Re: [HCP-Users] table for parcellation

[Glasser, Matthew]

(ii) Yes that is the right file.  I would use the already concatenated one from 
MR+FIX, else you need to use the _vn files to concatenate yourself (demean, 
divide by _vn files, and merge).

Matt.

From:  on behalf of Timothy Coalson 

Date: Friday, June 21, 2019 at 2:20 PM
To: Marta Moreno 
Cc: HCP Users 
Subject: Re: [HCP-Users] table for parcellation

(i) You can use wb_command -cifti-label-export-table on the dlabel file to get 
the order of the parcels in a fixed format, though there are extra lines and 
numbers in the output text file.  360 parcels is a rather long table, you might 
consider a matrix figure instead, and only mention the highlights.  If you make 
the figure in wb_view, then you can upload the scene to BALSA, which will 
include the data files used to make it, allowing others to use your data 
directly instead of looking through a table.

Someone else will need to answer (ii).

Tim


On Thu, Jun 20, 2019 at 10:32 PM Marta Moreno 
mailto:mmorenoort...@icloud.com>> wrote:
Dear experts,

After running:

1.  PreFreeSurfer
2.  FreeSurfer
3.  PostFreeSurfer
4.  fMRIVolume
5.  fMRISurface
6.  ICA+FIX (MR+FIX)
7.  MSMAll (Do MSM Surface Registration)
8.  dedrift and resample pipeline

2 questions:

(i) I used wb_command -cifti-parcellate and wb_command -cifti-correlation to 
create a parcellation.pconn.nii file per each subject. I have uploaded all 
files into matlab and now would like to create a table that includes all 
subjects’ correlation value from parcel 264 to all 360 parcels, and include the 
variable names for all 360 parcels. How can I do this?

(ii) Is the file “RS_fMRI_MR_Atlas_MSMAll_Test_hp0_clean.dtseries.nii” the 
final step after (8) to use for wb_command -cifti-parcellate and wb_command 
-cifti-correlation

Thanks,

L.



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Re: [HCP-Users] NIFTI to CIFTI

[Timothy Coalson]

I don't know what 3dDeconvolve does, but if you used it to try to do
anything spatial (spatial sharpening, PSF, etc), then the files produced by
wb_command -cifti-convert would be entirely inappropriate.  The only
meaningful operations that can be done on -cifti-convert "volume-ish" files
are temporal processing, because the spatial aspects are completely jumbled.

That said, yes, if you made a volume-ish file by -cifti-convert and put
that through an afni tool, the cifti-template can be the input file you
used in -cifti-convert to make the volume-ish input in the first place.  If
the cifti files you are using are standard 91k grayordinates, you could use
the appropriate file from the Pipelines/global/templates folder if that was
somehow more convenient.  Since we do not expect tools to preserve anything
about the volume-ish files except the dimensions, we can't use the
volume-ish file to also store the information required to put the "voxels"
back into the right vertices, which is why a cifti file is required as the
template, to define what "voxel" actually represents each vertex, etc.

You will likely need the -reset-scalars option, as I expect the statistics
output is a different number of frames than the timeseries.

Tim


On Fri, Jun 21, 2019 at 12:24 PM Pipoly, Marco A 
wrote:

> Hello All,
>
>
> I am relatively new to working with HCP tfMRI connectome data and am
> running into a bit of confusion about the following: I have statistical map
> outputs (in stats.nii.gz format) from, CIFTI data converted to NIFTI data
> that I put into AFNI 3dDeconvolve. I am interested in converting this
> output (stats.nii.gz) back into CIFTI in order to regain respect to the
> surface and structure information (that does not appear to remain when you
> wb_command CIFTI->NIFTI).
>
>
> It appears this will do the trick?:
>
> [-from-nifti] - convert a NIFTI (1 or 2) file made with this command back
>  into CIFTI
>   - the input nifti file
>   - a cifti file with the dimension(s) and mapping(s)
> that should be used
>   - output - the output cifti file
>
> If so, what exactly does it mean by "cifti-template?" Would this be the
> original dtseries file I used to procure the AFNI 3dDeconvolve outputs or
> is there a generic template brain(s) for the various CIFTI data types?
>
>
> Best,
>
>
> Marco A. Pipoly, B.S.
> NSF Graduate Research Fellow
> Graduate Student, PhD in Neuroscience
> University of Iowa
> marco-pip...@uiowa.edu
>
>
>
>
>
>
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Re: [HCP-Users] A question about scene file

[Harms, Michael]

As part of some other updates to the StructuralQC scenes themselves, I recently 
created a more sophisticated generation script that should use relative paths 
within the scene.

Please try the just updated master branch of
https://github.com/Washington-University/StructuralQC

We have tested this internally, but it would be good to get feedback from an 
outside user before I formally tag a new release.

Thanks,
-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 Aaron C 

Date: Friday, June 21, 2019 at 12:23 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] A question about scene file

Dear HCP experts,

The scene file (a structural processing QC scene) I generated in a Linux 
computer doesn't work in a Windows computer. It seems that the file paths were 
hard-coded in the scene file. Is there a way to make it more portable? Thank 
you.

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Re: [HCP-Users] A question about scene file

[Timothy Coalson]

Sorry, in my second paragraph I meant "breaking the usual convention of the
scene file XML".

