Re: [HCP-Users] Topup_AP dimension issue

2019-03-25 Thread Timothy Coalson 
That looks like you cut off some brain tissue.  I'm not really sure what
your goal is here, but if you have images with different voxel sizes, what
you may actually need to do is to resample an image (flirt, applywarp, or
wb_command -volume-*-resample), and not crop it.

Tim


On Sun, Mar 24, 2019 at 10:22 PM Marta Moreno 
wrote:

> Thanks for your response. The image is now cropped, image attached.
>
> Leah.
>
>
> ***
> Leah Moreno, PhD
> Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21
> New York, NY 10032
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu
>
> On Mar 24, 2019, at 10:58 PM, Glasser, Matthew  wrote:
>
> 0 66 to include all slices and probably 0 1 for timepoints tacked onto the
> end.
>
> Matt.
>
> From: Marta Moreno 
> Date: Sunday, March 24, 2019 at 9:54 PM
> To: Matt Glasser 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] Topup_AP dimension issue
>
> Thanks for your response. Still seams to be empty. I have attached both
> files into this email in case it helps.
>
> Leah.
>
>
>
> ***
> Leah Moreno, PhD
> Research Scientist
> Division of Experimental Therapeutics
> Department of Psychiatry
> Columbia University Medical Center
> 1051 Riverside Drive, Unit 21
> New York, NY 10032
> phone: (914) 218-7311
> email: mm4...@cumc.columbia.edu
>
> On Mar 24, 2019, at 10:47 PM, Glasser, Matthew  wrote:
>
> Not negative.
>
> Matt.
>
> From: Marta Moreno 
> Date: Sunday, March 24, 2019 at 9:45 PM
> To: Matt Glasser 
> Cc: HCP Users 
> Subject: Re: [HCP-Users] Topup_AP dimension issue
>
> Thanks for your response. Do you mean running this?: fslroi
> NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96
> 66 66
>
> If that is the case the test file seams to be empty.
>
> Leah.
>
>
>
> On Mar 24, 2019, at 8:25 PM, Glasser, Matthew  wrote:
>
> Subtract 128 from 96 and then take half of that as your start and 96 as
> your length.
>
> Matt.
>
> From:  on behalf of Marta Moreno <
> mmorenoort...@icloud.com>
> Date: Sunday, March 24, 2019 at 6:40 PM
> To: HCP Users 
> Subject: [HCP-Users] Topup_AP dimension issue
>
> Dear Experts,
>
> Maybe a trivial question but how can I change the Topup_AP dimension' size
> from 128 128 66 to 96 96 66? Using fslroi I am cutting the brain.
>
> Thanks,
>
> Leah.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
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> 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.
>
>
>
>
> --
> 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.
>
>
> ___
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Re: [HCP-Users] A question about the MSMSulc

2019-03-25 Thread Glasser, Matthew 
Please download the appropriate compiled release: 
https://github.com/ecr05/MSM_HOCR/releases

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, March 25, 2019 at 7:09 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] A question about the MSMSulc

but regarding this repository, you mean MSM_HOCR/src/MSM ?
because the files there are .cc, which is not what the pipeline codes look for..



On Mon, 25 Mar 2019 at 13:35, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
It should point to where the compiled MSM binary is.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, March 25, 2019 at 3:17 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>, Matt 
Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] A question about the MSMSulc

hey
following this issue, should the $MSMBINDIR point to this whole directory, or 
only to the src folder inside of it?

thanks,
Shachar


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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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 
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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] A question about the MSMSulc

2019-03-25 Thread Shachar Gal 
hey
following this issue, should the $MSMBINDIR point to this whole directory,
or only to the src folder inside of it?

thanks,
Shachar

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Re: [HCP-Users] A question about the MSMSulc

2019-03-25 Thread Shachar Gal 
but regarding this repository, you mean MSM_HOCR/src/MSM ?
because the files there are .cc, which is not what the pipeline codes look
for..



On Mon, 25 Mar 2019 at 13:35, Glasser, Matthew  wrote:

> It should point to where the compiled MSM binary is.
>
> Matt.
>
> From: Shachar Gal 
> Date: Monday, March 25, 2019 at 3:17 AM
> To: "hcp-users@humanconnectome.org" , Matt
> Glasser 
> Subject: Re: [HCP-Users] A question about the MSMSulc
>
> hey
> following this issue, should the $MSMBINDIR point to this whole directory,
> or only to the src folder inside of it?
>
> thanks,
> Shachar
>
>
> --
>
> 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.
>

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Re: [HCP-Users] A question about the MSMSulc

2019-03-25 Thread Glasser, Matthew 
It should point to where the compiled MSM binary is.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, March 25, 2019 at 3:17 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>, Matt 
Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] A question about the MSMSulc

hey
following this issue, should the $MSMBINDIR point to this whole directory, or 
only to the src folder inside of it?

thanks,
Shachar


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.

