Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right?
On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. > What you are trying to get is the expected variance of your difference > between the ces files (as a variance, it must be positive). To get this you > need > > cesvardiff = (cesvar1+cesvar2)/(2^2) > > The 2^2 is the number of inputs (2) squared. > > doug > > > SHAHIN NASR wrote: > >> Hi, >> >> I have generated two different functional connectivity maps for two >> different ROI-based seeds. These maps are based on group-average of the same >> subjects (generated by using separate isxconcat-sess commands ), and now I >> want to see the difference map. To do so, I used mris_calc as below. >> > mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub >> map2/rh.ces.nii >> >> Also, to generate the rh.cesvar.nii file I used this command: >> > mris_calc -o diff_map1/rh.cesvar.nii map1/rh.cesvar.nii sub >> map2/rh.cesvar.nii >> >> But then when I used the glmfit with WLS option as below: >> >> > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask >> ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf >> fsaverage rh --wls rh.cesvar.nii >> >> I faced an error saying: "Error: MRInormWeights: values less than or eq >> to 0" which I assumed is related to an error in rh.cesvar.nii file (am I >> right?). Would you tell me how can I fix this problem? >> >> P.S.: please note that sequence of subjects and all MRI parameters are >> exactly the same between the two maps. >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
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