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Dear vladimir, I epoched my data and changed the label by copy and paste from excel to trial ( or I used from “conditions(D, 1:Ntrials, 'Condition 1')” command in “spm_eeg_convert_arbitrary_data.m” but when I press prep and load the header for tial definition, again I have same problem( number of trial for each condition label is 100 instead of 20!!!) . As I checked mnn example with 480 trials for standard and 120 trials for deviant , I found spm can divide trials to 480 and 120 by their value which is 1 for standard and 3 for deviant. So I started to change each trial value to 1 or 2 or 3 or 4 or 5 by copy and paste numbers from excel to trial column but unfortunately after update it does not change !!! On Sun, Oct 18, 2015 at 1:20 PM, Vladimir Litvak <[log in to unmask]> wrote: > Dear Pari, > > On Sun, Oct 18, 2015 at 5:21 AM, pari eghbali <[log in to unmask]> > wrote: > >> Dear vladimir, >> >> >> Thank you for response. I could not find solution and I prefer to ask my >> questions with more detail. I would be appreciated to have your answers >> about them. >> >> >> I have ECoG signals recorded from 64 channels with 5 different stimuli >> and 100 trials in each channel stored in .mat file. I need to change my >> data format according to 3 dimensions as data (channel, data point, number >> of trials) in order to import it in >> “spm_eeg_convert_arbitrary_data.m”. After format conversion, for trial >> definition in “prep”, I have some problems: >> >> 1) 1- For my data, number of trials in each condition is 20 but GUI >> brings me 100, how can I define trial value for spm? >> > > It looks like your trial type is not encoded in the file so all off your > triggers are shown as the same type. You could epoch your dataset with that > one trigger type and then if you know the correct order of conditions you > could re-label your trials. One way to do it is to use the reviewing tool, > just make a list of labels in Excel and copy and paste into the trial type > column there, press 'update' and 'save'. Another way is: > > D = spm_eeg_load > D = conditions(D, ':', lbl); > save(D); > > where lbl is an array of labels. > > >> 2) 2- What is “time shift in trial definition”? >> > > It is sometimes useful to shift time zero in peri-stimulus time with > respect to the trigger (e.g. if there is a projector delay). > >> 3) 3- Is it necessary to have trial definition file for DCM >> analysis? >> > > DCM expects epoched or averaged data so you need an epoched dataset as > input. > > Best, > > Vladimir > >> >> On Fri, Oct 16, 2015 at 5:13 PM, Vladimir Litvak < >> [log in to unmask]> wrote: >> >>> Dear Pari, >>> >>> You should know at which samples of your recording the stimuli occur. If >>> you know that, you can either segment your data around triggers in your own >>> code and make trials or convert your data as continuous and then epoch it >>> with spm_eeg_epochs and a trial definition file as described on p. 108 of >>> the manual. >>> >>> Best, >>> >>> Vladimir >>> >>> On Fri, Oct 16, 2015 at 9:59 AM, pari eghbali <[log in to unmask]> >>> wrote: >>> >>>> Hello, >>>> >>>> my raw data has two dimensions (row=data points of 5 different stimuli >>>> , column=64 channel). the format of the data is .mat. In >>>> spm_eeg_convert_arbitrary file, the data has three dimensions ( >>>> ftdata.trial(i)= squeeze (data(:,:,i)) !!! >>>> >>>> what is the third dimension of data? how can I define it? >>>> >>>> thank you for any response, >>>> best, >>>> pari >>>> >>>> On Thu, Oct 15, 2015 at 1:41 PM, Vladimir Litvak < >>>> [log in to unmask]> wrote: >>>> >>>>> Dear Pari, >>>>> >>>>> Trial definition can be done based on triggers or using the 'trl' >>>>> matrix built with your own code. See the manual for details. Yes, you >>>>> should have both conditions in the same dataset to model them together with >>>>> DCM. >>>>> >>>>> Best, >>>>> >>>>> Vladimir >>>>> >>>>> On Thu, Oct 15, 2015 at 7:16 AM, pari eghbali < >>>>> [log in to unmask]> wrote: >>>>> >>>>>> Dear Vladimir, >>>>>> I want to examine modulation of effective connectivity by DCM >>>>>> algorithm during 100 repetitions of same stimulation in ECoG signals. >>>>>> Actually , the condition (20 stimuli vs. 100 stimuli) effects would >>>>>> be modelled by connectivity changes in the B matrix. How can I prepare >>>>>> trial definition in spm? should I concatenate two conditions to each other >>>>>> ? >>>>>> I would be really appreciated if you help me on this matter. >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Oct 12, 2015 at 10:17 PM, Vladimir Litvak < >>>>>> [log in to unmask]> wrote: >>>>>> >>>>>>> The part about callback is not important. There is some mismatch in >>>>>>> dimensionality. You should try to figure out why by putting a breakpoint in >>>>>>> spm_dcm_csd_data. >>>>>>> >>>>>>> Vladimir >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 13 Oct 2015, at 05:24, pari eghbali <[log in to unmask]> >>>>>>> wrote: >>>>>>> >>>>>>> Dear Vladimir, >>>>>>> >>>>>>> I changed the type of channel according to your suggestion and >>>>>>> parameterized DCM model according to rat anaesthesia data example ( >>>>>>> neuronal model 'CMC' and spatial model 'LFP') but I got this error: >>>>>>> >>>>>>> Error using feval >>>>>>> Undefined function 'Slocation_Callback' for input arguments of type >>>>>>> 'struct'. >>>>>>> evaluating CSD for condition 1 >>>>>>> Error using ./ >>>>>>> Matrix dimensions must agree. >>>>>>> >>>>>>> Thank you, >>>>>>> Pari >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sun, Oct 11, 2015 at 8:22 AM, Vladimir Litvak < >>>>>>> [log in to unmask]> wrote: >>>>>>> >>>>>>>> You should set the channel types of channels 20 and 50 to 'LFP' and >>>>>>>> that of the rest of the channels to 'Other'. Then specify 'LFP' as the >>>>>>>> spatial model and the names of the channels as source names. See the rat >>>>>>>> anaesthesia data example in the manual. >>>>>>>> >>>>>>>> Best, >>>>>>>> >>>>>>>> Vladimir >>>>>>>> >>>>>>>> On Sun, Oct 11, 2015 at 9:00 PM, pari eghbali < >>>>>>>> [log in to unmask]> wrote: >>>>>>>> >>>>>>>>> Thank you for your help. >>>>>>>>> I have one more question! In 64 channels I want to find >>>>>>>>> connectivity between channel 20 and channel 50. How can I define those >>>>>>>>> areas in electromagnetic model of DCM? Should I define source location ( >>>>>>>>> dimension of 64 channels) in Prep? >>>>>>>>> Thank you again for your prompt reply, >>>>>>>>> Best, >>>>>>>>> Arezoo >>>>>>>>> >>>>>>>>> On Sun, Oct 11, 2015 at 6:58 AM, Vladimir Litvak < >>>>>>>>> [log in to unmask]> wrote: >>>>>>>>> >>>>>>>>>> Dear Pari, >>>>>>>>>> >>>>>>>>>> The channel data should be in the dat file. I think the example >>>>>>>>>> script has a data variable which you can replace with your own data. >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> >>>>>>>>>> Vladimir >>>>>>>>>> >>>>>>>>>> On Sun, Oct 11, 2015 at 7:37 PM, pari eghbali < >>>>>>>>>> [log in to unmask]> wrote: >>>>>>>>>> >>>>>>>>>>> Hello >>>>>>>>>>> I am currently working with ECoG channel signals to investigate >>>>>>>>>>> brain effective connectivity(DCM). I used a sample script of LFP to convert >>>>>>>>>>> my data format to spm format. It gave me two format files:.dat and .mat. It >>>>>>>>>>> seems both of them have header information since there was not any function >>>>>>>>>>> in sample script to import my data. I am wondering to know where should I >>>>>>>>>>> import the channel signals? >>>>>>>>>>> >>>>>>>>>>> Thank you, >>>>>>>>>>> Pari >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >