date:20161103

Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

2016-11-03 Thread Hernke, Cynthia

Thank you, Jenn.

Hi Daniel,

Yes, the intensity scores are averaged. Also, please follow this 
link
 for the interpretation guide, then select the attachment in the article.  The 
other link is no longer active.

Thank you,

Cindy

From: "Elam, Jennifer" 
Date: Thursday, November 3, 2016 at 11:09 AM
To: "hcp-users@humanconnectome.org" , 
"daniel.hw...@qimrberghofer.edu.au" , 
"Hernke, Cynthia" 
Subject: Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude 
Scale


Hi Daniel,

More information on the raw scoring of the NIH Toolbox Taste Intensity test 
used for HCP is on p.22 of the NIH Toolbox Scoring and Interpretation 
Guide.
 And then there's general info about the norming and types of final scores 
provided on this page: 
http://www.healthmeasures.net/score-and-interpret/interpret-scores/nih-toolbox. 
Basically the raw score is from 0-100 intensity, but the Unadjusted Standard 
score we report is rescaled so that the mean =100, and the SD=15. The 
Age-adjusted Standard Score are compared to the other respondents in the 18-29 
or 30-39 age ranges (depending on the age of the subject) and similarly 
rescaled to a mean=100, SD=15. So the rescaling is why the values all fall 
between 56-135, which would be a range of about 3 standard deviations below the 
mean to about 2 above.



As far as I know, we combine the results from the intensity scores from the two 
tasting solutions, but Cindy Hernke (CC'd) will have to confirm that.



Best,

Jenn


314-362-9387
e...@wustl.edu
www.humanconnectome.org


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Daniel Hwang 

Sent: Thursday, November 3, 2016 1:33:45 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

Hi,

I was trying to relate the taste intensity score from the unrestricted data to 
the scale used for its measurement (the general Labelled Magnitude Scale).

In the HCP reference manual (Q3), it shows that the values for the taste 
intensity range from 60 to 130. I was wondering whether the range of 60-130 
covers the full scale of the general Labelled Magnitude Scale as shown in the 
NIH Toolbox Demo (https://www.youtube.com/watch?v=s7b8E8GTnIE)? If it is the 
case, a score of 60 would indicate there is no taste at all (the bottom of the 
scale) and a score of 130 would indicate the strongest imaginable (the top of 
the scale).

Or does the range reflect the actual responses from HCP participants? However, 
in the unrestricted data, the taste intensity scores range from 56.35 to 
134.60. This makes me wonder maybe the range of 60-130 do not cover the full 
scale and the full scale could be range from 0 to more than 130.

Could anyone help me to solve the puzzle? Thanks.

Best,
Daniel

___
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] Taste Intensity Score and general Labelled Magnitude Scale

2016-11-03 Thread Daniel Hwang

Hi Jenn, Hi Cindy,

Thanks for the quick reply.

As for the test solutions used, in an earlier email thread entitled "Taste 
Intensity Test", Dr. Gregory Burgess mentioned that the scores are the 
"primary" scores from NIH Toolbox, which are for quinine rather than the 
average of two. Can you please confirm this again?

Thanks a lot for your help.

Daniel

From: Hernke, Cynthia [hern...@wustl.edu]
Sent: Friday, November 04, 2016 2:42 AM
To: Elam, Jennifer; hcp-users@humanconnectome.org; Daniel Hwang
Subject: Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude 
Scale

Thank you, Jenn.

Hi Daniel,

Yes, the intensity scores are averaged. Also, please follow this 
link
 for the interpretation guide, then select the attachment in the article.  The 
other link is no longer active.

