[HCP-Users] Clarification of VSPLOT_OFF, Emotion_Task_Acc, Dexterity_Unadj, Taste_Unadj

2017-12-12 Thread Nicole Kuek 
Dear HCP Experts,

I have the following questions with regards to variables and their
description in the HCP data dictionary:

1) What does VLSPOT_OFF code for? The data dictionary states "Penn Line
Orientation: Total Positions Off for All Trials", does this refer to (1)
the number of times the subjects provided an incorrect response or the
number of times the line to match was initially presented in a position
that was "Off" from the target of (2)  the total number of trials given to
subjects that are OFF from the correct orientation?

2) Is there more detailed information on precisely what was tested for the
In-scanner tasks? e.g Emotion_Task_Acc is described as "Average accuracy
Percentage during EMOTION task", however, what does the emotion task
constitute?

3) Can I confirm that a higher score for Endurance_Unadj indicates greater
endurance (since a greater distance was walked), while a higher score for
Dexterity_Unadj indicates less dexterity (since the time taken to complete
a task was measured. i.e the more time taken to complete the task, the
poorer the dexterity)

4) Can I confirm that for Taste_Unadj, the seven anchor labels provided
(Strongest imaginable, Very strong, Strong, Moderate, Weak, Barely
detectable, No sensation) on a 0-100 scale, are administered as 0 is for no
sensation, and increases to 100 for strongest imaginable ?
Thank you for your time, any clarification would be greatly appreciated.

-- 
Best Regards,

Nicole K.

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Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map?

2017-12-12 Thread Xavier Guell Paradis 
It works, thank you!
The steps have been -cifti-separate to convert from dscalar (multiple maps) to 
nifti (multiple maps), and -volume-merge to divide the nifti file in separate 
maps.
Thank you very much,
Xavier.

From: Glasser, Matthew [glass...@wustl.edu]
Sent: Tuesday, December 12, 2017 7:37 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it 
possible to generate one nifti from each dscalar map?

wb_command -volume-merge allows you to select specific maps despite its name.  
It contains functionality similar to both fslmerge and bfslroi.

Peace,

Matt.

From: 
>
 on behalf of Xavier Guell Paradis >
Date: Tuesday, December 12, 2017 at 6:35 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it 
possible to generate one nifti from each dscalar map?

Dear HCP experts,
I have a dscalar file with 4 maps and would like to convert each map into one 
separate nifti file. I am not worried about the problem of surface information 
in a nifti file, because I am interested in subcortical data only.
I have been able to transform the dscalar into a nifti file using this:
wb_command -cifti-separate input.dscalar.nii COLUMN -volume-all output.nii
The output.nii is a nifti file which contains 4 maps if I open it with wb_view. 
Is there a way to generate 4 separate nifti files (one for each map) instead of 
one single nifti file with all 4 maps?

Thank you very much,
Xavier.

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Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map?

2017-12-12 Thread Glasser, Matthew 
wb_command -volume-merge allows you to select specific maps despite its name.  
It contains functionality similar to both fslmerge and bfslroi.

Peace,

Matt.

From: 
>
 on behalf of Xavier Guell Paradis >
Date: Tuesday, December 12, 2017 at 6:35 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it 
possible to generate one nifti from each dscalar map?

Dear HCP experts,
I have a dscalar file with 4 maps and would like to convert each map into one 
separate nifti file. I am not worried about the problem of surface information 
in a nifti file, because I am interested in subcortical data only.
I have been able to transform the dscalar into a nifti file using this:
wb_command -cifti-separate input.dscalar.nii COLUMN -volume-all output.nii
The output.nii is a nifti file which contains 4 maps if I open it with wb_view. 
Is there a way to generate 4 separate nifti files (one for each map) instead of 
one single nifti file with all 4 maps?

Thank you very much,
Xavier.

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[HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map?

2017-12-12 Thread Xavier Guell Paradis 
Dear HCP experts,
I have a dscalar file with 4 maps and would like to convert each map into one 
separate nifti file. I am not worried about the problem of surface information 
in a nifti file, because I am interested in subcortical data only.
I have been able to transform the dscalar into a nifti file using this:
wb_command -cifti-separate input.dscalar.nii COLUMN -volume-all output.nii
The output.nii is a nifti file which contains 4 maps if I open it with wb_view. 
Is there a way to generate 4 separate nifti files (one for each map) instead of 
one single nifti file with all 4 maps?

Thank you very much,
Xavier.

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[HCP-Users] tfMRI volume-based analysis

2017-12-12 Thread Sang-Young Kim 
Dear experts:

I’m trying to do tfMRI volume-based analysis and have tried to run the script 
"TaskfMRIAnalysisBatch.sh". 
When I set the variable VolumeBasedProcessing="NO" in the script, I was able to 
run the tfMRI data on grayordinate space without any error. But if I changed 
the variable to "YES", the error came up without success. Please see below:

***
Warning: Number of voxels = 0. Spatial smoothing of autocorrelation estimates 
is not carried out
Warning: Number of voxels = 0. Spatial smoothing of autocorrelation estimates 
is not carried out

While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -cifti-convert-to-scalar 
/Volumes/easystore/projects/HCP/209/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/StandardVolumeStats/cope1.feat/zstat1.dtseries.nii
 ROW 
/Volumes/easystore/projects/HCP/209/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/209_tfMRI_MOTOR_level2_CUE_hp200_s2.dscalar.nii
 -name-file 
/Volumes/easystore/projects/HCP/209/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/Contrasttemp.txt

ERROR: failed to open file 
'/Volumes/easystore/projects/HCP/209/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/StandardVolumeStats/cope1.feat/zstat1.dtseries.nii',
 file does not exist, or folder permissions prevent seeing it


I have tried to figure out why this error occurred, but I couldn’t figure out. 
Any insights would be greatly appreciated. 

