emma@clinicalneuro-desktop:~$ echo $FSLMACHTYPE
gnu_32-gcc4.2
emma@clinicalneuro-desktop:~$ ls -al /usr/local/fsl/bin
total 185120
drwxr-xr-x 3 7959 999 4096 2008-03-25 10:58 .
drwxr-xr-x 13 7959 999 4096 2008-03-31 16:08 ..
-rwxr-xr-x 1 7959 999 12941 2007-11-14 14:44 add4bytes
-rwxr-xr-x 1 7959 999 1890786 2007-11-14 14:43 applywarp
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 ApplyXFM -> Runtcl
-rwxr-xr-x 1 7959 999 1908897 2007-11-14 14:42 applyxfm4D
-rwxr-xr-x 1 7959 999 1143692 2007-11-14 16:06 atlasquery
-rwxr-xr-x 1 7959 999 1765673 2007-11-14 14:42 avscale
-rwxr-xr-x 1 7959 999 7128 2007-11-14 14:23 avw2fsl
-rwxr-xr-x 1 7959 999 1842738 2007-11-14 14:47 b0calc
-rwxr-xr-x 1 7959 999 3554 2007-11-14 14:23 bedpost
-rwxr-xr-x 1 7959 999 7866 2007-11-14 14:23 bedpostx
-rwxr-xr-x 1 7959 999 1609 2007-08-01 18:10 bedpostx_datacheck
-rwxr-xr-x 1 7959 999 1907 2007-07-30 12:06 bedpostx_postproc.sh
-rwxr-xr-x 1 7959 999 469 2007-08-01 18:24 bedpostx_preproc.sh
-rwxr-xr-x 1 7959 999 592 2007-10-03 13:38 bedpostx_single_slice.sh
-rwxr-xr-x 1 7959 999 13346 2007-11-14 14:23 bet
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Bet -> Runtcl
-rwxr-xr-x 1 7959 999 2612518 2008-01-18 13:00 bet2
-rwxr-xr-x 1 7959 999 2521689 2007-11-14 14:36 betsurf
-rwxr-xr-x 1 7959 999 1820942 2007-11-14 14:38 ccops
-rwxr-xr-x 1 7959 999 2048393 2007-11-14 14:36 cluster
-rwxr-xr-x 1 7959 999 5859 2007-11-14 14:23 cluster2html
-rwxr-xr-x 1 7959 999 4484 2007-11-14 14:23 concat_bvars
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 ConcatXFM -> Runtcl
-rwxr-xr-x 1 7959 999 1757201 2007-11-14 14:37 connectedcomp
-rwxr-xr-x 1 7959 999 1938351 2007-11-14 14:41 contrast_mgr
-rwxr-xr-x 1 7959 999 1877077 2007-11-14 14:43 convertwarp
-rwxr-xr-x 1 7959 999 1770080 2007-11-14 14:42 convert_xfm
-rwxr-xr-x 1 7959 999 581 2007-07-31 15:04 correctheader
-rwxr-xr-x 1 7959 999 13504 2007-11-14 14:45 create_lut
-rwxr-xr-x 1 7959 999 1804705 2007-11-14 14:45 cylsamp
-rwxr-xr-x 1 7959 999 922 2007-07-19 10:08 design_ttest2
-rwxr-xr-x 1 7959 999 904417 2007-11-14 14:39 diff_pvm
-rwxr-xr-x 1 7959 999 1811292 2007-11-14 14:46 distancemap
-rwxr-xr-x 1 7959 999 1529 2007-07-26 14:00 dof2warp
drwxr-xr-x 2 7959 999 4096 2007-11-14 14:31 DR
-rwxr-xr-x 1 7959 999 2588042 2007-11-14 14:33 drawmesh
-rwxr-xr-x 1 7959 999 1824341 2007-11-14 14:38 dtifit
-rwxr-xr-x 1 7959 999 4893 2007-11-14 14:23 easythresh
-rwxr-xr-x 1 7959 999 4075 2007-11-14 14:23 eddy_correct
-rwxr-xr-x 1 7959 999 1047 2003-09-16 17:52 eqn2gif
-rwxr-xr-x 1 7959 999 4673 2007-11-14 14:23 estnoise
-rwxr-xr-x 1 7959 999 5047 2007-11-14 14:24 extractfidparams
