2012/5/10 Douglas N Greve <greve@nmr.mgh.harvard.edu>

isxavg-fe-sess is an out-dated program that won't give you what you want. If you do the -per-run option, you are sort of on your own in that you'll have to run mri_glmfit, then that the results from that and concatenate across subject. A different question is why do you want to do this?
doug

On 05/10/2012 02:58 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
I am working with single subject data in native space. Can I run mri_glmfit without running isxconcat-sess first? isxconcat-sess does not seem to take a -space argument and then fails because it does not find the average subcortical mask. What about isxavg-fe-sess?
Thanks, Caspar

2012/5/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

You can run selxavg3-sess with -per-run and it will give you a
different output for each run. These results can then be combined
in a fixed effects analysis using mri_glmfit.
doug

On 05/09/2012 03:09 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,

I have done some more debugging of my analysis and tried
different filters. If I understand slxavg-sess correctly, the
runs are concatenated, and the pcc is computed over all runs.
Is it possible to run a single subject FFX instead (e.g., by
uncommenting lines 205-217, 305-310)?
Thanks, Caspar

2012/5/7 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@

rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>>

Hi,
is it possible that it is a data format problem? I tried
forcing
fslmaths to give float output using -odt float. This changed
mostly the autocorrelations computed during selxavg, but
not the pcc.
Caspar

2012/5/7 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>
<mailto:cschwiedrz@ rockefeller.edu

<mailto:cschwiedrz@rockefeller.edu>>>

the cutoff frequencies are 0.0025 Hz and 0.25 Hz.
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>>>

The mkanalysis command looks ok. I don't know how to
interpret those numbers for fslmaths. What are the
cutoff
frequencies?
doug

On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
I use the following command for fslmaths
fslmaths fmc.nii -bptf 200 2 fmcfilt.nii

where 200*(TR+2) is 400s, and 2*(TR=2)=4s.

and for mkanalysis-sess
-force
-fsd bold
-funcstem fmcfilt
-analysis name
-notask
-tr 2
-runlistfile name
-native
-nskip 5
-mask brain
-tpef name
-taskreg name

for debugging, I did not include nuisance
regressors.
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>>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. edu
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>>>

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>
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. edu
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>
. edu
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. edu
<mailto: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>>
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<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>>
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<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>
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<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>

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<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>
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<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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MGH-NMR Center
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The information in this e-mail is
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error and
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please
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. edu
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358
<tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>>

Bugs: surfer.nmr.mgh.harvard.edu/
<http://surfer.nmr.mgh.harvard.edu/>
<http://surfer.nmr.mgh. harvard.edu/
<http://surfer.nmr.mgh.harvard.edu/>> fswiki/BugReporting
<http://surfer.nmr.mgh. harvard.edu/fswiki/
<http://harvard.edu/fswiki/>
BugReporting
<http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
FileDrop: www.nmr.mgh.harvard.edu/
<http://www.nmr.mgh.harvard.edu/>
<http://www.nmr.mgh.harvard. edu/
<http://www.nmr.mgh.harvard.edu/>>
facility/filedrop/index.html
<http://www.nmr.mgh.harvard.
edu/facility/filedrop/index. html
<http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard. edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>

Bugs: surfer.nmr.mgh.harvard.edu/
<http://surfer.nmr.mgh.harvard.edu/> fswiki/BugReporting
<http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
FileDrop: www.nmr.mgh.harvard.edu/
<http://www.nmr.mgh.harvard.edu/>
facility/filedrop/index.html
<http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>

-- 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>
Fax: 617-726-7422 <tel: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>

--
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
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html