You need to get the relevant information for the fMRI series. A T1 MPRAGE is completely different.
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of Duong Nguyen [[log in to unmask]]
Sent: Sunday, January 30, 2011 9:03 PM
To: [log in to unmask]
Subject: [SPM] fMRI Beginner's Help
Hello All,
I've just begun digging into fMRI and using SPM to analyze it. I have so far downloaded and run SPM 9 using the SPM manuel along with the example aduitory fMRI data to test and see the capabilities of SPM.
Everything here worked as the manuel described. My next step was to take a set of fMRI data that I was interested in and run that through SPM, however, I've been unsuccesful thus far in doing so.
I was able to obtain a set of fMRI data from the fMRI data center regarding: "Frontal-Hippocampal Double Dissociation Between Normal Aging and Alzheimer's Disease."
My initial run using SPM did not go well, probably because I did not know how to set up the design matrix correctly ("Specifiy 1-st level" GUI Button).
Below is an excerpt of the experiment acquisition setup:
"All imaging was performed using a Siemens 1.5 Tesla Vision Scanner. Cushions and a thermoplastic mask were used during scanning to reduce head movement.
A scout image (TR=15ms, TE=6ms, flip angle=30 deg, 2.34x1.17x8 mm resolution) was acquired first in order to center the field of view on the brain. Four T1-weighted
sagittal MP-RAGE scans (TR=9.7ms, TE=4ms, flip angle=10, T1=20ms, TD=200ms, 1x1x1.25 mm resolution) were acquired in each subject. Inter and Intra-scan
motion correction and averaging were accomplished off-line. All raw MRI data are available to research investigators."
Thus, the experiment looks like the following:
Protocal Name: T1-weighted sagittal MP-RAGE
Num of Vols Acquired: 1
TR: 9.7 ms
TE: 4 ms
Field of View 256 mm
Num of Slices 128
I have the following questions:
1) For each subject, four scans were made. Which means each subject has 4 volumes worth of data consisting of 128 slices each. Is this correct?
2) What is the true TR in this case? I'm assuming that the time between one slice to the next is 9.7 ms, and since we 128 slices, the total scan time
for one volume is 9.7 ms x 128 slices?
3) Is the TE important? I do not see it used much in the manuel unless I'm horribly mistaken.
4) Using SPM, I was able to run through all the data preprocessing steps. However, when I got to the "model specification, review and estimation" step, I was unable
to move on due to not knowing how to set up certain attributes. For example, the tool asks me for a TR (in seconds), but according to the TR in my data set, it should be 9.7 ms.
I tried entering in 0.0097 s, but the tool seemed to only take in 0.001 s as the minimum value. In addition to this, I'm not sure what the onset input value should be either (tried searching through
the SPM mailing list archive, but only gained minimal understanding).
Any help or pointer in the right direction is greatly appreciated!
Thanks,
Duong
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