Re: [HCP-Users] How to find trial-level behavioral results

[Xinyang Liu]

Hi, Greg.
Thank you very much for your kind help.
The "TAB.txt"  provides the information for  within scanner behavioral results, 
which are quite nice. But we also wish to acquire behavioral data for out of 
scanner tasks, that is the "NIT Toolbox Assessment" as mentioned in the manual 
(p.177). Do you have any idea for this part of data? Thanks.


Best regards,
Xinyang



At 2017-07-12 23:11:17, "Burgess, Gregory"  wrote:
>Hi Xinyang,
>
>The accuracy and RT for individual stimuli within a scan are in the  
>preprocessed directory for that scan (i.e., preproc resources). The files end 
>with “TAB.txt”, and are tab-delimited E-Prime outputs. If you need detail 
>about the variables contained in those TAB.txt outputs, you can review 
>Appendix 6 in the documentation (see 
>https://www.humanconnectome.org/study/hcp-young-adult/document/1200-subjects-data-release).
>
>--Greg
>
>
>Greg Burgess, Ph.D.
>Staff Scientist, Human Connectome Project
>Washington University School of Medicine
>Department of Psychiatry
>Phone: 314-362-7864
>Email: gburg...@wustl.edu
>
>> On Jul 12, 2017, at 4:47 AM, Xinyang Liu  wrote:
>>
>> Dear HCP fellows,
>>
>> May I ask for some help?
>> We are very interested in the behavioral and individual difference 
>> measurement data, which are introduced in Chapter 5 of the Reference Manual. 
>> However, in the downloaded "behavioral data" file (in .csv version), I 
>> cannot find the result for single stimulus. The behavioral results for each 
>> subject are all median values. For example, in one emotion task, the 
>> reaction time was recorded as "Emotion_Task_Median_RT" in one column. Do you 
>> know how to get the trial-level behavioral results? Thank you very much.
>>
>> Best regards,
>> Xinyang Liu
>>
>>
>>
>>
>>
>>
>> ___
>> 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.

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Re: [HCP-Users] PreFreeSurfer: Cannot open volume None for reading!

[Glasser, Matthew]

This also needs to be set to NONE:


AvgrdcSTRING=“SiemensFieldMap"


Matt.

From: > on behalf of Sara 
Rafique >
Date: Wednesday, July 12, 2017 at 4:13 PM
To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] PreFreeSurfer: Cannot open volume None for reading!

Hi Matt,

Please see attached. I also attached the log that is generated, in case this 
helps.
Many thanks,
Sara

On 10 July 2017 at 22:12, Glasser, Matthew 
> wrote:
Can you post the code you are using the launch the pipeline?

Thanks,
Matt.

From: 
>
 on behalf of Sara Rafique >
Date: Sunday, July 9, 2017 at 7:44 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] PreFreeSurfer: Cannot open volume None for reading!

Hi HCP team,

I'm attempting to run the PreFreeSurfer.sh script, but I get the following 
error:

About to use fsl_sub to queue or run 
/Applications/HCP_Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh

Cannot open volume None for reading!

Is this error related to the variables I have set to "NONE" as indicated by the 
script? These being:
MagnitudeInputName
PhaseInputName
SpinEchoPhaseEncodeNegative
SpinEchoPhaseEncodePositive
DwellTime
SEUnwarpDir
TopupConfig
GEB0InputName
T1wSampleSpacing
T2wSampleSpacing
UnwarpDir
GradientDistortionCoeffs

Many thanks,
Sara

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Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences

[Harms, Michael]

Essa Yacoub from CMRR sent me the following for distribution to the HCP-User 
list on this issue:


"A lot of investigators have done comparisons between the sequences. Most of 
this data is not public, although there are some sites that have published 
things - e.g. 
https://practicalfmri.blogspot.com/2016/06/starting-points-for-sms-epi-at-3-t-part.html#more

It should be noted that there are many different variants of the sequences from 
WIP to Product to MGH-c2p and CMRR-c2p -and- that it is difficult to directly 
compare the sequences as they have different options/features. There are many 
differences from acquisition to image reconstruction for both fMRI and 
diffusion. That said, I have yet to see any feedback to suggest that the MGH 
sequence (or other) outperforms the CMRR sequence, let alone a consensus. We 
get this type of question all of the time and what we tell people is to run the 
comparison for their particular protocol and metrics of interest and decide for 
themselves which sequence better fits their needs.


