Re: [Freesurfer] problems with analysis after using fslmaths

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>

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>
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