FIR time course & canonical hrf

Hi dear Matthew, dear list, 

I have a quick question that I want to make clear. 
Does it make sense to present the FIR time courses when I use canonical hrf
for SPM (event-related)?  and to which limit? what is the additional
information that TC (either fittedTC or fitted_TC_FIR) could give in this
case? 

Thanks in advance,
Qing   :)

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Very slow estimation

Dear Friends:

I'm trying calculate % signal changes of ROIS using Marsbar. It usually
works very well. But, now the estimation is very slow and takes several
hours for one ROI.  It is much slower than the estimation of SPM2. SPM2
takes about 10 minutes to estimate for the whole brain analysis.

Another issue is that for the same subject, marsbar perform estimation
separately for each ROI. But, my previous experience is that Marsbar
estimate once and than spit out % signal changes for different ROIs.

Relative to my previous design, my current design use 6 motion parameters as
covariates. I also used RobustWLS
(http://www.bangor.ac.uk/~pss412/imaging/robustWLS.html) in my design to
reduce the effects of motion.

Marsbar print following message:

Summarizing data with summary function: mean
Re-estimating covariance
Re-estimating whitening filter
Initialising parameters
Covariance estimate
Model
Temporal non-sphericity (over voxels)
......
......

Any suggestions will be highly appreciated.

Re: comparability of data from different scanning sessions

Hi Julia,

Sorry, I realize this is a very late reply, and I'm sure you've found
solutions by now, but...

> Conditions A,B,and C of the first day usually show similar time courses.
> However, compared to these
> conditions, condition A2 stays always close to zero.

I wonder, were the lengths of the events or blocks for A and A2 the
same in your models?  Did you specify durations for one and not the
other for example?  Let's imagine you specified an event length of 0.1
for A and 0 for A2, then the regressors for A2 would be much larger
(an event length of 0 in SPM is effectively translated to an event
length of 1), and the parameters for events of the same magnitude
would be much larger for A than A2.

You could normalize by estimating percent signal change for the events
and comparing those instead...

Best,

Matthew

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Re: comparability of data from different scanning sessions

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SPM5 VOI

Hi

I am a new user of marsbar and I have a (simple?) question considering
the use of marsbar extracted ROI-data in SPM. Specifically, I want to
perform a PPI
analysis in SPM5 for which you normally have to use VOI-data
originating from the VOI-tool at the results section in the SPM-GUI. I
was wondering if it is
possible to create VOI .mat Files with marsbar which correspond to the
same format generated by SPM (e.g. y and xY structures containing the
BOLD-eigenvariates).
Thanks,
Joe

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SPM.mat set design from file windows problem

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select specific values within nifti image

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Re: select specific values within nifti image

Hi,

> I would like to include only one of these values in my ROI (in this case,
> 12), while excluding voxels with the value of 0 or 112. How can I indicate
> this in the batched version of marsbar?

I think you could do this by applying a function to the image as you
do ROI definition->Build->Image,  such as 'img == 12'.  Does that
work?

Best,

Matthew

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select specific values within nifti image

Dear Matthew and List,

I am using MarsBar with SPM5 to build ROIs from a set of input images 
(segmented subcortical structures, using FSL FIRST). 

These input (nifti) images contain three different numbers: for instance, 0 at 
voxels where there is no subcortical structure, 12 at locations where there is 
subcortical structure, and 112 at the border of that structure. 

I would like to include only one of these values in my ROI (in this case, 12), 
while excluding voxels with the value of 0 or 112. How can I indicate this in 
the batched version of marsbar?

Thanks a lot for your help!

Greetings, Rick

=========================================

Rick C.G. Helmich, MD (Ph.D student)

F.C. Donders Centre for Cognitive Neuroimaging 
P.O. Box 9101 
6500 HB Nijmegen 
The Netherlands 

T  00 31 (0)24 36 65077 
F  00 31 (0)24 36 10989 
E  rick.helmich <at> fcdonders.ru.nl
web: www.fcdonders.ru.nl 
=========================================

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Re: select specific values within nifti image

Dear Matthew,

Thanks for your rapid response!

> I think you could do this by applying a function to the image as you do ROI 
> definition->Build->Image,  such as 'img == 12'.  Does that work?

In the GUI mode that does seem to work, although the output image is not 
strictly binarized: some of the 112 values are now replaced by values between 0 
and 1 (and although most of the 12 values are now 1, some of them are also 
between 0 and 1). Do you have any idea why that is? And second, how to batch 
the application of a function to the image? My code is now as follows:

ROI = maroi_image('image.nii');
saveroi(ROI, 'name_roi.mat');
save_as_image(ROI, 'name.img');

addding: ROI = (ROI==12) doesn't work (i.e. it gives me exactly the same image 
as before, including both voxels with values 12 and 112). Save_as_image
(ROI==12,'name.img') also does not work, that gives me an empty image. Any 
other advice?

Thanks a lot! Rick

Rick Helmich <r.helmich <at> fcdonders.ru.nl> writes:

> 
> Dear Matthew and List,
> 
> I am using MarsBar with SPM5 to build ROIs from a set of input images 
> (segmented subcortical structures, using FSL FIRST). 
> 
> These input (nifti) images contain three different numbers: for instance, 0 
at 
> voxels where there is no subcortical structure, 12 at locations where there 
is 
> subcortical structure, and 112 at the border of that structure. 
> 
> I would like to include only one of these values in my ROI (in this case, 
12), 
> while excluding voxels with the value of 0 or 112. How can I indicate this in 
> the batched version of marsbar?
> 
> Thanks a lot for your help!
> 
> Greetings, Rick
> 
> =========================================
> 
> Rick C.G. Helmich, MD (Ph.D student)
> 
> F.C. Donders Centre for Cognitive Neuroimaging 
> P.O. Box 9101 
> 6500 HB Nijmegen 
> The Netherlands 
> 
> T  00 31 (0)24 36 65077 
> F  00 31 (0)24 36 10989 
> E  rick.helmich <at> fcdonders.ru.nl
> web: www.fcdonders.ru.nl 
> =========================================
> 
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> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
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> 

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