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Description

Prepares BOLD (Blood-Oxygen-Level Dependent) images for data analysis.

Specific actions performed: images converted to 4dfp format; corrected for asynchronous slice acquisition, odd-even slice differences, and movement; an average image is created of all the first BOLD frames; and atlas transformations are computed.

Can be run on

GenericBoldPreprocessing.xml runs on an MR session with a T1 scan.
GenericBoldPreprocessing_PetMR.xml runs on a PET MR session with T1 scan.

Project Inputs

Name
Description
Allowed Values
mprs
Specify the label of the T1 scan type in
the sessions
text
(single item or comma-separated list)
target
Enter the file location of the image to be used as a
representative target
Listing of locations here
text (single name)
cross_day_register
Indicate if the subject will receive multiple scans
during the project cycle
0, 1
1 = yes, 0 = no
fstd
Specify the label of BOLD scan type in
the session
text
(single item or comma-separated list)
TR_vol
Indicate time per frame in seconds
positive numeric value
skip
Indicate fames that should not be processed
positive numeric value
epidir
Indicate direction of EPI slices
0, 1
1 = superior to inferior
0 = inferior to superior
tse
Specify the label of the Turbo Spin Echo scans in the sessions
(use only one of the following: tse, t1w, or pdt2)
text
(single item or comma-separated list)
t1w
Specify the label of the T1 weighted scans in the sessions
(use only one of the following: tse, t1w, or pdt2)
text
(single item or comma-separated list)
pdt2
Specify the label of the T2 scans in the sessions
(use only one of the following: tse, t1w, or pdt2)
text
(single item or comma-separated list)
epi2atl
Specify if transform EPI to Atlas is required
0, 1, 2
1 = transform to 333 space
2 = proceed to t4_xr3d_4dfp
0 = keep as scanned
normode
Turn on or off per-frame volume intensity
equalization
0,1
1 = yes, 0 = no
economy
Specify which of the intermediate files should be saved
positive numeric value
Siemens_interleave
Indicate if slice reordering to account for Siemens Trio
scanner interleave process should be performed
0, 1, blank
1=yes, 0 or blank=no
nx
Number of voxels on the x axis
positive numeric value
ny
Number of voxels on the y axis
positive numeric value
TR_slc
Indicate the time per slice in seconds
0, positive numeric value
0 = no pauses in acquisition
fMRI Run Label Assignment
Select how the files should be named
Can use default or specify naming convention

Launch Inputs

Name
Description
Allowed Values
Atlas Representative Target
See target above
Include MPRAGE
Indicate if MPRAGE images should be included
checked, unchecked
Include TSE
Indicate if TSE images should be included
checked, unchecked
Include BOLD
Indicate which BOLD images should be included
checked, unchecked
Is a FC scan
Specify if functional connectivity was recorded
in the scan
checked, unchecked
Run Labels
Specify how files should be named
text
Slice TR
See TR_slc above
Volume TR
See TR_vol above
No of pre-functional frames
to skip
See skip above
EPI acquisition direction
See epidir above
Transform EPI to Atlas
See epi2atl above
Enable per-frame volume
See normode above
Economy
See economy above
Nx
See nx above
Ny
See ny above
Siemens interleave
See Siemens_interleave above
send additional confirmation
emails to
Indicate others who should receive a confirmation
of successful completion of pipeline
email addresses separated
by comma

Outputs

The following will result from a successful completion of the pipeline

  • The user who launched the pipeline will receive an email from the XNAT Team with the wording:
    "BOLD processing completed for..."
  • Multiple BOLD files are created during the process. They are found under the Resources directory within the session.
    BOLDFiles.jpg
    Screenshot of BOLD files


Additional Information

BOLD Update
FAQs
Related presentation on 4dfp tools
Sample 4dfp params file

References

Shulman, G.L., Pope, D.L.W., Astafiev, S.V., McAvoy, M.P., Snyder, A.Z., Corbetta, M., 2010. Right hemisphere dominance during spatial selective attention and target detection occurs outside the dorsal frontoparietal network. J. Neurosci. 30, 3640–3651. doi:10.1523/JNEUROSCI.4085-09.2010

Fox, M.D., Zhang, D., Snyder, A.Z., Raichle, M.E., 2009. The global signal and observed anticorrelated resting state brain networks. J. Neurophysiol. 101, 3270–3283. doi:10.1152/jn.90777.2008