Thanks Vladimir!
Unfortunately, the recording is 20 minutes long but the downsampling
takes 1h45. I cannot epoch as we are doing TF before cutting the data.
But yes I want to avoid aliasing so I'll guess it will be running during
lunch break.
Thank you for your fast and helpful answers.
Best
Jessica
On 5/28/2015 2:30 PM, Vladimir Litvak wrote:
> 10Gb and 214 channels at 10kHz sounds like a lot to me so I'd say 20
> min is not bad. You can just run your pipeline overnight and work with
> downsampled files in the morning. Also note that there is a way to
> epoch at conversion so if you don't need all your data you could start
> with a smaller dataset from the beginning.
>
> I usually specify something in a batch (like select a couple of files)
> and then save it as an m-file to see an example of what is a cell and
> what is a string etc.
>
> Vladimir
>
> On Thu, May 28, 2015 at 10:22 PM, Jessica Schrouff
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Thank you for your help Vladimir and Christophe.
>
> I used the spm_eeg_convert routine with the 'header' option to
> load the header then made 3 conversions (one for EEG channels, one
> for the diod and one for the mike). I was able to clear the input
> for the output filename in the batch. This is ECoG data, so the
> channel list is modified for each patient. Also, I am building a
> pipeline for my lab so it's easier if they can change parameters
> in the batches instead of in a script or history.
>
> It runs smoothly (although understanding which inputs should be
> cells of cells and which should only be cells was not
> straightforward). The downsampling is super slow though (10,000Hz
> to 500Hz, 214 channels, 20 minutes = 10Gb in .dat). Is there any
> way of improving this? How would using the 'decimate' function
> affect the signal compare to SPM's downsampling?
>
> Thank you,
> Best,
> Jessica
>
>
> On 5/28/2015 2:16 AM, Vladimir Litvak wrote:
>> Dear Jessica,
>>
>> I think you are over-complicating things. You could use the 'Load
>> header' option in 'Prepare' GUI to read just the header
>> information for your files and save a channel list that you could
>> then use to convert just the channels you need (see p. 360 in the
>> manual http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf). Not sure
>> why that list would be different every time if you record on the
>> same system. I would expect that you'd only need to create it once.
>>
>> If you specify a full path for the output file, SPM will use it.
>> I'm not sure about <-X but you can just save your batch as an .m
>> file and modify that field in your own code. You could also use a
>> low-level script which is more convenient for preprocessing. This
>> can be generated by saving the history from the reviewing tool.
>>
>> Best,
>>
>> Vladimir
>>
>> On Thu, May 28, 2015 at 12:55 AM, Jessica Schrouff
>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Dear All,
>>
>> I am playing with the edf format from our new acquisition
>> system. Unfortunately, we will have to sample the data as
>> high as 10kHz in some cases. Up to now, the data conversion
>> is fine. However, in the data file, there are extra channels
>> that need to be set aside before the data can be downsampled
>> (e.g. microphone, photodiod).
>>
>> As I don't know the names or indexes of those channels, I am
>> converting all the channels, then cloning the object for EEG
>> channels (based on the channel labels from the output file)
>> and trying to fill this new DEEG object with only EEG
>> channels. I have an out of memory error at line 24 of subsref
>>
>> if this.montage.Mind==0
>> varargout = {double(subsref(this.data, subs))};
>> else
>>
>> It appears that because I don't have a montage, accessing and
>> writing the data is not performed block by block (which I
>> would expect to be the case, as files are pretty big).
>>
>> Apart from going myself block by block, is there any other
>> way of doing this? E.g. How could I access the channel names
>> before file conversion to then get the indexes of the EEG
>> channels and not have to clone the converted data? (Although
>> this error should probably be corrected).
>>
>> Also, when converting, I would like to change the directory.
>> I am doing a 'move' after the conversion but it is slow
>> because my dataset is big. If I change the 'output' name,
>> will it consider the path I put it in? How to have an <-X in
>> the batch for later scripting in that case (as this is empty
>> by default)?
>>
>> Thank you,
>> Best regards,
>> Jessica
>>
>>
>
>
