Differences between revisions 9 and 10
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:

[[FsFastTutorialV5.1|top]] | [[FsFastTutorialV5.1|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct|next (Directory Structure)]]
 		[[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Back to list of all tutorials]] | [[FsTutorial|Back to course page]] | [[FsFastTutorialV5.1|Previous]] | [[FsFastTutorialV5.1/FsFastDirStruct|Next (Directory Structure)]]
Line 9: Line 7:
Line 16: Line 13:
 * FreeSurfer anatomical analyses   * FreeSurfer anatomical analyses
Line 19: Line 16:
The paradigm was designed to study the effects of emotional stimuli on the ability to recall items stored in working memory.
Line 20: Line 18:
The paradigm was designed to study the effects of emotional stimuli on
the ability to recall items stored in working memory.
 * Blocked design 		 * Blocked design
Line 24: Line 20:
  1. Encode (16 sec) - 8 stick figures to remember (no response)
   1. Distractor (16 sec) - 8 distractor images (response whether there is a face in the image)
      a. Emotional - Distractors are emotionally disturbing
      a. Neutral - Distractors are emotionally neutral
  1. Probe (16 sec) - 8 pairs of stick figures. Subject responds as to which of the pair was in the original Encode. 		  1. Encode (16 sec) - 8 stick figures to remember (no response)
  1. Distractor (16 sec) - 8 distractor images (response whether there is a face in the image)
   a. Emotional - Distractors are emotionally disturbing
   a. Neutral - Distractors are emotionally neutral
  1. Probe (16 sec) - 8 pairs of stick figures. Subject responds as to which of the pair was in the original Encode.
Line 34: Line 30:
  1. Encode
  1. Emotional Distractor
  1. Neutral Distractor
  1. Probe following Emotional Distractor
  1. Probe following Neutral Distractor
1. Encode
 1. Emotional Distractor
 1. Neutral Distractor
 1. Probe following Emotional Distractor
 1. Probe following Neutral Distractor
Line 43: Line 40:
Line 52: Line 48:
Line 55: Line 50:
= Getting the Data (not necessary for the Boston FreeSurfer Course) = = Getting the Data (not necessary for the Boston FreeSurfer Course) =
You can get the analyzed functional data (10G) from:
Line 57: Line 53:
You can get the analyzed functional data (10G) from:
Line 61: Line 56:
You can get the structural data (5G) from:
Line 62: Line 58:
You can get the structural data (5G) from:
Line 66: Line 61:
= Organizing the Tutorial (not necessary for the Boston FreeSurfer Course) =
cd to a place on your network where you have enough space to unpack the tutorial data.
Line 67: Line 64:


= Organizing the Tutorial (not necessary for the Boston FreeSurfer Course) =

cd to a place on your network where you have enough space to unpack
the tutorial data.
Line 77: Line 68:
Line 81: Line 73:
You will need to set the TUTORIAL_DATA environment variable. In bash, run:
Line 82: Line 75:
You will need to set the TUTORIAL_DATA environment variable. In bash, run:
Line 86: Line 78:
In tcsh or csh
Line 87: Line 80:
In tcsh or csh
Line 89: Line 81:
setenv TUTORIAL_DATA /place/with/space  setenv TUTORIAL_DATA /place/with/space
Line 91: Line 83:

You will also need to link the FreeSurfer anatomical subjeccts (data
in fsfast-tutorial.subjects) into your $SUBJECTS_DIR. 		You will also need to link the FreeSurfer anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR.
Line 96: Line 86:
Line 99: Line 90:
In tcsh or csh, run:
Line 100: Line 92:
In tcsh or csh, run:
Line 104: Line 95:


[[FsFastTutorialV5.1|top]] | [[FsFastTutorialV5.1|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct|next (Directory Structure)]] 		[[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Back to list of all tutorials]] | [[FsTutorial|Back to course page]] | [[FsFastTutorialV5.1|Previous]] | [[FsFastTutorialV5.1/FsFastDirStruct|Next (Directory Structure)]]

Back to list of all tutorials | Back to course page | Previous | Next (Directory Structure)

Contents

  1. FSFAST Tutorial Data Description
  2. Functional Paradigm
  3. Functional Data
  4. Anatomical Data
  5. Getting the Data (not necessary for the Boston FreeSurfer Course)
  6. Organizing the Tutorial (not necessary for the Boston FreeSurfer Course)

1. FSFAST Tutorial Data Description

The functional data were collected as part of the Functional Biomedical Research Network (fBIRN, www.nbirn.net).

  • Working-memory paradigm with distractors
  • 18 subjects
  • Each subject has 1 run (except sess01 which has 4 runs)
  • Collected at MGH Bay 4 (3T Siemens)

  • FreeSurfer anatomical analyses

2. Functional Paradigm

The paradigm was designed to study the effects of emotional stimuli on the ability to recall items stored in working memory.

  • Blocked design
  • Each block consisted of 3 phases
    1. Encode (16 sec) - 8 stick figures to remember (no response)
    2. Distractor (16 sec) - 8 distractor images (response whether there is a face in the image)
      1. Emotional - Distractors are emotionally disturbing
      2. Neutral - Distractors are emotionally neutral
    3. Probe (16 sec) - 8 pairs of stick figures. Subject responds as to which of the pair was in the original Encode.
  • Between each block was a 16 sec scrambled image used as baseline.

wmparadigm.jpg

The above yields 5 conditions:

  1. Encode
  2. Emotional Distractor
  3. Neutral Distractor
  4. Probe following Emotional Distractor
  5. Probe following Neutral Distractor

The scrambled image will be modeled as a baseline, not as a condition.

3. Functional Data

  • Original data: each subject had 8 runs
  • This data: each subject has 1 run (except for sess01 who has 4)
  • Each run lasts 142 time points
  • TR = 2 sec.
  • There is one run of rest data for 13 subjects
  • There is a B0 map for each subject

4. Anatomical Data

  • FreeSurfer analysis has been run for all 18 subjects

5. Getting the Data (not necessary for the Boston FreeSurfer Course)

You can get the analyzed functional data (10G) from: 

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz

You can get the structural data (5G) from: 

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz

6. Organizing the Tutorial (not necessary for the Boston FreeSurfer Course)

cd to a place on your network where you have enough space to unpack the tutorial data. 

cd /place/with/space

Untar the data 

tar xvfz fsfast-tutorial.tar.gz
tar xvfz fsfast-tutorial.subjects.tar.gz

You will need to set the TUTORIAL_DATA environment variable. In bash, run: 

export TUTORIAL_DATA=/place/with/space

In tcsh or csh 

setenv TUTORIAL_DATA /place/with/space

You will also need to link the FreeSurfer anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR.

You should set the FSFAST output format to be compressed NIFTI (nii.gz). In bash, run: 

export FSF_OUTPUT_FORMAT=nii.gz

In tcsh or csh, run: 

setenv FSF_OUTPUT_FORMAT nii.gz

Back to list of all tutorials | Back to course page | Previous | Next (Directory Structure)

FsFastTutorialV5.1/TutorialData (last edited 2016-09-01 16:37:09 by AllisonMoreau)