Hi Doug,
thanks for the response. The residual from unwhittening data is the same as
those produced by the full model. One more question. I transferred the
functional data from functional space to the anatomical space using mri_vol2vol
without resample: mri_vol2vol --reg register.dof6.dat --mov f.nii --o
test.noresample.nii --fstarg orig.1p5.mgz --no-save-reg --no-resample. From
the wiki, i know that resample parameter will change vox2ras only without
touching the raw data. When selxavg3-sess processes the functional data, does
it resample test.nosample.nii so that voxles from a run to another would
matches? The reason I am asking is that my functional data has slight
different slice position, I like to resample the raw data as little as possible.
Thanks,Xiaomin
Date: Mon, 17 Aug 2015 11:12:35 -0400
From: gr...@nmr.mgh.harvard.edu
To: yu...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess, -svres
They are not the "same". As you point out they have a correlation of
.98, not 1.0. What you are discovering is the inconvenient truth
that task signal accounts for a very small proportion of variation.
Welcome to fMRI:). I think the reason why the residual does not
equal y - X*beta is that they are whitened. Try it with whitening
turned off and see if you get the same (identical) result.
doug
On 8/9/15 10:50 PM, Xiaomin Yue wrote:
Hi Doug,
In order to understand my data better, I did the following
analysis. First, I did a full model analysis with all stimuli
conditions included in the analysis using: mkanalysis-sess
-fsd bold -paradigm xy_mky_category_eye_weights.par
-event-related -refeventdur 1 -no-inorm -delay 0 -polyfit 3
-gammafit 0 8 -gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg
eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2.0000 -nconditions
940 -funcstem f.mc.perrun.so.nativespace -acfbins 3 -analysis
perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run
-native -force -tpexclude xy_eye_tpe -runlistfile xyrunlist.
Then I run: selxavg3-sess -s beck -d . -analysis
perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-no-preproc -no-con-ok -overwrite -svres
second, I did a analysis without
the stimuli conditions: mkanalysis-sess
-fsd bold -paradigm xy_mky_category_eye_weights.par -notask
-no-inorm -delay 0 -nuisreg mcprextreg 3 -nuisreg
eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2.0000 -funcstem
f.mc.perrun.so.nativespace -acfbins 3 -analysis
NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-per-run -native -force -tpexclude xy_eye_tpe -runlistfile
xyrunlist. Then, I runselxavg3-sess
-s beck -d . -analysis
NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-no-preproc -no-con-ok -overwrite -svres
After that, I loaded the residuals
(res-00x.nii under the res directories) generated from the
full model analysis and those from the no task
analysis into the matlab. I expected that the results should
be different, but the residuals from the two analysis are
almost identical (correlation is 0.98) for a voxel where the
stimuli from different conditions should cause significant
response difference. Then, I tried to
generated the residual from the full model analysis by real
signal - design matrix (loaded from X.mat) *beta values
(loaded into matlab from beta.nii). This residual is
different from the residual of the NO task analysis. My
question is why the residual from the two different analysis
generated by fsfast are same? Are my commands wrong? Or
the model is wrong? Second, it is possible to generate raw
residuals without some kind of normalization?
Thanks very much for your help!
Xiaomin
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