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Re: [HCP-Users] Resting state networks

2019-03-25 Thread Glasser, Matthew 
Right.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Claude Bajada 
mailto:c.baj...@fz-juelich.de>>
Date: Monday, March 25, 2019 at 5:39 AM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Resting state networks


Thanks for your reply Tim, by "least pairing an LR with an RL" I assume you 
mean concatenate the time series, correct?

Claude

On 22/03/2019 19:19, Timothy Coalson wrote:
Inline replies.

Tim


On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada 
mailto:c.baj...@fz-juelich.de>> wrote:
Dear experts,

Could I just confirm that the data that is found in:

${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates

Yes.

and that these data can be used to then produce Resting state networks

Yes.

(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?

Yes, but the LR and RL runs have different locations of signal dropout, so we 
generally recommend at least pairing an LR with an RL to increase the overall 
coverage.


Am I also correct in assuming that these data are not smoothed?

No, there is a small amount of added smoothing done (2mm FWHM) while putting 
the data into ~2mm grayordinates space - this could be done without any added 
smoothing, but for historical reasons we have kept it consistent with earlier 
releases.  Of course, this amount doesn't approach the smoothing done in many 
non-HCP analysis streams.

Regards,

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Topup_AP dimension issue

2019-03-25 Thread Glasser, Matthew 
If this is in relation to matching it to a gradient echo image, do they now 
line up?

Matt.

From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 24, 2019 at 10:22 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Topup_AP dimension issue

Thanks for your response. The image is now cropped, image attached.

Leah.

[cid:A5254DC1-6600-41D6-8981-FBA6526606CF@home]

***
Leah Moreno, PhD
Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu

On Mar 24, 2019, at 10:58 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

0 66 to include all slices and probably 0 1 for timepoints tacked onto the end.

Matt.

From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 24, 2019 at 9:54 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Topup_AP dimension issue

Thanks for your response. Still seams to be empty. I have attached both files 
into this email in case it helps.

Leah.



***
Leah Moreno, PhD
Research Scientist
Division of Experimental Therapeutics
Department of Psychiatry
Columbia University Medical Center
1051 Riverside Drive, Unit 21
New York, NY 10032
phone: (914) 218-7311
email: mm4...@cumc.columbia.edu

On Mar 24, 2019, at 10:47 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

Not negative.

Matt.

From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 24, 2019 at 9:45 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Topup_AP dimension issue

Thanks for your response. Do you mean running this?: fslroi 
NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 66 
66

If that is the case the test file seams to be empty.

Leah.



On Mar 24, 2019, at 8:25 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

Subtract 128 from 96 and then take half of that as your start and 96 as your 
length.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Marta Moreno 
mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 24, 2019 at 6:40 PM
To: HCP Users 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Topup_AP dimension issue

Dear Experts,

Maybe a trivial question but how can I change the Topup_AP dimension' size from 
128 128 66 to 96 96 66? Using fslroi I am cutting the brain.

Thanks,

Leah.

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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.




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 
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Re: [HCP-Users] Resting state networks

2019-03-25 Thread Claude Bajada 
Thanks for your reply Tim, by "least pairing an LR with an RL" I assume 
you mean concatenate the time series, correct?


Claude

On 22/03/2019 19:19, Timothy Coalson wrote:

Inline replies.

Tim


On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada > wrote:


Dear experts,

Could I just confirm that the data that is found in:


${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates


Yes.

and that these data can be used to then produce Resting state networks


Yes.

(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four
subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?


Yes, but the LR and RL runs have different locations of signal 
dropout, so we generally recommend at least pairing an LR with an RL 
to increase the overall coverage.



Am I also correct in assuming that these data are not smoothed?


No, there is a small amount of added smoothing done (2mm FWHM) while 
putting the data into ~2mm grayordinates space - this could be done 
without any added smoothing, but for historical reasons we have kept 
it consistent with earlier releases.  Of course, this amount doesn't 
approach the smoothing done in many non-HCP analysis streams.


Regards,

Claude







Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt






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