Thank you,

Cindy

From: "Elam, Jennifer" 
Date: Thursday, November 3, 2016 at 11:09 AM
To: "hcp-users@humanconnectome.org" , 
"daniel.hw...@qimrberghofer.edu.au" , 
"Hernke, Cynthia" 
Subject: Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude 
Scale


Hi Daniel,

More information on the raw scoring of the NIH Toolbox Taste Intensity test 
used for HCP is on p.22 of the NIH Toolbox Scoring and Interpretation 
Guide.
 And then there's general info about the norming and types of final scores 
provided on this page: 
http://www.healthmeasures.net/score-and-interpret/interpret-scores/nih-toolbox. 
Basically the raw score is from 0-100 intensity, but the Unadjusted Standard 
score we report is rescaled so that the mean =100, and the SD=15. The 
Age-adjusted Standard Score are compared to the other respondents in the 18-29 
or 30-39 age ranges (depending on the age of the subject) and similarly 
rescaled to a mean=100, SD=15. So the rescaling is why the values all fall 
between 56-135, which would be a range of about 3 standard deviations below the 
mean to about 2 above.



As far as I know, we combine the results from the intensity scores from the two 
tasting solutions, but Cindy Hernke (CC'd) will have to confirm that.



Best,

Jenn


314-362-9387
e...@wustl.edu
www.humanconnectome.org


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Daniel Hwang 

Sent: Thursday, November 3, 2016 1:33:45 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

Hi,

I was trying to relate the taste intensity score from the unrestricted data to 
the scale used for its measurement (the general Labelled Magnitude Scale).

In the HCP reference manual (Q3), it shows that the values for the taste 
intensity range from 60 to 130. I was wondering whether the range of 60-130 
covers the full scale of the general Labelled Magnitude Scale as shown in the 
NIH Toolbox Demo (https://www.youtube.com/watch?v=s7b8E8GTnIE)? If it is the 
case, a score of 60 would indicate there is no taste at all (the bottom of the 
scale) and a score of 130 would indicate the strongest imaginable (the top of 
the scale).

Or does the range reflect the actual responses from HCP participants? However, 
in the unrestricted data, the taste intensity scores range from 56.35 to 
134.60. This makes me wonder maybe the range of 60-130 do not cover the full 
scale and the full scale could be range from 0 to more than 130.

Could anyone help me to solve the puzzle? Thanks.

Best,
Daniel

___
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

[HCP-Users] Fwd: -probtrackx-dot-convert volume label problem

2016-11-03 Thread Timothy Coalson

For the list's benefit.

Tim

-- Forwarded message --
From: Maarten Vaessen 
Date: Thu, Nov 3, 2016 at 3:45 AM
Subject: Re: [HCP-Users] -probtrackx-dot-convert volume label problem
To: Timothy Coalson 


The problem was that the coords_for_fdt_matrix3 file (from probtrackx2) has
5 colums (x,y,z,something,something), while the -probtrackx-dot-convert expects
just the x,y,z in a file.
It works now!

Thanks,

-Maarten

On Wed, Nov 2, 2016 at 9:43 PM, Timothy Coalson  wrote:

