date:20190423

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

2019-04-23 Thread Glasser, Matthew

Also ReApplyFixMultiRunPipeline.sh is not affected at all by this bug.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Matt Glasser mailto:glass...@wustl.edu>>
Date: Tuesday, April 23, 2019 at 7:47 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>, "Harms, Michael" 
mailto:mha...@wustl.edu>>
Cc: HCP Users 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz 
volume data for some (one?) subjects?

This is a bug affecting the use of ReApplyFix to re-clean data using a hand 
classification instead of the original FIX classification (and does not affect 
the use of ReApplyFix in MSMAll).  It has been present since the release of 
ReApplyFix and will affect the volume data of all HCP-YA subjects for which a 
hand classification was used (list will be forthcoming).  The bug will be fixed 
in the next bugfix release of the HCP Pipelines and the data corrected.  Sorry 
about this.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, April 23, 2019 at 6:12 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: HCP Users 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz 
volume data for some (one?) subjects?

Correction, the issue to follow is #107:

https://github.com/Washington-University/HCPpipelines/issues/107

Tim

On Tue, Apr 23, 2019 at 4:35 PM Harms, Michael 
mailto:mha...@wustl.edu>> wrote:

For users that want to follow this, please see:
https://github.com/Washington-University/HCPpipelines/issues/108

It has something to do with the fact that we needed to apply manual 
reclassification of the FIX output in that particular subject/run.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Keith Jamison mailto:kjami...@umn.edu>>
Date: Tuesday, April 23, 2019 at 3:59 PM
To: HCP Users 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume 
data for some (one?) subjects?

For subject 204218, both REST1_LR and REST1_RL, I noticed a linear trend in the 
*_hp2000_clean.nii.gz NIFTI time series, but the hp2000_clean.dtseries.nii 
CIFTI files do not have this trend. See attached figures showing this issue for 
both REST1_LR and REST1_RL for 204218. The overall mean time series has a 
negative trend for NIFTI, but in the voxel time series on the left you can see 
that some have positive trend and some have negative. To test, I did run 
fslmaths-based filtering on hp2000_clean.nii.gz and I no longer see any linear 
trend.

I tried one scan in one additional subject, 102311 REST1_LR, and did not see 
this linear trend in either NIFTI or CIFTI (also attached).

Note: I did remove the overall mean for each voxel timecourse before
plotting, and for the NIFTI I'm only showing gray matter voxels, as determined 
by downsampling aparc+aseg.nii.gz and excluding labels for WM,CSF,ventricles, 
and a few misc. I also tried looking at all non-zero voxels, as well as only 
those marked in RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz, but the issue 
of linear trends is the same.

Any idea what might be going on with this subject? I haven't tried this in 
anyone other than 204218 (bad) and 102311 (good).

-Keith

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Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

2019-04-23 Thread Glasser, Matthew

This is a bug affecting the use of ReApplyFix to re-clean data using a hand 
classification instead of the original FIX classification (and does not affect 
the use of ReApplyFix in MSMAll).  It has been present since the release of 
ReApplyFix and will affect the volume data of all HCP-YA subjects for which a 
hand classification was used (list will be forthcoming).  The bug will be fixed 
in the next bugfix release of the HCP Pipelines and the data corrected.  Sorry 
about this.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, April 23, 2019 at 6:12 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: HCP Users 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz 
volume data for some (one?) subjects?

Correction, the issue to follow is #107:

https://github.com/Washington-University/HCPpipelines/issues/107

Tim


On Tue, Apr 23, 2019 at 4:35 PM Harms, Michael 
mailto:mha...@wustl.edu>> wrote:

For users that want to follow this, please see:
https://github.com/Washington-University/HCPpipelines/issues/108

It has something to do with the fact that we needed to apply manual 
reclassification of the FIX output in that particular subject/run.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Keith Jamison mailto:kjami...@umn.edu>>
Date: Tuesday, April 23, 2019 at 3:59 PM
To: HCP Users 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume 
data for some (one?) subjects?

