New subject: problems with analysis after using fslmaths

7 May 2012


      What frequencies did you chose for the FSL bandpass filter? What is you 
mkanalysis-sess command?
On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
...
yes
2012/5/7 Douglas N Greve <greve@nmr.mgh.harvard.edu 
mailto:greve@nmr.mgh.harvard.edu>
Did you regenerate the seeds after filtering?


On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:

    I have tried analyses with only one seed time course (either 1
    voxel, mean of a sphere of 1 voxel radius, or mean of a
    functionally defined roi), as well as several seeds within the
    same design matrix, with the same problem.
    All of these analyses did yield higher pcc when done without
    filtering.
    Caspar

    2012/5/7 Douglas N Greve <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard. edu
    <mailto:greve@nmr.mgh.harvard.edu>>>


       Is this doing all of those seeds simultaneously or one seed
    at a time?

       On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
    > Hi,
    > I am trying to use fslmaths to filter my data before I plug it
       into a
    > resting state analysis. However, once I obtain a pcc map, all
    > correlation coefficients are <0.1, even the autocorrelation
    with the
    > seed voxel.
    > The data look fine when I open them in Matlab using MRIread; the
    > correlations between individual voxel time courses obtained in
       Matlab
    > is about 0.6.
    >
    > My analysis stream is as follows:
    > a) I filter the data using "fslmaths input -bptf highpass
    lowpass
    > output"; from this I obtain a filtered nii.gz file
    > b) I extract a seed timecourse from the filtered data in Matlab
    > c) I run mkanalysis-sess with -notask
    > d) I run selxavg3-sess
    > e) I overlay the pcc.nii
    >
    > I have tried this with smoothed and unsmoothed data, with and
       without
    > nuisance regressors, with different seeds, with mri_convert
       after step
    > a. It is not a problem with the overlay since the max values
    in pcc
    > are all <0.1.
    > I noticed that there are some differences in the nifti header
       (as read
    > with MRIread) before and after filtering, but it seemed to
    me that
    > they are gone after I used mri_convert.
    > I do find much higher correlations with unfiltered data.
    > Any advice what could be going wrong here? I am using
    Freesurfer 5.1
    > and FSL 4.1.9 on Linux.
    > Thanks, Caspar
    >
    >
    >
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] problems with analysis after using fslmaths