[HCP-Users] Structural Protocol

[Rachel Woodall]

Hello,

Is the Pheonix ZIP file available for the structural protocol on a 3T
Siemens Prisma?

Many thanks,
Rachel

-- 
Rachel Woodall

PhD Student
University of York
Department of Psychology
YO10 5DD

Email: rachel.wood...@york.ac.uk
Phone: 01904 567613

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Re: [HCP-Users] Structural Protocol

[Harms, Michael]

Hi,
You can find an importable protocol here:
http://protocols.humanconnectome.org/CCF/

The protocols that we are using for the HCP-Aging/Development projects are 
highly similar, but include a few additions (e.g., switch to 
navigator-corrected anatomicals; addition of PCASL scan).  Those will be posted 
once we can organize the documentation (sometime after OHBM).

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
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 Rachel Woodall 
>
Date: Wednesday, June 21, 2017 at 3:42 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Structural Protocol

Hello,

Is the Pheonix ZIP file available for the structural protocol on a 3T Siemens 
Prisma?

Many thanks,
Rachel

--
Rachel Woodall

PhD Student
University of York
Department of Psychology
YO10 5DD

Email: rachel.wood...@york.ac.uk
Phone: 01904 567613


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Re: [HCP-Users] Custom visualisation help

[Timothy Coalson]

As a sanity check, try adding "-drop-unused-labels".  If loading that
result still has the labels in the features box, then it means your input
file does have the values that your text files specifies.

To expend on my previous reply (we are a little busy with the HCP course),
the last element in the lines of numbers is the opacity value, so
previously your text file specified that the labels were almost completely
transparent.  You want them to be like this for them to be opaque:

TCpol_R
1255208208255
...

Tim



On Wed, Jun 21, 2017 at 9:26 AM, Seán Froudist Walsh 
wrote:

>
> Thanks a lot for the suggestion Timothy. Unfortunately I'm still getting a
> colourless map. I did get the result I wanted using the matlab gifti
> toolbox ( http://www.artefact.tk/software/matlab/gifti/ ), so no rush.
>
> Perhaps I'm saving under the wrong name, or doing something wrong when
> trying to visualise? Here's the actual command I'm using.
>
> wb_command -volume-label-import sequential_region_map_no_hipp.nii.gz
> hipp_pre_color_palette_table.txt sequential_region_map_no_hipp_
> hcp_label.nii.gz
>
> Then when I'm trying to visualise it, I'm just loading it in and trying to
> display over the atlas I'm using.
>
> Not sure if there's more info I can give.
>
> Thanks again for the help.
>
> Best wishes,
>
> Sean
>
>
> On 21 June 2017 at 11:42, Timothy Coalson  wrote:
>
>> The fourth "color" specifier in your text file should be 255, not 1.
>>
>> Tim
>>
>>
>> On Wed, Jun 21, 2017 at 8:34 AM, Seán Froudist Walsh 
>> wrote:
>>
>>> Sorry, made a mistake in my e-mail. I tried wb_command
>>> -volume-label-import and got the results explained previously. Any ideas?
>>>
>>> Thanks,
>>>
>>> Sean
>>>
>>> On 20 June 2017 at 20:08, Glasser, Matthew  wrote:
>>>
 I think you want wb_command -volume-label-import.

 Peace,

 Matt.

 From:  on behalf of Seán
 Froudist Walsh 
 Date: Tuesday, June 20, 2017 at 7:04 PM
 To: "hcp-users@humanconnectome.org" 
 Subject: [HCP-Users] Custom visualisation help

 Hey all,

 I'm trying to get a colour display on a surface to match a colormap I
 have set up in matlab, and have run into a whole world of pain. I would
 greatly appreciate your help.

 I have created a label text file of the following format:

 TCpol_R
 12552082081
 TCs_R
 22551581581
 Amyg_R
 325581811
 PFCoi_R
 42552312311

 I additionally have a nifti file, and a func.gii surface file (created
 with wb_command -volume-to-surface-mapping )

 Ideally I would like to display those colours on the surface, in the
 correct clusters.

 I thought I would try to display them on a volume as a first step, but
 that hasn't gone smoothly either.
 I used a command of the following format:
 wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
 my_label_volume.nii.gz

 Then I tried to display the label file over the volume in wb_view to no
 avail (I only see the underlying anatomical volume). Despite this, if I go
 to
 Overlay Tools --> Settings --> Edit Map's Labels
 I can see all of the labels I wanted listed, next to the correct
 colours.

 I would greatly appreciate if you could help fill in the gaps in my
 knowledge so that I can display my custom coloured labels on the surface.

 Many thanks,

 Sean

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 HCP-Users mailing list
 HCP-Users@humanconnectome.org
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>>>
>>> ___
>>> HCP-Users mailing list
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>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>

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Re: [HCP-Users] Custom visualisation help

[Timothy Coalson]

The fourth "color" specifier in your text file should be 255, not 1.