For subject 204218, both REST1_LR and REST1_RL, I noticed a linear trend in the 
*_hp2000_clean.nii.gz NIFTI time series, but the hp2000_clean.dtseries.nii 
CIFTI files do not have this trend. See attached figures showing this issue for 
both REST1_LR and REST1_RL for 204218. The overall mean time series has a 
negative trend for NIFTI, but in the voxel time series on the left you can see 
that some have positive trend and some have negative. To test, I did run 
fslmaths-based filtering on hp2000_clean.nii.gz and I no longer see any linear 
trend.

I tried one scan in one additional subject, 102311 REST1_LR, and did not see 
this linear trend in either NIFTI or CIFTI (also attached).

Note: I did remove the overall mean for each voxel timecourse before
plotting, and for the NIFTI I'm only showing gray matter voxels, as determined 
by downsampling aparc+aseg.nii.gz and excluding labels for WM,CSF,ventricles, 
and a few misc. I also tried looking at all non-zero voxels, as well as only 
those marked in RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz, but the issue 
of linear trends is the same.

Any idea what might be going on with this subject? I haven't tried this in 
anyone other than 204218 (bad) and 102311 (good).

-Keith



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Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

2019-04-23 Thread Timothy Coalson

Correction, the issue to follow is #107:

https://github.com/Washington-University/HCPpipelines/issues/107

Tim


On Tue, Apr 23, 2019 at 4:35 PM Harms, Michael  wrote:

>
>
> For users that want to follow this, please see:
>
> https://github.com/Washington-University/HCPpipelines/issues/108
>
>
>
> It has something to do with the fact that we needed to apply manual
> reclassification of the FIX output in that particular subject/run.
>
>
>
> 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 Keith
> Jamison 
> *Date: *Tuesday, April 23, 2019 at 3:59 PM
> *To: *HCP Users 
> *Subject: *[HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz
> volume data for some (one?) subjects?
>
>
>
> For subject 204218, both REST1_LR and REST1_RL, I noticed a linear trend
> in the *_hp2000_clean.nii.gz NIFTI time series, but the
> hp2000_clean.dtseries.nii CIFTI files do not have this trend. See attached
> figures showing this issue for both REST1_LR and REST1_RL for 204218. The
> overall mean time series has a negative trend for NIFTI, but in the voxel
> time series on the left you can see that some have positive trend and some
> have negative. To test, I did run fslmaths-based filtering on
> hp2000_clean.nii.gz and I no longer see any linear trend.
>
> I tried one scan in one additional subject, 102311 REST1_LR, and did not
> see this linear trend in either NIFTI or CIFTI (also attached).
>
> Note: I did remove the overall mean for each voxel timecourse before
> plotting, and for the NIFTI I'm only showing gray matter voxels, as
> determined by downsampling aparc+aseg.nii.gz and excluding labels for
> WM,CSF,ventricles, and a few misc. I also tried looking at all non-zero
> voxels, as well as only those marked in
> RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz, but the issue of linear
> trends is the same.
>
> Any idea what might be going on with this subject? I haven't tried this in
> anyone other than 204218 (bad) and 102311 (good).
>
> -Keith
>
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

2019-04-23 Thread Harms, Michael


For users that want to follow this, please see:
https://github.com/Washington-University/HCPpipelines/issues/108

It has something to do with the fact that we needed to apply manual 
reclassification of the FIX output in that particular subject/run.

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 Keith Jamison 

Date: Tuesday, April 23, 2019 at 3:59 PM
To: HCP Users 
Subject: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume 
data for some (one?) subjects?

For subject 204218, both REST1_LR and REST1_RL, I noticed a linear trend in the 
*_hp2000_clean.nii.gz NIFTI time series, but the hp2000_clean.dtseries.nii 
CIFTI files do not have this trend. See attached figures showing this issue for 
both REST1_LR and REST1_RL for 204218. The overall mean time series has a 
negative trend for NIFTI, but in the voxel time series on the left you can see 
that some have positive trend and some have negative. To test, I did run 
fslmaths-based filtering on hp2000_clean.nii.gz and I no longer see any linear 
trend.

I tried one scan in one additional subject, 102311 REST1_LR, and did not see 
this linear trend in either NIFTI or CIFTI (also attached).

