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| '''Index''' [[Navigation(children)]] |
#pragma section-numbers off [wiki:Self:FreeSurferWiki top] | [wiki:Self:Tutorials previous] This tutorial steps you through the analysis of an fMRI data set with the FreeSurfer Functional Analysis Stream (FSFAST), from organizing the data to group analysis. |
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| == Download the sample subjects data == == Get to know the Sessions Format == == Make a directory for your Study == == Make paradigm files for your experiment == == Motion correct the data using mc-sess == == Normalize signal intensity using inorm-sess == == Set up session-level analysis using mkanalysis-sessnew == == Average session-level data by condition using selxavg-sess == == Define an omnibus contrast using mkcontrast-sess == == Compute statistical maps of the omnibus contrast using stxgrinder-sess == == Run functional/structural registration using autoreg-sess == == Interfacing with FreeSurfer == == Functional/Anatomical Registration == == Visualization == === Visualization: slice-based using sliceview-sess === === Viewing Berts hemodynamic responses === === Visualization: surface-based using paint-sess and surf-sess === |
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| = Tutorial Data Description = The data being analyzed is part of the fBIRN Phase I data set. There are 5 subjects, each scanned twice at each of 10 sites. The data in the tutorial is the data collected at MGH. The task is a simple sensory motor blocked design experiment. During each task block the subject was shown a flashing checkerboard and presented with an auditory tone. During this time, the subject was asked to press bottons with both hands. The task blocks alternated with fixation blocks during which the subject stared at a fixation cross but performed no other task. Each block type was 15 sec long. Each run started with a fixation block followed by 8 pairs of task and fixation blocks (and so ends with a fixation block) for a total run duration of 255 sec. The TR was 3 sec, so there were 85 time points. This task was performed 4 times in each visit.Anatomicals were also collected and analyzed in FreeSurfer for each of these subjects. = Quick Visualization Tutorial (tkmedit/tksurfer) = = Assembling the Data in the FSFAST Hiearchy = == The Project (or Study) Directory == == Create a Session == == Create a Stimulus Schedule (Paradigm File) == == Link to the FreeSurfer Anatomical Recontruction == == Create a SessionID File == = Preprocessing of fMRI Data (preproc-sess) = == What preprocessing stages do you want to run? == == Run preprocessing == == Examine additions to hiearchy == == View motion correction plots == = First-Level Analysis = == Configure Analysis and Contrasts (mkanalysis-sess) == == Analyze First Level (selxavg3-sess) == == Visualize == === Volume-based visualization (tkmedit-sess) === === Surface-based visualization (tksurfer-sess) === == Examine additions to the hierarchy == = Function-Structure Registration = == View unregistered (tkregister-sess) == == Run automatic registration (fslregister-sess) == == Check automatic registration (tkregister-sess) == == Check talairach registration == = Higher-Level (Group) Analysis = == Assemble the Data (isxconcat-sess) == === Volume-based (talairach/MNI305) === ==== Quality Assurance ==== ==== Group Analysis ==== ===== Random and Fixed Effects ===== ===== Cluster Analysis ===== === Surface-based === = FsFast Tutorial SlideShow = [[Navigation(slideshow)]] * ["/000 Frontmatter"] * ["/300 Download data"] * ["/400 Get familiar with sessions format"] * ["/500 Make a directory for your study"] * ["/600 Make paradigm files for your experiment"] * ["/700 Motion correct the data"] * ["/800 Normalize signal intensity"] * ["/900 Set up session-level analysis"] * ["/905 Average session-level data by condition"] * ["/910 Define an omnibus contrast"] * ["/920 Compute statistical maps of the omnibus contrast"] * ["/930 Run functional and structural registration"] * ["/940 Visualization"] |
[wiki:FreeSurferWiki top] | [wiki:Tutorials previous]
This tutorial steps you through the analysis of an fMRI data set with the FreeSurfer Functional Analysis Stream (FSFAST), from organizing the data to group analysis.
Tutorial Data Description
The data being analyzed is part of the fBIRN Phase I data set. There are 5 subjects, each scanned twice at each of 10 sites. The data in the tutorial is the data collected at MGH. The task is a simple sensory motor blocked design experiment. During each task block the subject was shown a flashing checkerboard and presented with an auditory tone. During this time, the subject was asked to press bottons with both hands. The task blocks alternated with fixation blocks during which the subject stared at a fixation cross but performed no other task. Each block type was 15 sec long. Each run started with a fixation block followed by 8 pairs of task and fixation blocks (and so ends with a fixation block) for a total run duration of 255 sec. The TR was 3 sec, so there were 85 time points. This task was performed 4 times in each visit.Anatomicals were also collected and analyzed in FreeSurfer for each of these subjects.
Quick Visualization Tutorial (tkmedit/tksurfer)
Assembling the Data in the FSFAST Hiearchy
The Project (or Study) Directory
Create a Session
Create a Stimulus Schedule (Paradigm File)
Link to the FreeSurfer Anatomical Recontruction
Create a SessionID File
Preprocessing of fMRI Data (preproc-sess)
What preprocessing stages do you want to run?
Run preprocessing
Examine additions to hiearchy
View motion correction plots
First-Level Analysis
Configure Analysis and Contrasts (mkanalysis-sess)
Analyze First Level (selxavg3-sess)
Visualize
Volume-based visualization (tkmedit-sess)
Surface-based visualization (tksurfer-sess)
Examine additions to the hierarchy
Function-Structure Registration
View unregistered (tkregister-sess)
Run automatic registration (fslregister-sess)
Check automatic registration (tkregister-sess)
Check talairach registration
Higher-Level (Group) Analysis
Assemble the Data (isxconcat-sess)
Volume-based (talairach/MNI305)
Quality Assurance
Group Analysis
Random and Fixed Effects
Cluster Analysis
Surface-based
FsFast Tutorial SlideShow
- ["/000 Frontmatter"]
- ["/300 Download data"]
- ["/400 Get familiar with sessions format"]
- ["/500 Make a directory for your study"]
- ["/600 Make paradigm files for your experiment"]
- ["/700 Motion correct the data"]
- ["/800 Normalize signal intensity"]
- ["/900 Set up session-level analysis"]
- ["/905 Average session-level data by condition"]
- ["/910 Define an omnibus contrast"]
- ["/920 Compute statistical maps of the omnibus contrast"]
- ["/930 Run functional and structural registration"]
- ["/940 Visualization"]