-rwxr-xr-x 1 7959 999 667 2007-07-27 10:59 extracttxt
-rwxr-xr-x 1 7959 999 1262470 2007-11-14 14:43 fabber
-rwxr-xr-x 1 7959 999 1613 2007-07-31 16:00 fast
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Fast -> Runtcl
-rwxr-xr-x 1 7959 999 1706 2007-07-25 11:32 fast1
-rwxr-xr-x 1 7959 999 1988279 2008-03-20 14:26 fast4
-rwxr-xr-x 1 7959 999 1152663 2008-03-20 14:12 fast_exe
-rwxr-xr-x 1 7959 999 1809622 2007-11-14 14:45 fdr
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Fdt -> Runtcl
-rwxr-xr-x 1 7959 999 30004 2007-11-14 14:23 feat
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Feat -> Runtcl
-rwxr-xr-x 1 7959 999 1756798 2007-11-14 14:40 feat_model
-rwxr-xr-x 1 7959 999 16030 2007-11-14 14:23 featquery
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Featquery -> Runtcl
-rwxr-xr-x 1 7959 999 7548 2007-11-14 14:23 featregapply
-rwxr-xr-x 1 7959 999 2513483 2007-11-14 14:41 filmbabe
-rwxr-xr-x 1 7959 999 5512 2007-11-14 14:23 filmbabescript
-rwxr-xr-x 1 7959 999 1950549 2007-11-14 14:41 film_gls
-rwxr-xr-x 1 7959 999 1756746 2007-11-14 14:38 find_the_biggest
-rwxr-xr-x 1 7959 999 3712163 2007-11-14 14:47 first
-rwxr-xr-x 1 7959 999 5005 2007-11-14 14:23 first_flirt
-rwxr-xr-x 1 7959 999 5146 2007-11-14 14:23 first_roi_slicesdir
-rwxr-xr-x 1 7959 999 3712822 2007-11-14 14:47 first_utils
-rwxr-xr-x 1 7959 999 2032766 2007-11-14 14:41 flame
-rwxr-xr-x 1 7959 999 2078529 2008-03-20 14:19 flirt
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Flirt -> Runtcl
-rwxr-xr-x 1 7959 999 4752 2007-11-14 14:24 flirt_average
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 fsl -> Runtcl
-rwxr-xr-x 1 7959 999 1798784 2007-11-14 14:34 fsl2ascii
-rwxr-xr-x 1 7959 999 5397 2007-11-14 14:23 fslanimate
-rwxr-xr-x 1 7959 999 1251523 2007-11-14 14:45 fsl_boxplot
-rwxr-xr-x 1 7959 999 1806834 2007-11-14 14:34 fslcc
-rwxr-xr-x 1 7959 999 1843501 2007-11-14 14:36 fslcheck
-rwxr-xr-x 1 7959 999 4909 2007-11-14 14:23 fslchfiletype
-rwxr-xr-x 1 7959 999 4496 2008-03-25 10:40 fslchpixdim
-rwxr-xr-x 1 7959 999 1773432 2007-11-14 14:36 fslcomplex
-rwxr-xr-x 1 7959 999 261407 2007-11-14 14:34 fslcpgeom
-rwxr-xr-x 1 7959 999 266907 2007-11-14 14:35 fslcreatehd
-rwxr-xr-x 1 7959 999 6023 2007-11-14 14:23 fsledithd
-rwxr-xr-x 1 7959 999 9414 2007-11-14 14:23 fslerrorreport
-rwxr-xr-x 1 7959 999 1770739 2007-11-14 14:36 fslfft
-rwxr-xr-x 1 7959 999 1901367 2007-11-14 14:44 fsl_glm
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 fsl_gui -> Runtcl
-rwxr-xr-x 1 7959 999 269263 2007-11-14 14:34 fslhd
-rwxr-xr-x 1 7959 999 2331274 2007-11-14 14:45 fsl_histogram
