NITRC Robust Biological Parametric Mapping Forum: help

RE: BPM for SPM12 ?

Victor Altmayer — Fri, 06 Jan 2023 10:17:36 GMT

Hello,
Did you find any updtodate method to adress this problem please ?

Best,
Victor

RE: BPM for SPM12 ?

giacomo — Wed, 24 Nov 2021 13:59:38 GMT

Dear Isabelle,
I am facing the same problem as yours.
Did you find other tools to perfom multimodal voxemwise analysis?
Thank you very much in advance for your help
Giacomo

Robust BPM Matlab/2017

giacomo — Mon, 22 Nov 2021 10:02:27 GMT

Hello,
I am using rBPM with Matlab/R2017b and when I try to visualize the results with Contrast Manager, I obtain the following error: "Error using fileparts. Too many outputs arguments".
I read that I would need to download and install an older version of Matlab.
Is it possible to update rBPM in order to be fully supported by newer versions of Matlab?
Any other suggestions on how I can use rBPM on Matlab 2017?
Thank you very much in advance
Giacomo

Problems with model II regression

dalbrecht — Thu, 28 Mar 2019 19:34:03 GMT

Hello,

I'm attempting to perform regressions between PET and MRI (ASL, specifically) data using the BPM toolbox. When reading up on the model II regression, I thought that this would be the most appropriate option because there are observational errors associated with both modalities. However, when I change which modality is the dependent variable (e.g. PET as dependent, MRI as independent, and vice versa), I get wildly different results. I'm also using a single non-imaging covariate in the model, but entering the same way for both analyses.
The residual images I get from both analyses are also very different, although I expected them to be the same based on the publication in Neuroimage by Yang et al. I'm assuming this is not an expected outcome, do you have any ideas what might be happening? I'm happy to provide any files or outputs that might be helpful.

Thanks very much,

Dan

Contrasts on BPM in a regression?

Frances Q — Thu, 10 May 2018 14:37:58 GMT

Hi all,

I couldn't find in the guides about how contrasts are specified on BPM. I am using the Regression option with fMRI as the dependent modality, PET as the imaging covariate, and a vector of binary (0 or 1) non-imaging covariates.

I'd like to see if the non-imaging covariate has a moderating effect on the imaging modality. Would the correct contrast therefore be [0 -1 1]?

It would be great to have a section on how contrasts are defined on BPM.

Thanks!

Best wishes,

Frances

BPM for SPM12 ?

Isabelle Faillenot — Tue, 05 Sep 2017 12:55:53 GMT

Hi,
I would like to know if there is a SPM12 compatible version of BPMe or if you know another tools to use images as covariates ?
thank you
Isabelle

BnPM

Hengshuang LIU — Wed, 02 Mar 2016 12:28:28 GMT

Dear developers,
For the BnPM analysis,
I don't quite understand:

1. What is the submitted pbs file like? Is the one present in BPM manual Page15 an example, although that one looks more like ModelII instead of BnPM? Anyway, is it in ".m" format?
What does the following mean? How to get the "modII_slice1.m" and "Slice1job58669"? Is that the so-called "qsub based cluster"?
[i]matlab -nodesktop < /gpfs21/scratch/yangx6/Sim_Img/resultModelII1/Slice1/modII_slice1.m >matlab.output[/i]
[i]touch /gpfs21/scratch/yangx6/Sim_Img/resultModelII1/Slice1job58669.done[/i]
[i]
[/i]
what does the following mean?
[i]#PBS -l mem=2000mb
#PBS -o xue-cluster.txt
#PBS -j oe[/i]

2. If I have 1 imaging covariate "GM" and 2 non-imaging covariates "RT" and "ACC", and intend to set ACC as an regressor, then shall I choose F or T test (My guess is F) and set the contrast as "0 0 0 1"?

3. After entering new contrast, how to choose "SPM" directory and "BnPM" directory which pops out automatically? I thought to create one empty folder for each of them, am I right?

Thanks for any input,
Shuang

[i]
[/i]

too many agruments error with rBPM with SPM5

Gerard Bischof — Thu, 15 Oct 2015 11:55:06 GMT

Hello everyone and Hello Paul,

Did this ever got resolved for you? As I am getting the same error message (see below), when attempting to load the bpm.mat file into the contrast manager -- I tried it with and without loading the brainmask (in the latter case I used the one provided with a threshold of .1). Any help or advice here?

Thanks so much,

Gérard N Bischof, PhD

Error using fileparts
Too many output arguments.

Error in wfu_bpm_path_in_struct (line 22)
[pathstr, name, ext, version] = fileparts(BPM.mask);
Error in wfu_bpm_con_man (line 15)
BPM = wfu_bpm_path_in_struct(BPM_fname, BPM);
Error in wfu_bpm>button2Callback (line 193)
wfu_bpm_con_man;
Error while evaluating uicontrol Callback

RE: FWHM of the robust BPM analysis

Matthieu Vanhoutte — Tue, 28 Apr 2015 14:33:06 GMT

Hi Xue,

Many thanks for helping me and for this very interesting toolbox. Now Ihave
a new question : In the definition of the binary brain mask in the
"wfu_bpm_mask.m" file, could you explain me why l. 43 you compute
intersection mask with this formula :
*mask = (inter_mask > size(P1,1)-3);*
Thank you !

Matthieu

RE: FWHM of the robust BPM analysis

Xue Yang — Sat, 18 Apr 2015 11:34:43 GMT

Hi Matthieu,

Thank you for using robust BPM. The estimated FWHM is in the BPM.mat file. If you load BPM.mat in MATLAB, you could find it in BPM.fwhm. This parameter is estimated using the same method as SPM does.

Best,
Xue