rfxplot-users — mailing list or discussions on functionality of rfxplot

[rfxplot-users] Error in RFX plot

[Ankeeta S. <ank...@ya...>]

Dear developers 
I am new to use this toolbox and it says that it cannot read the directory of SPM.mat file.Please help
With Regards Ankeeta

Sent from Yahoo Mail on Android

[rfxplot-users] help: rfx plot error

[Joyce D. <JDi...@tr...>]

Hi All,

I have the following error:

RFXPLOT has terminated with an error. If you want to report this error, please type ''rfx_debug = 1" at the MATLAB prompt and rerun rfxplot

ERROR MESSAGE:
Cant open image file.
ERROR STACK:
66 rfx_get_data_img
425 rfx_main
200 rfxplot
981 spm

Does anyone know how to solve this problem? It appears almost near the end of using rfx plot while plotting effect sizes. While it is asking for Xtick positions.

Hope to hear from anyone.

Best,
Joyce

Met vriendelijke groet,
Joyce Dieleman
Promovendus - Jeugd

www.trimbos.nl<http://www.trimbos.nl>
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[rfxplot-users] Error plotting effect sizes for flexible factorial design

[Katharina V. <kat...@mo...>]

Hi all,


I’m currently trying to plot the interaction effect sizes for each of my conditions of a factorial design.
Unfortunately I get an error saying 'the field ‘u’ does not exist” .

Could you please let me know what might go wrong and how I can fix it?

Thank you,
Kati

___________________________________
Katharina Voigt
BSc(Hons), MSc, PhD
Postdoctoral Research Fellow

Turner Institute for Brain and Mental Health
Addiction and Mental Health Program
School of Psychological Sciences
Monash University
18 Innovation Walk, R618
Clayton campus, VIC 3800
Australia

T:  +61 3 9905 1402
E: kat...@mo...

[rfxplot-users] Please add me to the mailing list..Thanks

[Sungshin K. <sun...@no...>]

Sungshin Kim, PhD
Feinberg School of Medicine,
Northwestern University

[rfxplot-users] suprathreshold voxels

[Papegaaij, S (med) <s.p...@um...>]

Dear rfxplot-users,

I would like to plot the percent signal change within a region of interest. My question is when you select "only suprathreshold voxels" for the voxel selection whether this selection is done on group level or on individual level? I would like to have a mean value for all the suprathreshold voxels per individual. Is there a way to do this?

Thank you very much,

Selma Papegaaij
________________________________
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[rfxplot-users] Using rfxplot with PPI

[James Jones-R. <jj...@co...>]

Hello all,

We are attempting to use rfxplot to quantify effect sizes of the PPI
results we have calculated, all within SPM8 on a Mac OS. We have calculated
PPI on seed voxels of interest, which generated a list of target voxels
whose timecourses significantly correlate with the seed voxels. We are then
feeding those target voxels (and the accordant SPM.mat file that the PPI
toolbox generated for each target voxel) into rfxplot in order to quantify
the effect size of that target voxel's correlation/connectivity with its
respective seed voxel.

I have two questions for you all. First, when one goes through the rfxplot
GUI, one has the option of choosing "beta" or "con" as the substrate for
the analysis. In our study, we had two sessions/runs. Choosing "beta" in
rfxplot leads to two lists of variables to analyze (an essentially
identical list for each session), whereas choosing the "contrast" option
only gives a single list of variables to select from.

Here's our issue. When we run the "beta" option, the ".gdata" results
variable includes two unique columns of data, with two different values for
each participant (one for each of their two sessions); however, when we run
the "contrast" option, the ".gdata" results variable only has a single
column and it is identical to the first of the two ".gdata" columns from
the "beta"-based analysis. Why is this?

Secondly, and more broadly, does anyone have experience using rfxplot to
quantify connectivity analyses from PPI, and if so, can you point to any
resources or literature we can review? Specifically, we'd like to know more
about how to confirm that the rfxplot results actually pertain to the
connectivity estimate between the seed voxels and the target voxels. There
does not seem to be a lot of information out there about combining these
toolboxes in this way, although it seems theoretically to be a sound way of
conducting the analyses.

