcp-users@humanconnectome.org 
Subject: Re: [HCP-Users] Fw:

Load both of the volumes into wb_view (high-res mask and low-res fMRI - you may 
want to separate out a single frame from the fMRI to keep memory usage down) 
and see if they align with each other (if they don't display correctly, turn on 
oblique volume drawing mode).  If they do align, the answer is trivial, use 
wb_command -volume-affine-resample with the identity matrix as the transform 
(for smoother edges, use trilinear interpolation of the mask, then threshold it 
at 0.5 with -volume-math).  If not, you will need a transform of some kind, for 
instance, one that takes the fMRI into MNI space (which would need to be 
inverted before using it for this). 

workbench does not have the same issues as FSL with different FOV between 
different volume files - all alignment is done by millimeters, not by corner of 
FOV.


Tim


On Fri, Mar 16, 2018 at 12:58 PM, Glasser, Matthew  wrote:

  Perhaps if this were done with wb_command -volume-resample it would work 
better, but Tim would have to comment on this.

  Matt.

  From: HERACLES PANAGIOTIDES 
  Date: Friday, March 16, 2018 at 12:11 PM
  To: Matt Glasser 
  Subject: Re: [HCP-Users] Fw:


  This is what I used:  

  applywarp -i left_Accumbens.nii.gz -r rfMRI_REST1_LR_hp2000_clean.nii.gz -o 
left_Accumbens_in_FA.nii.gz 

  The position came our not in the right place.  

  -hp

  From: Glasser, Matthew
  Sent: Friday, March 16, 2018 9:39 AM
  To: HERACLES PANAGIOTIDES 
  Subject: Re: [HCP-Users] Fw:

  It should work if you use applywarp with no warp or affine.

  Peace,

  Matt.

  From: HERACLES PANAGIOTIDES 
  Date: Friday, March 16, 2018 at 11:17 AM
  To: Matt Glasser 
  Subject: Re: [HCP-Users] Fw:


  Thanks for the reply, Matt.  I did not define the problem properly.  The 
original mask is in MNI space (198 X 263 X 212) but does not have the same 
number of voxels in each dimensions the rfMRI (91 X 109 X 91).  Is it possible 
to transform the the mask to have the same dimensionality (number of voxels in 
each dimension) as the rfMRI?

  Best,
  -hp
  From: Glasser, Matthew 
  Sent: Friday, March 16, 2018 7:22 AM
  To: HERACLES PANAGIOTIDES ; HCP 
  Subject: Re: [HCP-Users] Fw:

  Why can’t you use an MNI space accumbens mask?  

  Peace,

  Matt.

  From:  on behalf of HERACLES 
PANAGIOTIDES 
  Date: Friday, March 16, 2018 at 8:04 AM
  To: HCP 
  Subject: [HCP-Users] Fw:


  Could someone please help me warp a mask  (left_Accumbens.nii) to an rfMRI in 
MNI space. 
  I used the following FLIRT command:

  flirt –in left_Accumbens.nii.gz -ref rfMRI_REST1_LR_hp2000_clean.nii.gz 
-applyxfm -init MNI2FA.mat –out left_Accumbens_in_FA.nii.gz


  I am attaching the input, output and mat files.  the rfMRI is too big for 
this email.  I am also attaching an image that shows the original ROI (green) 
and the transformed/output ROI (red).  They are not registered correctly.  



  Alternatively, I used the fnirt command with no better luck.  

  fnirt --ref=rfMRI_REST1_LR_hp2000_clean.nii.gz --in=left_Accumbens.nii.gz -- 
inmask=left_Accumbens.nii.gz --aff=MNI2FA.mat --iout=left_Accumbens_in_FA.nii.gz


  Any ideas or suggestions?

  Thanks,
  -hp
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Re: [HCP-Users] HCP Pipeline without T2w

[Pedro Costa Klein]

Well, in this case, I will be using your toolbox now as it is just to get
familiar with it. I am really looking forward to the update then!

Thank you so much for the support.