Thanks. 

Sang-Young
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Re: [HCP-Users] error open file in wb_view

2017-12-12 Thread Harwell, John 
It is possible the file is corrupted.  Please try to run “wb_command 
-file-information  ” on the file and see if that works.

On Dec 12, 2017, at 12:20 PM, Marta Moreno 
> wrote:

Thanks.

Yes, I can load spec files but when trying to see functional connectivity maps 
for the specific subject it crashes. I can load other type of files, i.e., seed 
used. This is the first time I cannot see this file, before I was able to do so 
without crashing. I have downloaded workbench v1.2.3. now but the problem 
persists. The only change I had these past weeks was the MATLAB_R2017b.


On Dec 12, 2017, at 1:12 PM, Harwell, John 
> wrote:


Hi Marta,

Does wb_view start up if you do not try to load any files?  Is this the first 
time you have run wb_view on this Mac?

Do you know which file is causing the crash?  You could use File Menu —> Open 
File and try opening just a surface file.


John Harwell


On Dec 12, 2017, at 11:25 AM, Marta Moreno 
> wrote:

Dear experts,

I am getting an error any time I am trying to open file in wb_view. Any idea 
how to solve this problem?

Thanks,

-L

Error attached below:

Process:   wb_view [56364]
Path:  
/usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:??? [56362]
Responsible:   wb_view [56364]
User ID:   501

Date/Time: 2017-12-12 12:21:10.852 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 270 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]


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Re: [HCP-Users] error open file in wb_view

2017-12-12 Thread Marta Moreno 
Thanks.

Yes, I can load spec files but when trying to see functional connectivity maps 
for the specific subject it crashes. I can load other type of files, i.e., seed 
used. This is the first time I cannot see this file, before I was able to do so 
without crashing. I have downloaded workbench v1.2.3. now but the problem 
persists. The only change I had these past weeks was the MATLAB_R2017b.


> On Dec 12, 2017, at 1:12 PM, Harwell, John  wrote:
> 
> 
> Hi Marta,
> 
> Does wb_view start up if you do not try to load any files?  Is this the first 
> time you have run wb_view on this Mac?  
> 
> Do you know which file is causing the crash?  You could use File Menu —> Open 
> File and try opening just a surface file.  
> 
> 
> John Harwell
> 
> 
>> On Dec 12, 2017, at 11:25 AM, Marta Moreno  wrote:
>> 
>> Dear experts,
>> 
>> I am getting an error any time I am trying to open file in wb_view. Any idea 
>> how to solve this problem? 
>> 
>> Thanks,
>> 
>> -L
>> 
>> Error attached below:
>> 
>> Process:   wb_view [56364]
>> Path:  
>> /usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
>> Identifier:workbench
>> Version:   1.1.1 (1.1.1)
>> Code Type: X86-64 (Native)
>> Parent Process:??? [56362]
>> Responsible:   wb_view [56364]
>> User ID:   501
>> 
>> Date/Time: 2017-12-12 12:21:10.852 -0500
>> OS Version:Mac OS X 10.12.5 (16F73)
>> Report Version:12
>> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
>> 
>> 
>> Time Awake Since Boot: 270 seconds
>> 
>> System Integrity Protection: enabled
>> 
>> Crashed Thread:0  Dispatch queue: com.apple.main-thread
>> 
>> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
>> Exception Codes:   KERN_INVALID_ADDRESS at 0x
>> Exception Note:EXC_CORPSE_NOTIFY
>> 
>> Termination Signal:Segmentation fault: 11
>> Termination Reason:Namespace SIGNAL, Code 0xb
>> Terminating Process:   exc handler [0]
>> 
>> 
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> 


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Re: [HCP-Users] error open file in wb_view

2017-12-12 Thread Harwell, John 

Hi Marta,

Does wb_view start up if you do not try to load any files?  Is this the first 
time you have run wb_view on this Mac?  

Do you know which file is causing the crash?  You could use File Menu —> Open 
File and try opening just a surface file.  


John Harwell
  

> On Dec 12, 2017, at 11:25 AM, Marta Moreno  wrote:
> 
> Dear experts,
> 
> I am getting an error any time I am trying to open file in wb_view. Any idea 
> how to solve this problem? 
> 
> Thanks,
> 
> -L
> 
> Error attached below:
> 
> Process:   wb_view [56364]
> Path:  
> /usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
> Identifier:workbench
> Version:   1.1.1 (1.1.1)
> Code Type: X86-64 (Native)
> Parent Process:??? [56362]
> Responsible:   wb_view [56364]
> User ID:   501
> 
> Date/Time: 2017-12-12 12:21:10.852 -0500
> OS Version:Mac OS X 10.12.5 (16F73)
> Report Version:12
> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
> 
> 
> Time Awake Since Boot: 270 seconds
> 
> System Integrity Protection: enabled
> 
> Crashed Thread:0  Dispatch queue: com.apple.main-thread
> 
> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes:   KERN_INVALID_ADDRESS at 0x
> Exception Note:EXC_CORPSE_NOTIFY
> 
> Termination Signal:Segmentation fault: 11
> Termination Reason:Namespace SIGNAL, Code 0xb
> Terminating Process:   exc handler [0]
> 
> 
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[HCP-Users] error open file in wb_view

2017-12-12 Thread Marta Moreno 
Dear experts,

I am getting an error any time I am trying to open file in wb_view. Any idea 
how to solve this problem? 

Thanks,

-L

Error attached below:

Process:   wb_view [56364]
Path:  
/usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:??? [56362]
Responsible:   wb_view [56364]
User ID:   501

Date/Time: 2017-12-12 12:21:10.852 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 270 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]


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