Dear Muhammad and other users interested in the topography-based
artefact correction,
Laurence Hunt prepared a tutorial for artefact detection and rejection
in SPM and has kindly made it available on
http://www.fmrib.ox.ac.uk/~woolrich/artifact_session.zip . The file
contains example data, code and a tutorial for using them. Enjoy and
thanks again to Laurence.
Best,
Vladimir
On Wed, Dec 1, 2010 at 10:42 AM, Vladimir Litvak
<[log in to unmask]> wrote:
> 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
>>> >> >
>>> >> >
>>> >
>>> >
>>
>>
>
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