--
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 Mahmoud >
Date: Tuesday, July 11, 2017 at 8:18 PM
To: "Glasser, Matthew" >
Cc: "HCP-Users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences

And please let us know if you figured it out which sequence is better.

Thank you,
Mahmoud

On Tue, Jul 11, 2017 at 4:44 PM, Glasser, Matthew 
> wrote:
I am not part of such a consensus.  I don’t know if there have been rigorous 
comparison of the two sequences or by what metrics it is being asserted that 
MGH outperforms CMRR.  Perhaps you could ask your source for this 
recommendation why they say that?

Peace,

Matt.

From: 
>
 on behalf of "Juranek, Jenifer" 
>
Date: Tuesday, July 11, 2017 at 10:34 AM
To: "HCP-Users@humanconnectome.org" 
>
Subject: [HCP-Users] CMRR vs MGH multiband/SMS sequences

Just curious if anyone is aware of head-to-head comparisons of CMRR and MGH 
MB/SMS sequences?
Someone recently mentioned to me that “the general consensus is that MGH 
outperforms CMRR”.
Is there a “general consensus” in the research community on this issue? Any 
differences between dMRI and fMRI applications?
I’m interested in using an HCP-style acquisition protocol for a 5yr study about 
to start…from what I can tell, CMRR MB sequences have been selected across the 
board for HCP-style studies currently funded by NIH.
Does anyone have any thoughts they can share?
Many Thanks,
Jenifer
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
Associate Professor
Department of Pediatrics
UTHealth
Houston, TX 77030
713.500.8233


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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.

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Re: [HCP-Users] How to find trial-level behavioral results

[Burgess, Gregory]

Hi Xinyang,

The accuracy and RT for individual stimuli within a scan are in the  
preprocessed directory for that scan (i.e., preproc resources). The files end 
with “TAB.txt”, and are tab-delimited E-Prime outputs. If you need detail about 
the variables contained in those TAB.txt outputs, you can review Appendix 6 in 
the documentation (see 
https://www.humanconnectome.org/study/hcp-young-adult/document/1200-subjects-data-release).

--Greg


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu

> On Jul 12, 2017, at 4:47 AM, Xinyang Liu  wrote:
>
> Dear HCP fellows,
>
> May I ask for some help?
> We are very interested in the behavioral and individual difference 
> measurement data, which are introduced in Chapter 5 of the Reference Manual. 
> However, in the downloaded "behavioral data" file (in .csv version), I cannot 
> find the result for single stimulus. The behavioral results for each subject 
> are all median values. For example, in one emotion task, the reaction time 
> was recorded as "Emotion_Task_Median_RT" in one column. Do you know how to 
> get the trial-level behavioral results? Thank you very much.
>
> Best regards,
> Xinyang Liu
>
>
>
>
>
>
> ___
> 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.

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[HCP-Users] How to find trial-level behavioral results

[Xinyang Liu]

Dear HCP fellows,


May I ask for some help? 
We are very interested in the behavioral and individual difference measurement 
data, which are introduced in Chapter 5 of the Reference Manual. However, in 
the downloaded "behavioral data" file (in .csv version), I cannot find the 
result for single stimulus. The behavioral results for each subject are all 
median values. For example, in one emotion task, the reaction time was recorded 
as "Emotion_Task_Median_RT" in one column. Do you know how to get the 
trial-level behavioral results? Thank you very much.


Best regards,
Xinyang Liu






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