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Hi Mark I ran the analysis on a different machine and it worked. I guess there is something wrong with my laptop. Thanks, Rajani On Tue, Nov 24, 2009 at 2:55 AM, Mark Jenkinson <[log in to unmask]> wrote: > 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 >> >> >> >>