Tim


On Wed, Jun 21, 2017 at 8:34 AM, Seán Froudist Walsh 
wrote:

> Sorry, made a mistake in my e-mail. I tried wb_command
> -volume-label-import and got the results explained previously. Any ideas?
>
> Thanks,
>
> Sean
>
> On 20 June 2017 at 20:08, Glasser, Matthew  wrote:
>
>> I think you want wb_command -volume-label-import.
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Seán Froudist
>> Walsh 
>> Date: Tuesday, June 20, 2017 at 7:04 PM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Custom visualisation help
>>
>> Hey all,
>>
>> I'm trying to get a colour display on a surface to match a colormap I
>> have set up in matlab, and have run into a whole world of pain. I would
>> greatly appreciate your help.
>>
>> I have created a label text file of the following format:
>>
>> TCpol_R
>> 12552082081
>> TCs_R
>> 22551581581
>> Amyg_R
>> 325581811
>> PFCoi_R
>> 42552312311
>>
>> I additionally have a nifti file, and a func.gii surface file (created
>> with wb_command -volume-to-surface-mapping )
>>
>> Ideally I would like to display those colours on the surface, in the
>> correct clusters.
>>
>> I thought I would try to display them on a volume as a first step, but
>> that hasn't gone smoothly either.
>> I used a command of the following format:
>> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
>> my_label_volume.nii.gz
>>
>> Then I tried to display the label file over the volume in wb_view to no
>> avail (I only see the underlying anatomical volume). Despite this, if I go
>> to
>> Overlay Tools --> Settings --> Edit Map's Labels
>> I can see all of the labels I wanted listed, next to the correct colours.
>>
>> I would greatly appreciate if you could help fill in the gaps in my
>> knowledge so that I can display my custom coloured labels on the surface.
>>
>> Many thanks,
>>
>> Sean
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
> ___
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Custom visualisation help

[Seán Froudist Walsh]

Sorry, made a mistake in my e-mail. I tried wb_command -volume-label-import
and got the results explained previously. Any ideas?

Thanks,

Sean

On 20 June 2017 at 20:08, Glasser, Matthew  wrote:

> I think you want wb_command -volume-label-import.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Seán Froudist
> Walsh 
> Date: Tuesday, June 20, 2017 at 7:04 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Custom visualisation help
>
> Hey all,
>
> I'm trying to get a colour display on a surface to match a colormap I have
> set up in matlab, and have run into a whole world of pain. I would greatly
> appreciate your help.
>
> I have created a label text file of the following format:
>
> TCpol_R
> 12552082081
> TCs_R
> 22551581581
> Amyg_R
> 325581811
> PFCoi_R
> 42552312311
>
> I additionally have a nifti file, and a func.gii surface file (created
> with wb_command -volume-to-surface-mapping )
>
> Ideally I would like to display those colours on the surface, in the
> correct clusters.
>
> I thought I would try to display them on a volume as a first step, but
> that hasn't gone smoothly either.
> I used a command of the following format:
> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
> my_label_volume.nii.gz
>
> Then I tried to display the label file over the volume in wb_view to no
> avail (I only see the underlying anatomical volume). Despite this, if I go
> to
> Overlay Tools --> Settings --> Edit Map's Labels
> I can see all of the labels I wanted listed, next to the correct colours.
>
> I would greatly appreciate if you could help fill in the gaps in my
> knowledge so that I can display my custom coloured labels on the surface.
>
> Many thanks,
>
> Sean
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Custom visualisation help

[Seán Froudist Walsh]

Thanks a lot for the suggestion Timothy. Unfortunately I'm still getting a
colourless map. I did get the result I wanted using the matlab gifti
toolbox ( http://www.artefact.tk/software/matlab/gifti/ ), so no rush.

Perhaps I'm saving under the wrong name, or doing something wrong when
trying to visualise? Here's the actual command I'm using.

wb_command -volume-label-import sequential_region_map_no_hipp.nii.gz
hipp_pre_color_palette_table.txt sequential_region_map_no_hipp_
hcp_label.nii.gz

Then when I'm trying to visualise it, I'm just loading it in and trying to
display over the atlas I'm using.

Not sure if there's more info I can give.

Thanks again for the help.

Best wishes,

Sean


On 21 June 2017 at 11:42, Timothy Coalson  wrote:

> The fourth "color" specifier in your text file should be 255, not 1.
>
> Tim
>
>
> On Wed, Jun 21, 2017 at 8:34 AM, Seán Froudist Walsh 
> wrote:
>
>> Sorry, made a mistake in my e-mail. I tried wb_command
>> -volume-label-import and got the results explained previously. Any ideas?
>>
>> Thanks,
>>
>> Sean
>>
>> On 20 June 2017 at 20:08, Glasser, Matthew  wrote:
>>
>>> I think you want wb_command -volume-label-import.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From:  on behalf of Seán
>>> Froudist Walsh 
>>> Date: Tuesday, June 20, 2017 at 7:04 PM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] Custom visualisation help
>>>
>>> Hey all,
>>>
>>> I'm trying to get a colour display on a surface to match a colormap I
>>> have set up in matlab, and have run into a whole world of pain. I would
>>> greatly appreciate your help.
>>>
>>> I have created a label text file of the following format:
>>>
>>> TCpol_R
>>> 12552082081
>>> TCs_R
>>> 22551581581
>>> Amyg_R
>>> 325581811
>>> PFCoi_R
>>> 42552312311
>>>
>>> I additionally have a nifti file, and a func.gii surface file (created
>>> with wb_command -volume-to-surface-mapping )
>>>
>>> Ideally I would like to display those colours on the surface, in the
>>> correct clusters.
>>>
>>> I thought I would try to display them on a volume as a first step, but
>>> that hasn't gone smoothly either.
>>> I used a command of the following format:
>>> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
>>> my_label_volume.nii.gz
>>>
>>> Then I tried to display the label file over the volume in wb_view to no
>>> avail (I only see the underlying anatomical volume). Despite this, if I go
>>> to
>>> Overlay Tools --> Settings --> Edit Map's Labels
>>> I can see all of the labels I wanted listed, next to the correct
>>> colours.
>>>
>>> I would greatly appreciate if you could help fill in the gaps in my
>>> knowledge so that I can display my custom coloured labels on the surface.
>>>
>>> Many thanks,
>>>
>>> Sean
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>

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