Thank you very much for your time!

James
-- 
James Jones-Rounds
Laboratory Manager
Human Development EEG and Psychophysiology (HEP) Laboratory,
Department of Human Development,
--------------------------------------------
Cornell University | Ithaca, NY
607-255-9883
ee...@co...

[rfxplot-users] Can I use four different studies data?

[Yuko <ilo...@gm...>]

Dear all,

I would like to use four different studies data.

Each study has "Task A", however, in each study, trial number of "Task A"
was difference. For example, in study one, I presented "Task A" 12 times,
and in study two, I presented "Task A" 11 times......
Could I use con_images of Task A from those different four studies?

Any suggestion would be highly appreciated.

Thank you so much,
Yuko

[rfxplot-users] Individual Subject PSTH

[Horatio D. <hor...@gm...>]

Dear Jan,

Firstly - thank you for such a well-written and -documented toolbox, its a
new discovery for me and Im finding it a pleasure to use. Ill be sure to
cite you in upcoming manuscripts.

I have primarily been using the toolbox for extracting PSTHs, but I would
like to be able to extract PSTHs for each individual in my sample to run
some stats and correlations with behaviour. Ive played around with some of
the data structures but can't seem to find how to do this. Do you have any
pointers for me?

With regards,
Horatio

[rfxplot-users] different colors for groups plotting psth

[Domsalla, M. <Mel...@zi...>]

Hi rfxplot-users,

 

I was just trying to plot psth separately for 2 groups. Do you know if
there is the possibility to plot the psth for the two groups in
different colours? In the manual the colour specification only is
described for different effects or different bins. Can anybody help?

 

Thanks in advance and best wishes

 

 

Melanie Domsalla, Dipl.Psych.


Research unit 'Experimental Psychology' 

Central Institute of Mental Health 

Department of Psychosomatic Medicine and Psychotherapy

Medical Faculty Mannheim, University of Heidelberg

J 5, D-68159 Mannheim, Germany

phone: +49-621-1703 4417, fax: +49-621-1703-4405

 

 

[rfxplot-users] Error: Improper index matrix reference; batch script?

[Gina J. <jo...@hu...>]

Hi,

I'm trying to get started with rfxplot and scripting a simple plot based on the rfxplot manual but am getting the following error:

ERROR MESSAGE:
Improper index matrix reference.
ERROR STACK:
31      spm_read_vols
14      rfx_get_ffx_voxel_mask
214     rfx_main
204     rfxplot

I'm not even sure where to begin asking questions or what info to provide. I turned on "rfx_debug = 1". Doing "dbstop if error" or putting breakpoints in rfx or SPM code doesn't seem to stop the execution where the error/breakpoint is. 


Any suggestions? Does anyone maybe have a sample batch script?

Thanks for any help,
g

[rfxplot-users] Problem with rfxplot: Cant open image file (files *not* moved)

[Klossika, I. <Iri...@zi...>]

Dear experts,

 

I'm having problems with a voi analysis using rfxplot. It keeps
terminating with the following error:

 

ERROR MESSAGE:

Cant open image file.

ERROR STACK:

66      rfx_get_data_img

425     rfx_main

200     rfxplot

914     spm

 

... after displaying the results of only one subject. Whole brain
results of First and Second Level analyses (spm8) are displayed without
problems for all subjects. And no, I most certainly did not move the
files around (that's apparently what everybody thinks at first, but I
know for sure because I re-did the whole preprocessing in the faint hope
that this might help; it didn't). Neither should limited access be a
problem.

 

What really mystifies me is that the problem appears in only one group
of subject. The other runs smoothly. Can anybody help?

 

 

Iris Klossika
Central Institute of Mental Health
Mannheim, Germany

 

[rfxplot-users] PSTH and Beta values

[Burak E. <bur...@gm...>]

Dear RFX users,

I have 3 questions

1) While plotting psth I am getting error saying that rfx can't access to
individuals time series subject 1.... and stopping. Even though the group
folder is in different folder than single subject
they are both under the same big folder and got no problem in plotting
percent signal changes. I only got problems with psth.

