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Dear Muhammad, You can put it before this part. Just note that usually the file you would use to define spatial confounds is not the same file that you correct. The former would be an averaged eyeblink file and the latter your actual dataset of interest. The head model should be in this second dataset. Best, Vladimir On Wed, Dec 1, 2010 at 4:21 AM, MP <[log in to unmask]> wrote: > Hi Vladimir, > Thanks so much for your detailed response. I am now able to generate the > script for the 3D head model. My follow up question to you is, where exactly > should I insert it in the eye blink correction routine? > Currently the eye blink removal section of the script looks like the > following: > % Eye Blink Correction > S = []; > S.D = fullname6; > S.method = 'SVD'; > S.timewin = [-0.498 > 2]; > S.ncomp = 2; > D = spm_eeg_spatial_confounds(S); > save(D); > S = []; > S.D = fullname6; > S.correction = 'Berg'; > D = spm_eeg_correct_sensor_data(S); > save (D); > > Where should I insert the 3D Head modelling script? > Thanks > - Muhammad > > > On Tue, Nov 30, 2010 at 5:54 AM, Vladimir Litvak <[log in to unmask]> > wrote: >> >> Dear Muhammad, >> >> Press the 'Batch' button, go to SPM->M/EEG->M/EEG Source >> reconstruction->M/EEG head model specification >> >> Then you need to specify the configuration. The parameters are the >> same as in 3D source reconstruction window. Once you specify a >> complete configuration that can run (the triangle at the top turns >> grin) you can go to File->Save batch as script and save your >> configuration as an .m file. You can then modify the code if necessary >> and add it to your script. >> >> Best, >> >> Vladimir >> >> >> On Mon, Nov 29, 2010 at 6:47 PM, MP <[log in to unmask]> wrote: >> > Hi Vladimir, >> > Many thanks for your help. Could you please guide how can I pre-compute >> > the >> > head model for my dataset using SPM batch tool? I want to do this so >> > that I >> > can include the eye-blink correction using Berg algorithm in a script. >> > Thanks, >> > - Muhammad >> > >> > On Sat, Nov 13, 2010 at 7:48 AM, Vladimir Litvak >> > <[log in to unmask]> >> > wrote: >> >> >> >> Dear Muhammad, >> >> >> >> On Sat, Nov 13, 2010 at 3:46 AM, MP <[log in to unmask]> wrote: >> >> > Hello all, >> >> > I am doing eye-blink correction through Berg algorithm. I have a >> >> > couple >> >> > of >> >> > questions in this regard: >> >> > 1. Once the data has been run through the Berg algorithm, is the >> >> > output >> >> > data >> >> > corrected for the eye-blinks, or is there anything that needs to be >> >> > done? >> >> >> >> If you've done everything correctly the data is corrected. If it's >> >> continuous data you could average it around eyeblinks again to make >> >> sure they are gone. >> >> >> >> > 2. While running the Berg algorithm, a prompt comes up asking "Which >> >> > Head >> >> > Model?" for the MEEG/MRI coregistration. Which script is this prompt >> >> > coming >> >> > from? >> >> >> >> Head model is necessary for the 'Berg' option (but not for SSP) >> >> because Berg algorithm uses lead fields of cortical sources. If you >> >> want to batch it you can pre-compute the head model for your dataset >> >> using the batch tool before correcting it. >> >> >> >> > 3. How does the Berg algorithm affect the spectral information in the >> >> > data? >> >> > Is it OK to do TF-decomposition and then stat analysis on this data? >> >> >> >> In principle it is OK, but it depends on the question and the data so >> >> you should still be careful. The principles of this correction are >> >> very similar to those of ICA and ICA is very frequently used for >> >> removing eye blinks prior to all kinds of analyses so you can use the >> >> ICA literature as a precedent. In any case perhaps you should repeat >> >> your analysis with and without eye blink correction and convince >> >> yourself that the differences you see can be attributed to eye blink >> >> removal. >> >> >> >> Best, >> >> >> >> Vladimir >> >> >> >> >> >> > Thanks >> >> > - Muhammad >> >> > >> >> > >> >> > On Fri, Nov 12, 2010 at 12:08 PM, Vladimir Litvak >> >> > <[log in to unmask]> wrote: >> >> >> >> >> >> No, this function is used for detecting eyeblinks in continuous data >> >> >> as part of eyeblink correction procedure. See >> >> >> >> >> >> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=SPM;adf47ab2.1007 >> >> >> >> >> >> Vladimir >> >> >> >> >> >> On Fri, Nov 12, 2010 at 5:02 PM, MP <[log in to unmask]> wrote: >> >> >> > Hi all, >> >> >> > It may be a very naive question, but does >> >> >> > 'spm_eeg_detect_eyeblinks' remove >> >> >> > the eye-blinks after detecting them? >> >> >> > Thanks >> >> >> > - Muhammad >> >> > >> >> > >> > >> > > >