> As a guess, did you use "-crop" when you used -cifti-separate to get the
> amygdala ROI?  If so, that changes the volume space (specifically the FOV),
> so indices don't correspond with the normal 2mm volume space.  This would
> mean that you now need to make a label volume in this new FOV space.
> Alternatively, you could get the ROI without using -crop, rerun probtrackx,
> and then the standard Atlas_ROIs file will work.
>
> The  must have the same dimensions and origin/spacing as the
> roi file you used in probtrackx, otherwise the indices won't match.  I
> would not call an amygdala-only volume "Atlas_ROIs", that would be
> misleading, and you should double check your amygdala ROI file for its
> value, as it probably uses 1 rather than 18, and fix the labels text file
> based on that, but the -volume-label-import command otherwise looks like it
> would produce something that should work for your current probtrackx
> results.
>
> Tim
>
>
> On Wed, Nov 2, 2016 at 7:20 AM, Maarten Vaessen 
> wrote:
>
>> Hello,
>>
>> I'm trying to convert a .dot from probtrackx2 with -matrix3 option to a
>> dconn.nii. The -lrtarget was a list containing all volumes and surfaces
>> conforming to the HCP grayordinate file. The -target3 is the L (or R)
>> amygdala from Atlas_ROI.2.nii.gz. The output from probtrackx2 looks
>> sensible.
>>
>> I use the following command and get this error:
>> wb_command -probtrackx-dot-convert fdt_matrix3.dot fdt_matrix3.dconn.nii
>> -col-cifti 91282_Greyordinates.dscalar.nii COLUMN -row-voxels
>> coords_for_fdt_matrix3 amyL_label_from_Atlas.nii.gz
>>
>> ERROR: voxel index in list file did not match a structure: 0, 1, 56
>>
>>
>> Now, I am not sure what to use as input for -probtrackx-dot-convert
>> -row-voxels:
>>
>> [-row-voxels] - the output mapping along a row will be voxels
>>
>>  - a text file containing IJK indices for the voxels
>>  used
>> --> this should be the coords_for_fdt_matrix3 right?
>>
>>  - a label volume with the dimensions and sform used, with
>> structure labels
>> --> here I am a bit lost. I tried several options, the probably most
>> sensible being:
>> wb_command -volume-label-import subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii
>> amyL_label.txt amyL_label_from_Atlas.nii.gz -discard-others
>>
>> amyL_label.txt =
>> AMYGDALA_LEFT
>> 18 103 255 255 255
>>
>> What would be the correct input to get this to work?
>>
>> Thx,
>>
>> -Maarten
>>
>> ___
>> 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

Re: [HCP-Users] result resolution

2016-11-03 Thread nailin yao

I see! Thank you Michael and Matt!

Best,
Nailin

2016-11-03 15:10 GMT-04:00 Glasser, Matthew :

> Indeed, for most analyses 32k (2mm average vertex spacing) is the ‘main
> mesh’.
>
> Peace,
>
> Matt.
>
> From:  on behalf of "Harms,
> Michael" 
> Date: Thursday, November 3, 2016 at 2:05 PM
> To: nailin yao , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] result resolution
>
>
> The structural results (surfaces, thickness, myelin maps) are available on
> a 164k mesh because the structural data was acquired at a resolution (0.7
> mm) that supports such a fine grained mesh.  The functional data were
> acquired at 2 mm resolution, which is approximately the average spacing in
> the 32k mesh.  Plus, working with the fMRI data on a 164k mesh would
> require 5x the memory and storage for a dense timeseries (and 25x the
> memory/storage for a dense connectome).
>
> 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 nailin yao <
> ynai...@gmail.com>
> Date: Thursday, November 3, 2016 at 12:43 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] result resolution
>
> Hi,
>
> May I know why the main results are 164k resolution, while the functional
> output are only 32k resolution, and I have to overlay them on the 32k
> surface in the fsaverage_LR32k subdirectory? Thank you very much!
>
> Best,
> Nailin
>
> --
> Nailin Yao,  PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
> ___
> 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
>
>
> --
>
> 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.
>



-- 
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

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

Re: [HCP-Users] result resolution

2016-11-03 Thread Glasser, Matthew

Indeed, for most analyses 32k (2mm average vertex spacing) is the 'main mesh'.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Thursday, November 3, 2016 at 2:05 PM
To: nailin yao mailto:ynai...@gmail.com>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] result resolution

The structural results (surfaces, thickness, myelin maps) are available on a 
164k mesh because the structural data was acquired at a resolution (0.7 mm) 
that supports such a fine grained mesh.  The functional data were acquired at 2 
mm resolution, which is approximately the average spacing in the 32k mesh.  
Plus, working with the fMRI data on a 164k mesh would require 5x the memory and 
storage for a dense timeseries (and 25x the memory/storage for a dense 
connectome).

