NITRC GIMME (Group Iterative Multiple Model Estimation) Forum: help

high beta values

gonnis — Thu, 21 Jan 2021 0:09:50 GMT

Hi gimme community,

I am running a resting-state analysis on timeseries extracted from 7 ROIS from the Hammers atlas (IC_ant, IC_post, AC, PC, IFG, Thalamus, Accumbens) for 55 subjects.
Data Pipeline:
1) minimal preprocessing with fMRIPrep
2) smoothing (FWHM=4mm) and denoising using CONN (some confounds removal)
3) extract timeseries from ROIs with nilearn
4) run gimme (method='Fast_greedy') on denoised timeseries

(Step2 could be done in python too, but this is the state of the matter).

After running gimme, looking at the IndivPathEstimates.csv file,
I get some high beta values (absolute value larger than 1.2): examples
# A tibble: 11 x 1
beta
1 -2.00
2 6.90
3 -5.17
4 -1.31
5 1.31
6 -1.23
7 1.30
8 -3.55
9 17.4
10 5.52
11 -60.4

from as low as -60.4 up to 17.4!

Does anybody know where could these high values come from / what could be the reason they are so high?

Thank you in advance for your comments / help

gio

RE: GIMME for event related designs?

Chih-Ting Chang — Wed, 07 Mar 2018 22:41:11 GMT

Hi, Dr. Gates,

Thank you for making GIMME available!

I have the same question here. I am facing a difficulty with feeding the onsets of stimuli into the R environment. Is euSEM with GIMME under R available now?

Really appreciate!

Best,
Chih-Ting

How could I download the GIMME toolbox for MATLAB?

Josie Huang — Fri, 26 Jan 2018 16:57:34 GMT

Hello,

I could not find any file in the Downloads. How could I download the GIMME toolbox for MATLAB?
Thank you!

Josie

RE: GIMME for event related designs?

Oliver Contier — Tue, 25 Jul 2017 16:22:01 GMT

Hello,

I have the same request. We are currently contemplating using GIMME (euSEM) to explore the effect of the task on connectivity in our event-related fmri dataset. It would be much appreciated to know if this would be implemented in the R toolbox within the foreseeable future.

We are also confronted with the question of how to deal with analysing multiple runs, i.e. if it would be appropriate to simply concatinate the ROI time series. So far we haven't found any standard recommendations in the literature and would be very interested if you have any ideas or suggestions.

Thanks!
Oliver

number of nodes

Toni Abe — Mon, 22 May 2017 21:17:08 GMT

Hello,

Thank you very much for this tool.

Is there any way to use GIMME to obtain functional connectivity between more than 25 nodes? (e.g. 90 nodes?)

Also, what would be the shortcomings of using a larger number of nodes?

Best,
Toni

RE: GIMME for event related designs?

Kathleen Gates — Wed, 10 May 2017 22:17:17 GMT

Hello,

Sorry for the delayed response. We have transitioned into R and no longer maintain the Matlab toolbox.

euSEM is possible with GIMME and has been implemented. We are currently integrating this into the R program and should be done by the end of the summer.

Thanks for your patience. Please email if you'd like help implementing euSEM with gimme in the meantime.

Katie

RE: Configuration

Kathleen Gates — Wed, 10 May 2017 22:15:50 GMT

Hello,

The Matlab version is not maintained. Lisrel requires windows, so we have moved to R so that users with any platform can utilize GIMME.

Sorry for any inconvenience. Please message us if you have any questions.

RE: Configuration

Rajpreet Chahal — Wed, 10 May 2017 0:30:16 GMT

Hi Peter,

I'm getting the same error, though I am using the latest versions of Matlab and Lisrel.
Were you able to resolve this?

Thank you,
Rajpreet Chahal

RE: Group Level SEM

Kathleen Gates — Fri, 17 Mar 2017 16:58:14 GMT

Hi Brittany,

The problem seems to be the location of the Lisrel program. Is it on a server?

We experience a number of problems with Lisrel since they are no longer supporting licenses on servers. Additionally, Lisrel is no longer supported for Linux & Mac.

For this reason we highly recommend using our R package [i]gimme[/i]. It also has a GUI and is quite easy to use (even if you've never used R). Directions for using the GUI can be found here: http://gimme.web.unc.edu/63-2/

Best,
Katie

GIMME for event related designs?

Michael Tennekoon — Wed, 15 Mar 2017 12:49:50 GMT

Just a quick question. In the 2012 GIMME paper it says that using euSEM it would be possible to use GIMME with event related data. However the documentation for GIMME now says it can be used with block design data. So I just wanted to clarify if it was possible to use GIMME for event related data?

Thanks,

Michael