Pedro


2018-03-16 21:40 GMT+01:00 Erin W. E. Dickie :

> In cases where you don't have a T2w image. You would run freesurfer's 
> `*recon_all`
> *on your T1w scans and then *`ciftify_recon_all` * to essentially mimic
> the HCPPipelines Anatomical. * `ciftify_recon_all` *contains a little bit
> of PreFreesurfer.sh and all of PostFreesurfer.sh and is meant to be run
> after freesurfer.
>
> In the next release (i.e. next week), ciftify_recon_all will use the
> MSMSulc surface based registration (matching the HCP outputs) instead of
> the freesurfer registration. I would recommend waiting for that.
>
> For fMRI, the current workflow will be fMRIprep followed by
> ciftify_subject_fmri.
>
> We will also try to clarify this more in the documentation over the next
> few weeks.
>
> Thanks,
> Erin
>
> On Fri, Mar 16, 2018 at 11:12 AM, Pedro Costa Klein  > wrote:
>
>> Thank you Matt for the indication and thank you Erin for such a quick
>> response!
>>
>> Erin, this toolbox seems to be exactly what I was looking for!
>>
>> Does this toolbox replaces all the stages of the pipeline or should I use
>> it at some point of the HCP pipeline (e.g. after running the
>> PreFressurfer.sh)?
>>
>> Best regards,
>>
>> 2018-03-16 15:56 GMT+01:00 Erin W. E. Dickie :
>>
>>> Thanks for the recommendation Matt!
>>>
>>> Pedro, the ciftify toolbox link is here (https://edickie.github.io/cif
>>> tify). The toolbox started with exactly with what you are suggesting
>>> (modifying the .sh files to make them run without T2w images). Over time we
>>> ended up translating the key parts to python and adding more detailed
>>> logging and less intermediate output files.
>>>
>>> The current state of the package is a little unstable as I'm currently
>>> working in a few final changes. I'm aiming to publish a more stable release
>>> within the next two weeks.
>>>
>>> Let me know if you have any questions.
>>>
>>> Thanks,
>>> Erin
>>>
>>>
>>>
>>> On Fri, Mar 16, 2018 at 10:28 AM, Glasser, Matthew 
>>> wrote:
>>>
 I would recommend the ciftify toolbox if your data do not meet HCP
 Pipelines acquisition requirements (lacking highres T2w scan and or
 Fieldmap).  The ciftify toolbox is currently beta, but should be fully
 available in the very near future (Erin Dickie the author is CCed and can
 give more details).

 Peace,

 Matt.

 From:  on behalf of Pedro Costa
 Klein 
 Date: Friday, March 16, 2018 at 3:49 AM
 To: "hcp-users@humanconnectome.org" 
 Subject: [HCP-Users] HCP Pipeline without T2w

 Dear all,

 I have a dataset that I wish to use with the HCP pipeline scripts from
 the repository in https://github.com/Washington-University/Pipelines,
 but I don't have the T2w images for the subjects. Is it possible (perhaps
 with some modification on the .sh files) to use pipeline without the T2w?
 If so, what would be the impact on the outputs and what are the most
 "critical" steps that I must pay attention to while changing the scripts?

 Another idea would be to replace the T2w images by a synthetic image
 (e.g. a T2w atlas, like the MNI). Is this option acceptable? If so, what
 would be the best approach for using a atlas replacing the T2w?

 Thank you very much for your insights.

 --
 *Pedro Costa Klein **(*https://scholar.google.
 com.br/citations?user=ll3ukqMJ)
 *PhD Student*
 *Klinik und Poliklink für Psychiatrie und Psychotherapie
 - Ludwig-Maximilians Universität*
 pedrockl...@gmail.com





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>>>
>>>
>>
>>
>> --
>> *Pedro Costa Klein **(*https://scholar.google.
>> com.br/citations?user=ll3ukqMJ)
>> *PhD Student*
>> *Klinik und Poliklink für Psychiatrie und Psychotherapie
>> - Ludwig-Maximilians Universität*
>> pedrockl...@gmail.com
>>
>>
>>
>>
>>
>>
>


-- 
*Pedro Costa Klein **(*
https://scholar.google.com.br/citations?user=ll3ukqMJ)
*PhD Student*
*Klinik und Poliklink für Psychiatrie und Psychotherapie
- Ludwig-Maximilians Universität*
pedrockl...@gmail.com

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