Note: I did remove the overall mean for each voxel timecourse before
plotting, and for the NIFTI I'm only showing gray matter voxels, as determined 
by downsampling aparc+aseg.nii.gz and excluding labels for WM,CSF,ventricles, 
and a few misc. I also tried looking at all non-zero voxels, as well as only 
those marked in RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz, but the issue 
of linear trends is the same.

Any idea what might be going on with this subject? I haven't tried this in 
anyone other than 204218 (bad) and 102311 (good).

-Keith



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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [HCP-Users] EXT MSG Re: Parcellation

2019-04-23 Thread Briend, Frederic

Thanks for your very helpful advice Tim,
I am going to use ciftify.


Best,

Frederic




From: Timothy Coalson 
Sent: Tuesday, April 23, 2019 12:26:13 PM
To: Briend, Frederic
Cc: hcp-users@humanconnectome.org
Subject: EXT MSG Re: [HCP-Users] Parcellation

We recommend mapping the individual cortical data to surfaces before doing 
anything else with the data.  If you have fieldmaps, and high-res T1w and T2w, 
you may be able to use the HCP pipelines to do this:

https://github.com/Washington-University/HCPpipelines

If you don't have these scans, another possibility is ciftify:

https://github.com/edickie/ciftify

Either of these will output your data in cifti format, and you can then use 
wb_command -cifti-parcellate on it.

You can accurately map the parcellation into an individual's volume space using 
their surfaces, but that uses the same information needed to map the subject's 
data to the surface anyway.  However, it is generally not possible to 
accurately map the parcellation to group-averaged volume data, because existing 
volume registration does not achieve the same alignment precision across 
subjects that surface registration does, see our recent paper:

https://www.ncbi.nlm.nih.gov/pubmed/29925602

Tim


On Tue, Apr 23, 2019 at 12:27 PM Briend, Frederic 
mailto:fbri...@uabmc.edu>> wrote:

Dear hcp-users members,

I would like to use a parcellation (Glasser's atlas 360), to reduce the 
dimensionality from my image (resting-state images in .nii) from voxels to 
parcels (averaging my timeseries across each parcel).

How is it possible to do that, as advice by Matthew 
here,
 by the Connectome Workbench’s wb_command -cifti-parcellate ?

Thanks a lot.

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Re: [HCP-Users] Parcellation

2019-04-23 Thread Timothy Coalson

We recommend mapping the individual cortical data to surfaces before doing
anything else with the data.  If you have fieldmaps, and high-res T1w and
T2w, you may be able to use the HCP pipelines to do this:

https://github.com/Washington-University/HCPpipelines

If you don't have these scans, another possibility is ciftify:

https://github.com/edickie/ciftify

Either of these will output your data in cifti format, and you can then use
wb_command -cifti-parcellate on it.

You can accurately map the parcellation into an individual's volume space
using their surfaces, but that uses the same information needed to map the
subject's data to the surface anyway.  However, it is generally not
possible to accurately map the parcellation to group-averaged volume data,
because existing volume registration does not achieve the same alignment
precision across subjects that surface registration does, see our recent
paper:

https://www.ncbi.nlm.nih.gov/pubmed/29925602

Tim

On Tue, Apr 23, 2019 at 12:27 PM Briend, Frederic  wrote:

> Dear hcp-users members,
>
>
> I would like to use a parcellation (Glasser's atlas 360), to reduce the
> dimensionality from my image (resting-state images in .nii) from voxels to
> parcels (averaging my timeseries across each parcel).
>
> How is it possible to do that, as advice by Matthew here
> ,
> by the Connectome Workbench’s wb_command -cifti-parcellate ?
>
>
> Thanks a lot.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] Parcellation

2019-04-23 Thread Briend, Frederic

Dear hcp-users members,

I would like to use a parcellation (Glasser's atlas 360), to reduce the 
dimensionality from my image (resting-state images in .nii) from voxels to 
parcels (averaging my timeseries across each parcel).

How is it possible to do that, as advice by Matthew 
here,
 by the Connectome Workbench’s wb_command -cifti-parcellate ?

Thanks a lot.

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Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

Re: [HCP-Users] EXT MSG Re: Parcellation

Re: [HCP-Users] Parcellation

[HCP-Users] Parcellation

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