Hi,
I am surprised that you would have trouble with an image of this
size, as it should less than 256MB in size when unpacked in
memory, so even multiple internal copies should be OK.
What happens if you try to run it on an ROI?
Say do the following:
fslroi xyz xyz_roi 0 512 0 512 30 60
then run FAST on xyz_roi.
I'm assuming that xyz here is brain extracted (as all inputs
to FAST need to be).
Let us know how you get on with this.
All the best,
Mark
On 23 Nov 2009, at 23:45, rajani sebastian wrote:
> Hi Mark and Matt
> Here is the o/p of fslhd
>
> <nifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = 'xyz.nii.gz'
> image_filename = 'xyz.nii.gz'
> image_offset = '352'
> ndim = '3'
> nx = '512'
> ny = '512'
> nz = '120'
> dx = '0.4688'
> dy = '0.4688'
> dz = '1.3'
> datatype = '4'
> datatype_name = 'INT16'
> nvox = '31457280'
> nbyper = '2'
> byteorder = 'LSB_FIRST'
> xyz_units = '2'
> xyz_units_name = 'mm'
> time_units = '8'
> time_units_name = 's'
> descrip = 'FreeSurfer Jun 11 2009'
> qform_code = '1'
> qform_code_name = 'Scanner Anat'
> qto_xyz_matrix = '-0.4688 0 0 122.107 0 -0.4688 0 157.034 0 0 1.3
> -56.8624 0 0 0 1'
> qto_ijk_matrix = '-2.13311 0 0 260.467 0 -2.13311 0 334.97 0 0
> 0.769231 43.7403 0 0 0 1'
> quatern_b = '0'
> quatern_c = '0'
> quatern_d = '1'
> qoffset_x = '122.107'
> qoffset_y = '157.034'
> qoffset_z = '-56.8624'
> qfac = '1'
> qform_i_orientation = 'Right-to-Left'
> qform_j_orientation = 'Anterior-to-Posterior'
> qform_k_orientation = 'Inferior-to-Superior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '-0.4688 0 -0 122.107 0 -0.4688 -0 157.034 0 0
> 1.3 -56.8624 0 0 0 1'
> sto_ijk matrix = '-2.13311 -0 -0 260.467 -0 -2.13311 -0 334.97 0 0
> 0.769231 43.7403 0 0 0 1'
> sform_i_orientation = 'Right-to-Left'
> sform_j_orientation = 'Anterior-to-Posterior'
> sform_k_orientation = 'Inferior-to-Superior'
> num_ext = '0'
>
> Thanks,
> Rajani
>
>
> On Mon, Nov 23, 2009 at 5:40 PM, rajani sebastian <[log in to unmask]
> > wrote:
> 512X512X120
> rajani
>
>
> On Mon, Nov 23, 2009 at 5:35 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> It isn't the sequence parameters that I need, it is the size of
> the image. How many voxel by how many voxels by how many
> voxels (or slices) is it? e.g. 256x256x240
>
> All the best,
> Mark
>
>
>
> On 23 Nov 2009, at 23:31, rajani sebastian wrote:
>
> It's a T1 weighted image ( TR=9.44, TE=3.88, TI=450.00, flip
> angle=20.00). Also, i choose 4 as the number of classes to be
> segmented because there is a lesion.
> Thanks,
> Rajani
>
>
> On Mon, Nov 23, 2009 at 5:24 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> What are the dimensions of the image you are trying to segm
>
> All the best,
> Mark
> sl
>
>
> On 23 Nov 2009, at 23:18, rajani sebastian wrote:
>
> Hi everybodysl
> I am trying to run FAST on Ubuntu version 8.04 (32 bit system with
> 2GB RAM) . Every time i run FAST, i keep getting the message
> 'killed' or aborted. Does anybody know the reason as to why this is
> happening? I have 35 GB free disk space on my laptop.
> Thanks,
> Rajani
>
>
>
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