subject:"Re\: \[HCP\-Users\] Some questions about the HCP structural processing pipeline"

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

2019-04-10 Thread Aaron C

Hi Matt,

I called the FreeSurfer pipeline using the script "FreeSurferPipelineBatch.sh" 
in the "Examples" folder. Do you mean that these brain extracted T1w and T2w 
images "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the FreeSurfer 
pipeline? Thank you.

Aaron


From: Glasser, Matthew 
Sent: Monday, April 8, 2019 10:50 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Some questions about the HCP structural processing 
pipeline

The brain masked file should not be used for surface estimation.  How are you 
calling the FreeSurfer pipeline?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Monday, April 8, 2019 at 9:41 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about the HCP structural processing pipeline

Dear HCP experts,

I have some questions about the HCP structural processing pipeline.

  1.  The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w 
folder has excessive voxels removed in the cortical surface, which resulted in 
erroneous pial surface estimation. Is there a way that I could adjust any 
parameters of brain extraction in the PreFreeSurfer.sh file to have a larger 
brain mask?
  2.  There is another file "brainmask_fs.nii.gz". Is this the same mask 
derived from "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz"?
  3.  In the structural processing QC scene, is there a way that I could also 
display the boundary of the extracted brain alongside with pial and white 
surfaces in the coronal brain?

Thank you.

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Re: [HCP-Users] Some questions about the HCP structural processing pipeline

2019-04-09 Thread Timothy Coalson

To add some context, the _acpc_dc_restore_brain versions of the files are
*outputs* of the structural pipelines.  We do not run freesurfer on masked
T1w images.

Matt is asking for the exact arguments you provided to
FreeSurferPipeline.sh, by providing the full command line that was run that
contains "FreeSurferPipeline.sh" (not the ...Batch.sh).

Tim


On Tue, Apr 9, 2019 at 9:21 AM Glasser, Matthew  wrote:

> How did YOU call the FreeSurfer Pipeline in your subject with an issue?
>
> Matt.
>
> From: Aaron C 
> Date: Tuesday, April 9, 2019 at 8:42 AM
> To: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] Some questions about the HCP structural
> processing pipeline
>
> Hi Matt,
>
> I called the FreeSurfer pipeline using the script
> "FreeSurferPipelineBatch.sh" in the "Examples" folder. Do you mean that
> these brain extracted T1w and T2w images "T1w_acpc_dc_restore_brain.nii.gz"
> and "T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the
> FreeSurfer pipeline? Thank you.
>
> Aaron
>
> --
> *From:* Glasser, Matthew 
> *Sent:* Monday, April 8, 2019 10:50 PM
> *To:* Aaron C; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Some questions about the HCP structural
> processing pipeline
>
> The brain masked file should not be used for surface estimation.  How are
> you calling the FreeSurfer pipeline?
>
> Matt.
>
> From:  on behalf of Aaron C <
> aaroncr...@outlook.com>
> Date: Monday, April 8, 2019 at 9:41 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Some questions about the HCP structural processing
> pipeline
>
> Dear HCP experts,
>
> I have some questions about the HCP structural processing pipeline.
>
>1. The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the
>T1w folder has excessive voxels removed in the cortical surface, which
>resulted in erroneous pial surface estimation. Is there a way that I could
>adjust any parameters of brain extraction in the PreFreeSurfer.sh file to
>have a larger brain mask?
>2. There is another file "brainmask_fs.nii.gz". Is this the same mask
>derived from "T1w_acpc_dc_restore_brain.nii.gz" and
>"T2w_acpc_dc_restore_brain.nii.gz"?
>3. In the structural processing QC scene, is there a way that I could
>also display the boundary of the extracted brain alongside with pial and
>white surfaces in the coronal brain?
>
> Thank you.
>
> ___
> 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.
>
>
> --
>
> 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] Some questions about the HCP structural processing pipeline

2019-04-09 Thread Glasser, Matthew

How did YOU call the FreeSurfer Pipeline in your subject with an issue?

Matt.

From: Aaron C mailto:aaroncr...@outlook.com>>
Date: Tuesday, April 9, 2019 at 8:42 AM
To: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Some questions about the HCP structural processing 
pipeline

Hi Matt,

I called the FreeSurfer pipeline using the script "FreeSurferPipelineBatch.sh" 
in the "Examples" folder. Do you mean that these brain extracted T1w and T2w 
images "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the FreeSurfer 
pipeline? Thank you.

Aaron

From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Monday, April 8, 2019 10:50 PM
To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Some questions about the HCP structural processing 
pipeline

The brain masked file should not be used for surface estimation.  How are you 
calling the FreeSurfer pipeline?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Monday, April 8, 2019 at 9:41 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about the HCP structural processing pipeline

Dear HCP experts,

I have some questions about the HCP structural processing pipeline.

  1.  The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w 
folder has excessive voxels removed in the cortical surface, which resulted in 
erroneous pial surface estimation. Is there a way that I could adjust any 
parameters of brain extraction in the PreFreeSurfer.sh file to have a larger 
brain mask?
  2.  There is another file "brainmask_fs.nii.gz". Is this the same mask 
derived from "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz"?
  3.  In the structural processing QC scene, is there a way that I could also 
display the boundary of the extracted brain alongside with pial and white 
surfaces in the coronal brain?

Thank you.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.

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

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

2019-04-08 Thread Glasser, Matthew

The brain masked file should not be used for surface estimation.  How are you 
calling the FreeSurfer pipeline?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Monday, April 8, 2019 at 9:41 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about the HCP structural processing pipeline

Dear HCP experts,

I have some questions about the HCP structural processing pipeline.

  1.  The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w 
folder has excessive voxels removed in the cortical surface, which resulted in 
erroneous pial surface estimation. Is there a way that I could adjust any 
parameters of brain extraction in the PreFreeSurfer.sh file to have a larger 
brain mask?
  2.  There is another file "brainmask_fs.nii.gz". Is this the same mask 
derived from "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz"?
  3.  In the structural processing QC scene, is there a way that I could also 
display the boundary of the extracted brain alongside with pial and white 
surfaces in the coronal brain?

Thank you.

___
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

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

Re: [HCP-Users] Some questions about the HCP structural processing pipeline

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