Differences between revisions 1 and 9 (spanning 8 versions)
⇤ ← Revision 1 as of 2017-02-22 17:22:26 →
Size: 3277
Editor: AllisonMoreau
Comment: created FSFAST 6.0 TutorialData page
← Revision 9 as of 2018-02-24 20:33:25 → ⇥
Size: 3216
Editor: EmmaBoyd
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
[[FsFastTutorialV5.1_freeview|top]] | [[FsFastTutorialV5.1_freeview|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct_freeview|next (Directory Structure)]]
<<TableOfContents>>		 [[FsFastTutorialV6.0|top]] | [[FsFastTutorialV6.0|previous]]| [[FsFastTutorialV6.0/FsFastDirStruct_freeview|next (Directory Structure)]] <<TableOfContents>>
Line 5: Line 5:
The functional data were collected as part of the Functional Biomedical Research Network (fBIRN, www.nbirn.net). The functional data were collected as part of the Functional Biomedical Research Network (fBIRN).
Line 10: Line 11:
 * FreeSurfer anatomical analyses  * !FreeSurfer anatomical analyses
Line 12: Line 14:
The paradigm was designed to study the effects of emotional stimuli on
the ability to recall items stored in working memory.
 * Blocked design		 The paradigm was designed to study the effects of emotional stimuli on the ability to recall items stored in working memory.

 * Block design
Line 16: Line 18:
  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 22: Line 24:
{{attachment:wmparadigm.jpg}}
The above yields 5 conditions:
  1. Encode
  1. Emotional Distractor
  1. Neutral Distractor
  1. Probe following Emotional Distractor
  1. Probe following Neutral Distractor
{{attachment:wmparadigm.jpg}} <<BR>> The above yields 5 conditions:

 1. Encode
 1. Emotional Distractor
 1. Neutral Distractor
 1. Probe following Emotional Distractor
 1. Probe following Neutral Distractor
Line 30: Line 34:
Line 37: Line 42:
Line 39: Line 45:
'''If you are at a !FreeSurfer Course, continue on to the next page now'''
[[FsFastTutorialV5.1_freeview|top]] | [[FsFastTutorialV5.1_freeview|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct_freeview|next (Directory Structure)]]
'''If you are at a !FreeSurfer Course, continue on to the next page now''' <<BR>><<BR>> [[FsFastTutorialV6.0|top]] | [[FsFastTutorialV6.0|previous]]| [[FsFastTutorialV6.0/FsFastDirStruct|next (Directory Structure)]]
Line 42: Line 49:
= Getting the Data (not necessary for the Boston FreeSurfer Course)  = = Getting the Data (not necessary for the Boston !FreeSurfer Course) =
Line 44: Line 51:
Line 48: Line 56:
Line 51: Line 60:
= 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.		 = 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 58: Line 67:
Line 62: Line 72:
You will need to set the TUTORIAL_DATA environment variable. In tcsh
or csh		 You will need to set the TUTORIAL_DATA environment variable.  In bash
Line 67: Line 77:
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):		 You will also need to link the !FreeSurfer anatomical subjects (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR. You should set the FSFAST output format to be compressed NIFTI (nii.gz):
Line 73: Line 82:
[[FsFastTutorialV5.1_freeview|top]] | [[FsFastTutorialV5.1_freeview|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct_freeview|next (Directory Structure)]] [[FsFastTutorialV6.0|top]] | [[FsFastTutorialV6.0|previous]]| [[FsFastTutorialV6.0/FsFastDirStruct|next (Directory Structure)]]

top | 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).

  • 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.

  • Block 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

If you are at a FreeSurfer Course, continue on to the next page now

top | previous| next (Directory Structure)

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 

export TUTORIAL_DATA=/place/with/space

You will also need to link the FreeSurfer anatomical subjects (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR. You should set the FSFAST output format to be compressed NIFTI (nii.gz): 

export FSF_OUTPUT_FORMAT=nii.gz

top | previous| next (Directory Structure)

FsFastTutorialV6.0/TutorialData (last edited 2018-09-30 09:41:07 by AndrewHoopes)