help > T1-equilibration dummy scans
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May 2, 2012 05:05 PM | Ged Ridgway
T1-equilibration dummy scans
Hi,
In the functional data for the FC-1000 (or, if they vary, more specifically for the NYU test-retest data http://www.nitrc.org/projects/nyu_trt/ ), have some "dummy scans" (to allow for T1-equilibration) been automatically dropped by the scanner and/or dropped from the distributed data?
If not, were a few of the 197 scans dropped in any of the papers on the NYU TRT data? And/or should future papers consider dropping the first few scans?
For example, see the last sentence of section 2.2 of this paper http://dx.doi.org/10.1016/j.neuropsychol...
"An additional four (dummy) EPI volumes were acquired before the start of each session to account of T1-equilibrium effects."
Many thanks,
Ged
In the functional data for the FC-1000 (or, if they vary, more specifically for the NYU test-retest data http://www.nitrc.org/projects/nyu_trt/ ), have some "dummy scans" (to allow for T1-equilibration) been automatically dropped by the scanner and/or dropped from the distributed data?
If not, were a few of the 197 scans dropped in any of the papers on the NYU TRT data? And/or should future papers consider dropping the first few scans?
For example, see the last sentence of section 2.2 of this paper http://dx.doi.org/10.1016/j.neuropsychol...
"An additional four (dummy) EPI volumes were acquired before the start of each session to account of T1-equilibrium effects."
Many thanks,
Ged
May 2, 2012 05:05 PM | Ged Ridgway
RE: T1-equilibration dummy scans
Oops, just slightly too late I have seen that it's mentioned in the
preprocessing document for FC-1000 here:
http://www.nitrc.org/docman/view.php/296...
that "The first 5 timepoints of each timeseries were discarded" for rest.nii
However, the equivalent document for NYU TRT:
http://www.nitrc.org/docman/view.php/274...
does not mention this (preproc for functional data: "none")
I hope I have the right forum for a question about the TRT data; there don't seem to be any forums for it specifically on NITRC: http://www.nitrc.org/support/?group_id=2...
Many thanks,
Ged
http://www.nitrc.org/docman/view.php/296...
that "The first 5 timepoints of each timeseries were discarded" for rest.nii
However, the equivalent document for NYU TRT:
http://www.nitrc.org/docman/view.php/274...
does not mention this (preproc for functional data: "none")
I hope I have the right forum for a question about the TRT data; there don't seem to be any forums for it specifically on NITRC: http://www.nitrc.org/support/?group_id=2...
Many thanks,
Ged
May 2, 2012 07:05 PM | Maarten Mennes
RE: T1-equilibration dummy scans
Hi Ged,
Yes, for the FCP-1000 analysis we removed the first 5 timepoints of every scan (regardles of whether we had information about that from each site). We choose this option as it gave us ease of use and certainty that we allowed magnetization stabilization in every dataset (some datasets might have more removed, but that is ok).
For the TRT data we did not do this. The number of volumes of the scan is 197. However, if I remember correctly there were indeed 4 dummy volumes collected with that sequence. Those volumes were automatically discarded by the scanner and not considered during the reconstruction. So you can safely use all 197 volumes (as was done in the paper that reports on the TRT data http://www.ncbi.nlm.nih.gov/pubmed/19221144).
Cheers,
Maarten
Yes, for the FCP-1000 analysis we removed the first 5 timepoints of every scan (regardles of whether we had information about that from each site). We choose this option as it gave us ease of use and certainty that we allowed magnetization stabilization in every dataset (some datasets might have more removed, but that is ok).
For the TRT data we did not do this. The number of volumes of the scan is 197. However, if I remember correctly there were indeed 4 dummy volumes collected with that sequence. Those volumes were automatically discarded by the scanner and not considered during the reconstruction. So you can safely use all 197 volumes (as was done in the paper that reports on the TRT data http://www.ncbi.nlm.nih.gov/pubmed/19221144).
Cheers,
Maarten