Re: ffx bug - Freesurfer

13 May 2008


      Sorry, It's not "live" yet -- meaning that the stable version has not 
been updated yet. Usually, this happens overnight. You can tell by running:
ls -l $FREESURFER_HOME/fsfast/toolbox/fast_selxavg.m
doug
xiaomin wrote:
...
Hi Doug,
The significance of ffx with percent is still very small from -0.0249 
to 0.0682, which is similar to what I got before.  I am using stable 4.
Xiaomin
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Tuesday, May 13, 2008 5:32 PM
To: xiaomin
Cc: 'Roger Tootell'; 'Daphne Holt'; 'Brittany Cassidy'; 'Free Surfer'
Subject: Re: ffx bug
There were a bunch of voxels with no significance because the ffx 
noise had essentially been multiplied by 100 (so 100 times more noise 
than there really was). make sense?
xiaomin wrote:
Hi Doug,
Thanks for fixing it.  I will rerun the group analysis and let you 
know if it works.  However, it is still puzzling to me why the 
significant histogram from the ffx without percent (as attached in my 
last email) looks so weird.  The maximum is too large.   Also, the 
shape of the significant ffx histogram should not be different for 
percent vs. non-percent.
Xiaomin
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Tuesday, May 13, 2008 5:13 PM
To: xiaomin
Cc: analysis-bugs@nmr.mgh.harvard.edu 
mailto:analysis-bugs@nmr.mgh.harvard.edu; 'Roger Tootell'; 'Daphne 
Holt'; 'Brittany Cassidy'; Free Surfer
Subject: Re: ffx bug
Hi Xiaomin, I finally got around to looking at this, and this is a 
bug. The "cespct" is not actually a percent, rather it is a fraction 
of the mean functional. However, the "cesvarpct" is a percent, which 
makes the group ffx analysis with percent fail. I have fixed this in 
both dev and stable such that cespct is actually a percent, live on 
next update. Let me know if this does not fix your problem.
doug
xiaomin wrote:
Hi,
I am running the following command for group fixed factor and random factor
analysis with and without percent parameter on.
Here are the commands:

for the no percent:

isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats
-hemis -o . -subject fsaverage
mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask
../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf
fsaverage rh

for the percent:

isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats
-percent -hemis -o . -subject fsaverage
mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask
../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf
fsaverage rh
However, the significance between percent and no percent is inconsistent.
For testing if the data has problem, I run it with rfx design.  The
significance between percent and no percent is almost same. (see attached
graph)  Second, the significance with percent parameter for the fixed factor
analysis is very small, which is abnormal.  We need to use ffx significant
map to define a ROI.
The data is here:
/autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D
epth.
Xiaomin Yue
Research Fellow
NMR center, MGH

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting