Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Glasser, Matthew 
I would have a look at this file for the task design matrix:

${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${AnalysisName}.feat/design.mat

Not sure if it is released or if you have to run the task analysis pipeline to 
generate it.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Thursday, February 22, 2018 at 5:22 PM
To: Javier Zapata <jzap...@ucsb.edu<mailto:jzap...@ucsb.edu>>
Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

On the technical end, cifti dtseries are arranges such that a row is a 
timecourse - you will need to select columns rather than rows.  wb_command 
-cifti-merge can do this.

On the math side, I don't know the details needed to sync the EV files with the 
dtseries (whether the 0s from the EVs match the 0s from the processed data), 
but the typical task analysis uses the hemodynamic response function to 
estimate the BOLD effect waveform to expect from the stimulus, rather than 
simply chopping out the various segments.

Tim


On Thu, Feb 22, 2018 at 2:02 PM, Javier Zapata 
<jzap...@ucsb.edu<mailto:jzap...@ucsb.edu>> wrote:
Dear Professors,

I am pretty new to task fMRI data and I would like to check how to use the 
files in the EVs folder to extract information from the .dtseries.nii file for 
the MOTOR dataset. As an example I chose subject 100307 with the LR phase and I 
was able to build this table from the files in the EVs folder:

typestart time (s)
countdown0
cue_rightHand8.05
rightHand11.009
cue-leftFoot23.164
leftFoot 38.291

So suppose I would like to extract from a .dtseries.nii file (having 284 rows x 
91282 grayordinates) the part of the time series corresponding to the Right 
Hand task listed above. Then:

Should I pick all the rows covering the time interval [11.009;23.164] ?

If so, should I pick rows 15 through 33 from the .dtseries.nii file which cover 
the time interval starting from 10.8 (=0.72*15) until 23.76(=0.72*33) ?

Moreover, does the same interpretation hold for obtaining the .dtseries.nii 
rows corresponding to the cues and the fixation blocks?

Thank you very much,


Javier Zapata
-
PhD Student
UC Santa Barbara





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Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Timothy Coalson 
On the technical end, cifti dtseries are arranges such that a row is a
timecourse - you will need to select columns rather than rows.  wb_command
-cifti-merge can do this.

On the math side, I don't know the details needed to sync the EV files with
the dtseries (whether the 0s from the EVs match the 0s from the processed
data), but the typical task analysis uses the hemodynamic response function
to estimate the BOLD effect waveform to expect from the stimulus, rather
than simply chopping out the various segments.

Tim


On Thu, Feb 22, 2018 at 2:02 PM, Javier Zapata  wrote:

> Dear Professors,
>
> I am pretty new to task fMRI data and I would like to check how to use the
> files in the EVs folder to extract information from the .dtseries.nii file
> for the MOTOR dataset. As an example I chose subject 100307 with the LR
> phase and I was able to build this table from the files in the EVs folder:
>
> *type start time (s)*
> countdown 0
> cue_rightHand 8.05
> rightHand 11.009
> cue-leftFoot 23.164
> leftFoot 38.291
>
> So suppose I would like to extract from a .dtseries.nii file (having 284
> rows x 91282 grayordinates) the part of the time series corresponding to
> the Right Hand task listed above. Then:
>
> Should I pick all the rows covering the time interval [11.009;23.164] ?
>
> If so, should I pick rows 15 through 33 from the .dtseries.nii file which
> cover the time interval starting from 10.8 (=0.72*15) until 23.76(=0.72*33)
> ?
>
> Moreover, does the same interpretation hold for obtaining the
> .dtseries.nii rows corresponding to the cues and the fixation blocks?
>
> Thank you very much,
>
>
> Javier Zapata
> -
> PhD Student
> UC Santa Barbara
>
>
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] About interpreting EVs and .dtseries.nii files

2018-02-22 Thread Sang-Yun Oh 
Dear HCP-Users,

I am pretty new to task fMRI data and I would like to check how to use the
files in the EVs folder to extract information from the .dtseries.nii file
for the MOTOR dataset. As an example, I chose subject 100307 with the LR
phase and I was able to build this table from the files in the EVs folder:

*type start time (s)*
countdown 0
cue_rightHand 8.05
rightHand 11.009
cue-leftFoot 23.164
leftFoot  38.291

So suppose I would like to extract from a .dtseries.nii file (having 284
rows x 91282 grayordinates) the part of the time series corresponding to
the Right-Hand task listed above. Then:

Should I pick all the rows covering the time interval [11.009;23.164] ?

If so, should I pick rows 15 through 33 from the .dtseries.nii file which
cover the time interval starting from 10.8 (=0.72*15) until 23.76(=0.72*33)
?

Moreover, does the same interpretation hold for obtaining the .dtseries.nii
rows corresponding to the cues and the fixation blocks?

Thank you for your help!

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[HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Javier Zapata 
Dear Professors,

I am pretty new to task fMRI data and I would like to check how to use the 
files in the EVs folder to extract information from the .dtseries.nii file for 
the MOTOR dataset. As an example I chose subject 100307 with the LR phase and I 
was able to build this table from the files in the EVs folder:

typestart time (s)
countdown   0
cue_rightHand   8.05
rightHand   11.009
cue-leftFoot23.164
leftFoot38.291

So suppose I would like to extract from a .dtseries.nii file (having 284 rows x 
91282 grayordinates) the part of the time series corresponding to the Right 
Hand task listed above. Then:

Should I pick all the rows covering the time interval [11.009;23.164] ? 

If so, should I pick rows 15 through 33 from the .dtseries.nii file which cover 
the time interval starting from 10.8 (=0.72*15) until 23.76(=0.72*33) ? 

Moreover, does the same interpretation hold for obtaining the .dtseries.nii 
rows corresponding to the cues and the fixation blocks?

Thank you very much,


Javier Zapata
-
PhD Student
UC Santa Barbara


 


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