Tim


On Fri, Jun 21, 2019 at 2:28 PM Timothy Coalson  wrote:

> The paths inside a scene file's XML are supposed to be relative to the
> location of the scene file.  You are expected to usually have the scene
> file in a directory nearby where the data it refers to is, to reduce how
> far it crosses your filesystem structure to generate the relative paths.
> You can use wb_command -scene-file-relocate to move the scene file and
> regenerate its internal paths to put it closer to the data directory.  If
> you need to move it to a system that doesn't have the same filesystems
> mounted the same way, there is wb_command -zip-scene-file (or the "Zip..."
> button in the wb_view scene window), which will generate a self-contained
> archive with all the referenced files and the necessary directory layout.
>
> If the QC scene was generated with a script, it may be that the
> substituted paths were absolute, breaking the usual convention of the
> script.  Using -scene-file-relocate or loading and saving the scene file
> may convert these paths to relative.
>
> Tim
>
>
> On Fri, Jun 21, 2019 at 12:23 PM Aaron C  wrote:
>
>> Dear HCP experts,
>>
>> The scene file (a structural processing QC scene) I generated in a Linux
>> computer doesn't work in a Windows computer. It seems that the file paths
>> were hard-coded in the scene file. Is there a way to make it more portable?
>> Thank you.
>>
>> ___
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>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>

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Re: [HCP-Users] A question about scene file

[Timothy Coalson]

The paths inside a scene file's XML are supposed to be relative to the
location of the scene file.  You are expected to usually have the scene
file in a directory nearby where the data it refers to is, to reduce how
far it crosses your filesystem structure to generate the relative paths.
You can use wb_command -scene-file-relocate to move the scene file and
regenerate its internal paths to put it closer to the data directory.  If
you need to move it to a system that doesn't have the same filesystems
mounted the same way, there is wb_command -zip-scene-file (or the "Zip..."
button in the wb_view scene window), which will generate a self-contained
archive with all the referenced files and the necessary directory layout.

If the QC scene was generated with a script, it may be that the substituted
paths were absolute, breaking the usual convention of the script.  Using
-scene-file-relocate or loading and saving the scene file may convert these
paths to relative.

Tim


On Fri, Jun 21, 2019 at 12:23 PM Aaron C  wrote:

> Dear HCP experts,
>
> The scene file (a structural processing QC scene) I generated in a Linux
> computer doesn't work in a Windows computer. It seems that the file paths
> were hard-coded in the scene file. Is there a way to make it more portable?
> Thank you.
>
> ___
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] table for parcellation

[Timothy Coalson]

(i) You can use wb_command -cifti-label-export-table on the dlabel file to
get the order of the parcels in a fixed format, though there are extra
lines and numbers in the output text file.  360 parcels is a rather long
table, you might consider a matrix figure instead, and only mention the
highlights.  If you make the figure in wb_view, then you can upload the
scene to BALSA, which will include the data files used to make it, allowing
others to use your data directly instead of looking through a table.

Someone else will need to answer (ii).

Tim


On Thu, Jun 20, 2019 at 10:32 PM Marta Moreno 
wrote:

> Dear experts,
>
> After running:
>
> 1.  PreFreeSurfer
> 2.  FreeSurfer
> 3.  PostFreeSurfer
> 4.  fMRIVolume
> 5.  fMRISurface
> 6.  ICA+FIX (MR+FIX)
> 7.  MSMAll (Do MSM Surface Registration)
> 8.  dedrift and resample pipeline
>
> 2 questions:
>
> (i) I used wb_command -cifti-parcellate and wb_command -cifti-correlation
> to create a parcellation.pconn.nii file per each subject. I have uploaded
> all files into matlab and now would like to create a table that includes
> all subjects’ correlation value from parcel 264 to all 360 parcels, and
> include the variable names for all 360 parcels. How can I do this?
>
> (ii) Is the file “RS_fMRI_MR_Atlas_MSMAll_Test_hp0_clean.dtseries.nii”
> the final step after (8) to use for wb_command -cifti-parcellate and 
> wb_command
> -cifti-correlation
>
> Thanks,
>
> L.
>
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] NIFTI to CIFTI

[Pipoly, Marco A]

Hello All,


I am relatively new to working with HCP tfMRI connectome data and am running 
into a bit of confusion about the following: I have statistical map outputs (in 
stats.nii.gz format) from, CIFTI data converted to NIFTI data that I put into 
AFNI 3dDeconvolve. I am interested in converting this output (stats.nii.gz) 
back into CIFTI in order to regain respect to the surface and structure 
information (that does not appear to remain when you wb_command CIFTI->NIFTI).


It appears this will do the trick?:

[-from-nifti] - convert a NIFTI (1 or 2) file made with this command back
 into CIFTI
  - the input nifti file
  - a cifti file with the dimension(s) and mapping(s)
that should be used
  - output - the output cifti file

If so, what exactly does it mean by "cifti-template?" Would this be the 
original dtseries file I used to procure the AFNI 3dDeconvolve outputs or is 
there a generic template brain(s) for the various CIFTI data types?


Best,


Marco A. Pipoly, B.S.
NSF Graduate Research Fellow
Graduate Student, PhD in Neuroscience
University of Iowa
marco-pip...@uiowa.edu







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[HCP-Users] A question about scene file

[Aaron C]

Dear HCP experts,

The scene file (a structural processing QC scene) I generated in a Linux 
computer doesn't work in a Windows computer. It seems that the file paths were 
hard-coded in the scene file. Is there a way to make it more portable? Thank 
you.

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