Dear Soroor,
You can keep the normalised structural (w*) and smoothed normalised
functional images (sw*) only.
How did you define the centre of the two spheres for WM and CSF? Did you
take the ones used in chapter 38 of the SPM manual? You might want to
check on your data where they correspond to and adjust accordingly if,
say, the field of view of your images is different. An alternative would
be to use the WM and CSF masks obtained from segmentation (i.e. don't
delete the c* and y_* files) and compute the first component of a PCA
within them.
Best regards,
Guillaume.
On 06/11/2019 11:24, Soroor wrote:
> Dear all
>
> I preprocess the ABIDE dataset with spm12, this dataset consists of rest fMRI with one session for each subject and most of the data have less than 200 scans.
> The procedure that I use for preprocessing data is:
> 1.segmentation of the anatomical image
> 2.skull-stripped
> 3.normalise anatomical image
> 4.discarding first 5 scans of functional image
> 5.slice timing
> 6.realignment to first functional scan
> 7.coregisteration:
> -Reference image: skull stripped anatomical image
> -Source image: mean functional image
> -Other images: realignment functional image
> 8.normalise functional image to MNI space
> 9.smoothing with using 6mm FWHM
>
> First: I want to know after these steps how can I figure out which data must be deleted and after that, I will continue to process the data, for example, extract WM time series?
>
> Second: when I extract WM (7mm ROI) or CSF (5mm ROI) time series for some subjects I receive a warning (empty region), you think the reason for this depends on data or have another reason? (I didn't remove any data after preprocessing)
>
> Best regards,
> soroor
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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