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of nailin yao mailto:ynai...@gmail.com>>
Date: Thursday, November 3, 2016 at 12:43 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] result resolution

Hi,

May I know why the main results are 164k resolution, while the functional 
output are only 32k resolution, and I have to overlay them on the 32k surface 
in the fsaverage_LR32k subdirectory? Thank you very much!

Best,
Nailin

--
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

___
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

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] result resolution

2016-11-03 Thread Harms, Michael


The structural results (surfaces, thickness, myelin maps) are available on a 
164k mesh because the structural data was acquired at a resolution (0.7 mm) 
that supports such a fine grained mesh.  The functional data were acquired at 2 
mm resolution, which is approximately the average spacing in the 32k mesh.  
Plus, working with the fMRI data on a 164k mesh would require 5x the memory and 
storage for a dense timeseries (and 25x the memory/storage for a dense 
connectome).

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of nailin yao mailto:ynai...@gmail.com>>
Date: Thursday, November 3, 2016 at 12:43 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] result resolution

Hi,

May I know why the main results are 164k resolution, while the functional 
output are only 32k resolution, and I have to overlay them on the 32k surface 
in the fsaverage_LR32k subdirectory? Thank you very much!

Best,
Nailin

--
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University


___
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

[HCP-Users] result resolution

2016-11-03 Thread nailin yao

Hi,

May I know why the main results are 164k resolution, while the functional
output are only 32k resolution, and I have to overlay them on the 32k
surface in the fsaverage_LR32k subdirectory? Thank you very much!

Best,
Nailin

-- 
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

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

Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

2016-11-03 Thread Elam, Jennifer

Hi Daniel,

More information on the raw scoring of the NIH Toolbox Taste Intensity test 
used for HCP is on p.22 of the NIH Toolbox Scoring and Interpretation 
Guide.
 And then there's general info about the norming and types of final scores 
provided on this page: 
http://www.healthmeasures.net/score-and-interpret/interpret-scores/nih-toolbox. 
Basically the raw score is from 0-100 intensity, but the Unadjusted Standard 
score we report is rescaled so that the mean =100, and the SD=15. The 
Age-adjusted Standard Score are compared to the other respondents in the 18-29 
or 30-39 age ranges (depending on the age of the subject) and similarly 
rescaled to a mean=100, SD=15. So the rescaling is why the values all fall 
between 56-135, which would be a range of about 3 standard deviations below the 
mean to about 2 above.


As far as I know, we combine the results from the intensity scores from the two 
tasting solutions, but Cindy Hernke (CC'd) will have to confirm that.


Best,

Jenn


Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Daniel Hwang 

Sent: Thursday, November 3, 2016 1:33:45 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

Hi,

I was trying to relate the taste intensity score from the unrestricted data to 
the scale used for its measurement (the general Labelled Magnitude Scale).

In the HCP reference manual (Q3), it shows that the values for the taste 
intensity range from 60 to 130. I was wondering whether the range of 60-130 
covers the full scale of the general Labelled Magnitude Scale as shown in the 
NIH Toolbox Demo (https://www.youtube.com/watch?v=s7b8E8GTnIE)? If it is the 
case, a score of 60 would indicate there is no taste at all (the bottom of the 
scale) and a score of 130 would indicate the strongest imaginable (the top of 
the scale).

Or does the range reflect the actual responses from HCP participants? However, 
in the unrestricted data, the taste intensity scores range from 56.35 to 
134.60. This makes me wonder maybe the range of 60-130 do not cover the full 
scale and the full scale could be range from 0 to more than 130.

Could anyone help me to solve the puzzle? Thanks.

Best,
Daniel

___
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

Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

[HCP-Users] Fwd: -probtrackx-dot-convert volume label problem

Re: [HCP-Users] result resolution

Re: [HCP-Users] result resolution

Re: [HCP-Users] result resolution

[HCP-Users] result resolution

Re: [HCP-Users] Taste Intensity Score and general Labelled Magnitude Scale

8 matches

Site Navigation

Mail list logo

Footer information