2) Should I apply filtering for psth what is the rationale for that ?

3) In order to make a statistical test for comparing the  percent signal
changes for two contrasts for a  local maximum voxel or sphere does anybody
know the name of the variable in

the matlab data structure. Or is there an automatic procedure implemented in
rfx to say statistical significance. If anybody have a matlab script for
that, it would be very useful for the community.

Best wishes


-- 
Burak Erdeniz
Phd Student
Psychology & Computer Science Department
Health & Human Sciences Research Institute
2f240 Health Building
University of Hertfordshire
College Lane
Hatfield
Herts
AL 10 9AB

[rfxplot-users] Different colors for groups

[Vikram r. <vik...@gm...>]

Hi rfxplot users,

I was wondering if there was a way to plot psth with different colors for
each group (not effects or bins!)...the rfxplot gui doesnt prompt for any
options where we can define different colors for different groups. I am
plotting SEM s as area. Has anybody tried to play with this. Thanks in
anticipation.

Cheers!
Vikram Rao
UC Berkeley, Psychology Dept.
Berkeley, California, USA
"A pizza with radius "z" and thickness "a" has a volume of pi*z*z*a"

[rfxplot-users] Using rfxplot in mixed model design

[Marcus H. <mar...@me...>]

I planning to use rfxplot with a mixed model made with SPMs flexible factorial design (1 beween subjects, 2 within subjects factors). Since there is a long discussion regarding the correct calculation of error terms in a mixed model design, I wanna know of anybody has used rfxplot in a mixed model design.

Thanks in advance,

Marcus 

[rfxplot-users] important bug fixes in rfxplot. Please update.

[Jan G. <gla...@hs...>]

Dear all,

I have just posted a new version of rfxplot (Rev 30) online that contains a
couple of important bug fixes:
1. In previous version the percent signal change for negative betas was
computed incorrectly.
2. In case of multiple basis function (e.g. HRF+TD+DISP) the parameter
estimate plots were not correct.

Both errors are fixed in the current version and I urge you to update,
since these will affect your data plots, if the conditions above meet your
fMRI design.

The most recent version is available at:
http://rfxplot.sourceforge.net/download

Just unzip the most recent version in your SPM toolbox folder overwriting
the previous one.

Apologies, if you received this email multiple times.

Thanks,
Jan


-- 
Jan Gläscher, Ph.D.         Div. Humanities & Social Sciences
+1 (626) 395-3898 (office)  Caltech, Broad Center, M/C 114-96
+1 (626) 395-2000 (fax)     1200 E. California Blvd
gla...@hs...    Pasadena, CA 91125

[rfxplot-users] new version of rfxplot

[Jan G. <gla...@hs...>]

Dear all,

I have just posted a new version (Revision 7) of rfxplot online at
http://rfxplot.sourceforge.net.

New features include:
* Bug fixes related to multiple basis function and full factorial designs.
* Change of version numbering to reflect the subversion development stage
* Get regional labels from AAL templates (needs user configuration in
  rfx_defaults.m, details are found in the manual, section 9.1)
* The generation of the rfx*.mat file can be suppressed (configure this in
  rfx_defaults.m, see section 9.4 in the manual). This can be advantageous
  for the rfx_timeseries.mat, because on fast computers saving and loading
  of .mat files can take longer than (re-)generating the structures for
  each SPM session.
* In case of multiple basis functions, the user should only select the
  first BF from the image description table. The toolbox will select the
  remaining BFs automatically if necessary.
* The accompanying paper is now in press at Neuroinformatics. The approved
  manuscript is available in the Credits section of the website

As always, if you come across some errors, please let me know, so that I
can improve the code.

Best wishes,
Jan



-- 
Jan Gläscher, Ph.D.         Div. Humanities & Social Sciences
+1 (626) 395-3898 (office)  Caltech, Broad Center, M/C 114-96
+1 (626) 395-2000 (fax)     1200 E. California Blvd
gla...@hs...    Pasadena, CA 91125