Dear Jane,
there are several ways to do this (it also depends on which version of
SPM you are using):
* create a new 4D file without the dummy scans and proceed as normal:
SPM > Util > 3D to 4D File Conversion
See
http://en.wikibooks.org/wiki/SPM/Working_with_4D_data#Creating_4D_NIfTI_files_in_SPM
* use the dedicated batch module:
SPM > Util > Expand image frames
* use spm_select('ExtFPList',...) where you can specify your frames of
interest:
spm_select('ExtFPList',SCAN_dir,'^SCAN\.nii$',6:180)
* use spm_select('expand',fullfile(SCAN_dir,'SCAN.nii')) in SPM12 to get
the entire list of 3D scans and then select a subset
tmp = spm_select('expand',fullfile(SCAN_dir,'SCAN.nii'));
tmp = cellstr(tmp(6:180,:));
Best wishes,
Guillaume.
On 06/10/14 09:03, Jane Garrison wrote:
> I have a relatively large number of 4D nifti files that I need to
> manipulate. The first 5 volumes of each file are dummy scans which need
> to be discarded for the analysis.
>
> I am reading the volume information using spm_vol() and have determined
> the number of volumes in each scan. I now need to pass a subset of the
> volumes to various SPM functions for analysis. I am struggling to find
> the correct syntax and would appreciate some assistance.
>
> Suppose the scan in question is called SCAN.nii, it resides in SCAN_dir,
> and the number of volumes has been determined to be 180. I am trying to
> run code similar to the following example (which is failing):
>
> tmp = strcat(spm_select('FPList', SCAN_dir,SCAN.nii),',6:180));
> matlabbatch{1}.spm.spatial.realignunwarp.data(1).scans = cellstr(tmp);
>
> Please could someone offer some advice with the correct syntax here.
>
> Thanks so much
> Jane.
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
