Dear experts
In my center we are studying cortico-striatal functional connectivity, and
cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample.
For that we are using Choi's functional parcellation, distributed as a
volumetric NIFTI file, in MNI152 space. We want to validate
Dear Experts,
If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I
need to set DeDriftAndResamplePipelineBatch.sh as MotionRegression=TRUE?
Thanks,
Leah.
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A .dscalar.nii output, I think. Basically I want an equivalent of the nifti
ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if
outside. Would a dlabel file be better for this application?
El lun., 27 may. 2019 a las 19:03, Glasser, Matthew ()
escribió:
> Are you wanting a
Yes.
Matt.
From: on behalf of Marta Moreno
Date: Monday, May 27, 2019 at 11:15 AM
To: HCP Users
Subject: [HCP-Users] DeDriftAndResamplePipelineBatch.sh
Dear Experts,
If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I
need to set
To make the .dscalar.nii file, you seem to be on the right track. If the Choi
ROIs are properly in MNI space, hopefully you could simply use applywarp
--interp=nn -i -r
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
and then the wb_command
I thought you said you were using a locally collected sample you ran the HCP
Pipelines on?
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 3:10 PM
To: "Glasser, Matthew"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Ok, thank you! I will try that.
I
Are you wanting a .dlabel.nii output or a .dscalar.nii output?
Matt.
From: on behalf of Jaime Caballero
Date: Monday, May 27, 2019 at 10:37 AM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts
In my center we are studying
The objective is to extract functional connectivity between cortical and
striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
Up to this point I have imported each subject's dtseries.nii file into
MATLAB, and also the previously defined ROIs in an HCP-compatible format.
For the
OK. Thanks!
Leah.
> On May 27, 2019, at 12:59 PM, Glasser, Matthew wrote:
>
> Yes.
>
> Matt.
>
> From: on behalf of Marta Moreno
>
> Date: Monday, May 27, 2019 at 11:15 AM
> To: HCP Users
> Subject: [HCP-Users] DeDriftAndResamplePipelineBatch.sh
>
> Dear Experts,
>
> If I run MR
What do you plan to do with the file?
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 12:08 PM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an
Sorry for the confusion.
Locally acquired data wasn't processed using the HCP pipelines, it is in a
different resolution and it was processed in volume space, no problem there.
I want to use Choi's parcellation with HCP data. All the process I
described is mi workaround to adapt Choi files to
That file does exist in the structural package then.
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 3:20 PM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Sorry for the confusion.
Locally
Thanks Matt. and are acceptable ranges for values of those files less than 2
also?
Moataz
On Mon, May 27, 2019 at 5:47 AM +0100, "Glasser, Matthew"
mailto:glass...@wustl.edu>> wrote:
Hi Moataz,
I check the StrainJ (isotropic areal distortion) and StrainR (shape distortion)
and the overall
StrainR values are 2x higher than StrainJ in general. As for acceptable
values, keep in mind things like areal distortion/StrainJ are Log2 of the
number. That means that +/-2 means 4 fold expansion or contraction. What is
acceptable might vary from application to application. In general,
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