Dear Professor Wolf and Professor Tom Nichols,
I greatly appreciate your answer Professor Wolf, However I am a little confused because I think that it is valid to do a conjunction analysis using "easythresh_conj" without including the smoothness, although I do understand that is more accurately to use a smoothness. Thus, I was thinking to apply "easythresh_conj" without a smoothness. Am I understanding correctly?
So, My primary question was: if I have z-maps UN-thresholded which of the following call of "easythresh_conj" is correct:
1) easythresh_conj group1_min_group2_zstat group3_zstat1 2.3 MNI152_T1_2mm_brain.nii.gz grot
or
2) easythresh_conj group1_min_group2_zstat group3_zstat1 mask.nii.gz 2.3 0.01 MNI152_T1_2mm_brain.nii.gz grot
I thought the correct option was my option "2" However I found this post from Professor Tom Nichols ( https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1112&L=fsl&P=R21238&1=fsl&9=A&J=on&X=6CCA4C4BB86C137993&Y=lojicas%40yahoo.com&d=No+Match%3BMatch%3BMatches&z=4 ) where he described the opposite to what I was thinking. So I would like to Know which of the above calls of "easythresh_conj" is right for uncorrected stat.
I would appreciate any correction and insight on this matter,
Thanks a lot
Lorena
-- Lorena Jimenez-Castro, MD
Postdoctoral Fellow
Research Imaging Institute
University of Texas Health Science Center
8403 Floyd Curl Drive
San Antonio, TX 78229
________________________________
Hi,
I guess in principle it is no that wrong what you are doing. But you could take the minimum of all three maps with one call:
fslmaths group1_zstat1 -min group2_zstat1 -min group3_zstat1 groups_conj
You can feed the output into easythresh, or apply any other form of correction.
When using a cluster based thresholding, you might have a small bias when estimating the smoothness just for the resulting image (I read once here, that this is not severe, but can;t asses by myself). In Tom Nichols script there are several methods mentioned, to get a better estimate of the smoothness. FOr example, run smoothest on each group imagem and take the maximum of DLH and RESELS as smoothness estimate for the clusterthresholding, e.g.
SM1=`smoothest -z $zstat1 -m $tmpdir/mask`
SM2=`smoothest -z $zstat2 -m $tmpdir/mask`
SM3=`smoothest -z $zstat3 -m $tmpdir/mask`
VOLUME=`echo $SM1 | grep VOLUME | awk '{print $4}'` # Same mask, so volume should be identical
DLH1=`echo $SM1 | grep DLH | awk '{print $2}'`
DLH2=`echo $SM2 | grep DLH | awk '{print $2}'`
DLH3=`echo $SM3 | grep DLH | awk '{print $2}'`
# that's a quick and dirty way, not very elegant...
DLH=`echo "if ($DLH1 > $DLH2) $DLH1 else $DLH2" | bc -l`
DLH=`echo "if ($DLH3 > $DLH) $DLH3 else $DLH" | bc -l`
RESELS=`echo "if ($RESELS1 > $RESELS2) $RESELS1 else $RESELS2" | bc -l`
RESELS=`echo "if ($RESELS3 > $RESELS) $RESELS3 else $RESELS" | bc -l`
echo "DLH $DLH" > groups_conj_smoothness
echo "VOLUME $VOLUME" >> groups_conj_smoothness
echo "RESELS $RESELS" >> groups_conj_smoothness
Alternatively, you might use the mean instead of the max as less conservative approach:
DLH=`echo "( $DLH1 + $DLH2 + $DLH3) / 3.0" | bc -l`
RESELS=`echo "( $RESELS1 + $RESELS2 + $RESELS3 ) / 3.0" | bc -l`
I hope, this helps (and I hope I did nothing wrong here...),
wolf
On 12/06/2012 11:41 PM, Lorena Jimenez-Castro wrote:
Hello FS experts and users,
I want to do a conjunction analysis on three groups that I have, So I am using their three z-maps UN-thresholded (uncorrected stats). I did the following:
A) fslmaths group1_zstat1.nii.gz -min group2_zstat1.nii.gz group1_min_group2_zstat
B) easythresh_conj group1_min_group2_zstat group3_zstat1 2.3 MNI152_T1_2mm_brain.nii.gz grot
So, my question is:
1) Am I using correctly the easythresh_conj tool? or for uncorrected stats Do I need to call easythresh_conj like this:
easythresh_conj group1_min_group2_zstat group3_zstat1 mask.nii.gz 2.3 0.01 MNI152_T1_2mm_brain.nii.gz grot
I confused even so I have read the archives, so I would appreciate any clarification on this matter,
Thank you very much
Lorena
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