I am comparing the final beta.nii.gz by importing it to matlab and this is on individual subjects. The subjects have not moved much (less than 3 mm). But the number of voxels that have different values in betta.nii.gz are a handful which does not seem right since the fmc.nii.gz and fmcpr.nii.gz are much more differet. Also the X.mat file should contain the motion correction values since I have asked the analysis to use motion as an external regressor. But the two X.mat files in the analysis folder in the bold directory are very very similar (not identical but the difference seems to be in the 0.000001 range that might be due to some rounding errors)

One thing that puzzles me is the -funcstem in the analysis.info which is set to fmc by default. Does this force the analysis to use fmc.nii.gz az the input to the analysis? Should I make it to use fmcpr for the perrun analysis to get different results? 

M

On Tue, Jan 22, 2013 at 2:49 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect.

doug

On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote:

Hi Dough,

This might be a very basic question:
I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line:

*mkanalysis-sess \*

*-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \*

*-native -mcextreg -stc siemens -fwhm 0 \*

*-event-related  -paradigm para_cat.par -nconditions 5 \*

*-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2*

*
*
*
*

*
And here is what I have in my analysis info

analysis Cat_1
mcstem fmc
fsd bold
runlistfile run_1.txt
TR 2
RegDOF 6
RawSpace volume native
mask brain
RawFWHM 0
RawSTC siemens
UseB0DC 0
inorm 100
acfbins 30
fixacf  1
acffwhm 20
acfsvd  0
designtype event-related
nskip 0
polyfit 2
HPFCutoffHz 0
HeteroGCor 0
nconditions 5
parname para_cat.par
RefEventDur 3
timewindow 40.000000
prestim 0
TER 0.050000
spmhrf 0
stimulusdelay -1.00000000000000000000
Condition 1 Condition01
Condition 2 Condition02
Condition 3 Condition03
Condition 4 Condition04
Condition 5 Condition05
nuisreg mcextreg 3



I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1.

M

*

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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