Hi, FEAT doesn't use the TR in the header, but uses it as set in the
GUI (because 4D image headers rarely have this value set correctly).
So you should find that by the time it has finished the
preprocessing, FEAT has set the value in the header to the correct
value (as set in the GUI) in seconds.
Cheers, Steve.
On 20 Feb 2007, at 19:52, Syam Gadde wrote:
> Hello,
>
> We are running version 3.3.7 of FEAT on NIFTI data with a 1500 ms
> TR. However, the first time FEAT writes a 4-D file (with mcflirt)
> it seems to change the temporal units to seconds without scaling the
> actual time spacing. I ran mcflirt manually using version 3.3.9 and
> the same thing happens. I saw a reference to a similar problem with
> another tool (ip?) in the archives, with the statement that it would
> be fixed in the next release, but I don't know if this is the same
> problem.
>
> Any ideas? avwhd output and the mcflirt command line are below.
>
> Many thanks,
>
> -syam
>
>
> [gadde@cushing run1.feat]$ avwhd -x /data/psych/mask02/data/
> 20030328_41839/run1
> <nifti_image
> nifti_type = 'NIFTI-1'
> header_filename = '/data/psych/mask02/data/20030328_41839/run1.hdr'
> image_filename = '/data/psych/mask02/data/20030328_41839/run1.img'
> image_offset = '0'
> ndim = '4'
> nx = '64'
> ny = '64'
> nz = '34'
> nt = '148'
> dx = '3.75'
> dy = '3.75'
> dz = '3.8'
> dt = '1500'
> datatype = '4'
> datatype_name = 'INT16'
> nvox = '20611072'
> nbyper = '2'
> byteorder = 'LSB_FIRST'
> xyz_units = '2'
> xyz_units_name = 'mm'
> time_units = '16'
> time_units_name = 'ms'
> ... etc. ...
>
> [gadde@cushing run1.feat]$ /home/gadde/fsl-3.3.9/bin/mcflirt -in /
> data/psych/mask02/data/20030328_41839/run1 -out
> prefiltered_func_data_mcf -mats -plots -refvol 74 -rmsrel -rmsabs
>
> [gadde@cushing run1.feat]$ avwhd -x prefiltered_func_data_mcf.nii.gz
> <nifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = 'prefiltered_func_data_mcf.nii.gz'
> image_filename = 'prefiltered_func_data_mcf.nii.gz'
> image_offset = '352'
> ndim = '4'
> nx = '64'
> ny = '64'
> nz = '34'
> nt = '148'
> dx = '3.75'
> dy = '3.75'
> dz = '3.8'
> dt = '1500'
> datatype = '4'
> datatype_name = 'INT16'
> nvox = '20611072'
> nbyper = '2'
> byteorder = 'LSB_FIRST'
> scl_slope = '1'
> scl_inter = '0'
> xyz_units = '2'
> xyz_units_name = 'mm'
> time_units = '8'
> time_units_name = 's'
> ,,, etc. ...
------------------------------------------------------------------------
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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