Dear Wolf: Thanks for helping out Lorena! I concur she's using it
correctly.
Lorena: If you want to make the results more accurate, I'd do as Wolf
suggests and combine the smoothness files together.
-Tom
On Fri, Dec 7, 2012 at 4:40 PM, wolf zinke <[log in to unmask]> wrote:
> Hi,
>
> As far as I can see, these steps follow the example from Tom Nichols post
> you linked the last time. So it should be fine.
>
> good luck,
> wolf
>
>
>
> On 12/07/2012 10:29 PM, Lorena Jimenez-Castro wrote:
>
>> Dear Wolf,
>>
>> Thank you so much for your prompt response and explanation,
>>
>> Just a quick confirmation, if I want to use "easythres_conj" script
>> (without a smoothness) instead of "easythres", to see the common
>> activation of three z-maps UN-thresholded and to obtain the corrected
>> statistics, Am I doing the right thing using the following steps?
>>
>> A) fslmaths group1_zstat1.nii.gz -min group2_zstat1.nii.gz
>> group1_min_group2_zstat
>> B) easythresh_conj group1_min_group2_zstat group3_zstat1 mask.nii.gz 2.3
>> 0.01 MNI152_T1_2mm_brain.nii.gz grot
>>
>> Once again thank you very much,
>>
>> Lorena
>>
>>
>> -- Lorena Jimenez-Castro, MD
>> Postdoctoral Fellow
>> Research Imaging Institute
>> University of Texas Health Science Center
>> 8403 Floyd Curl Drive
>> San Antonio, TX 78229
>> __________
>>
>> 2012/12/7 wolf zinke <[log in to unmask]>
>> Hi,
>>
>> [I am no Prof but just wolf ;-)]
>>
>> I am sorry that I can't really follow you right now, or see, where you
>> approach contradicts that in the linked post.
>>
>> The use of this different numbers of arguments lead to some different
>> behavior of the easythres_conj script regarding its output. If you provide
>> a mask, as well as the two subsequent numbers specifying a cluster z and
>> thresholds, this script applies a conjunction analysis using the minimum
>> statistics approach AND also applies a cluster thresholding in order to
>> obtain corrected statistics. If you just provide a z-threshold, this is
>> only used for rendering the stats on the background image.
>>
>> So maybe the usage depends a bit on what you want to get out of this
>> script. If you look into this script (and maybe compare it with FSLs
>> easythresh script), you will see, that basically the 'conjunction analysis'
>> is the fslmaths call with the -m options. All the rest is about correcting
>> stats and rendering them.
>>
>> Therefore I made in my last reply the suggestion just to run fslmaths
>> with -min option using all your three groups, and use a subsequent call on
>> the output with easythresh in order to get cluster corrected statistics, If
>> I am not wrong, this should be quiet similar to what was described in the
>> linked post, but you might have a small (neglectable?) bias because of the
>> less accurate estimation of the smoothness.
>>
>> I hope this helps,
>> wolf
>>
>>
>>
>>
>>
>> On 12/07/2012 04:30 PM, Lorena Jimenez-Castro wrote:
>> 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<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
>>
>
--
__________________________________________________________
Thomas Nichols, PhD
Principal Research Fellow, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick, Coventry CV4 7AL, United Kingdom
Web: http://go.warwick.ac.uk/tenichols
Email: [log in to unmask]
Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
Fax: +44 24 7652 4532