-rwxr-xr-x 1 7959 999 3628 2007-11-14 14:23 fslinfo
-rwxr-xr-x 1 7959 999 1804006 2007-11-14 14:34 fslinterleave
-rwxr-xr-x 1 7959 999 2242655 2008-03-20 14:09 fslmaths
-rwxr-xr-x 1 7959 999 1802352 2007-11-14 14:36 fslmeants
-rwxr-xr-x 1 7959 999 1824551 2007-11-14 14:34 fslmerge
-rwxr-xr-x 1 7959 999 1790613 2007-11-14 14:34 fslnvols
-rwxr-xr-x 1 7959 999 1833456 2007-11-14 14:34 fslorient
-rwxr-xr-x 1 7959 999 10815 2007-11-14 14:24 fslpres
-rwxr-xr-x 1 7959 999 1765478 2007-11-14 14:34 fslpspec
-rwxr-xr-x 1 7959 999 1889243 2007-11-14 14:44 fsl_regfilt
-rwxr-xr-x 1 7959 999 1812261 2007-11-14 14:34 fslroi
-rwxr-xr-x 1 7959 999 3558 2007-11-14 14:23 fslsize
-rwxr-xr-x 1 7959 999 1816369 2007-11-14 14:36 fslslice
-rwxr-xr-x 1 7959 999 1816359 2007-11-14 14:34 fslsplit
-rwxr-xr-x 1 7959 999 1787113 2007-11-15 12:29 fslstats
-rwxr-xr-x 1 7959 999 13050 2007-11-14 14:24 fsl_sub
-rwxr-xr-x 1 7959 999 1816718 2007-11-14 14:36 fslswapdim
-rwxr-xr-x 1 7959 999 446 2007-07-19 16:48 fsltclsh
-rwxr-xr-x 1 7959 999 1256714 2007-11-14 14:45 fsl_tsplot
-rwxr-xr-x 1 7959 999 3833 2007-11-14 14:23 fslval
-rwxr-xr-x 1 7959 999 4453 2007-11-14 14:24 fslvbm_1_bet
-rwxr-xr-x 1 7959 999 6215 2007-11-14 14:24 fslvbm_2_template
-rwxr-xr-x 1 7959 999 5645 2007-11-14 14:24 fslvbm_3_proc
-rwxr-xr-x 1 7959 999 117 2007-11-14 16:06 fslview
-rwxr-xr-x 1 7959 999 4294991 2007-11-14 16:06 fslview_bin
-rwxr-xr-x 1 7959 999 446 2007-07-19 16:47 fslwish
-rwxr-xr-x 1 7959 999 1942385 2007-11-14 14:41 ftoz
-rwxr-xr-x 1 7959 999 1913975 2007-11-14 14:43 fugue
-rwxr-xr-x 1 7959 999 5424 2007-11-14 14:24 generate_b0
-rwxr-xr-x 1 7959 999 4521 2007-11-14 14:24 generate_brain
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Glm -> Runtcl
-rwxr-xr-x 1 7959 999 1819468 2007-11-14 14:46 groupttest
-rwxr-xr-x 1 7959 999 1285091 2007-11-14 14:41 halfcosbasis
-rwxr-xr-x 1 7959 999 8373 2007-11-14 14:44 hist2prob
-rwxr-xr-x 1 7959 999 5323 2007-11-14 14:24 imcp
-rwxr-xr-x 1 7959 999 1768194 2007-11-14 14:42 img2imgcoord
-rwxr-xr-x 1 7959 999 1768642 2007-11-14 14:42 img2stdcoord
-rwxr-xr-x 1 7959 999 4469 2007-11-14 14:24 imglob
-rwxr-xr-x 1 7959 999 4274 2007-11-14 14:24 imln
-rwxr-xr-x 1 7959 999 5269 2007-11-14 14:24 immv
-rwxr-xr-x 1 7959 999 3805 2007-11-14 14:24 imrm
-rwxr-xr-x 1 7959 999 4364 2007-11-14 14:24 imtest
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 InvertXFM -> Runtcl
-rwxr-xr-x 1 7959 999 1959268 2007-11-14 14:43 invwarp
-rwxr-xr-x 1 7959 999 1764935 2007-11-14 14:39 make_dyadic_vectors
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Make_flobs -> Runtcl
-rwxr-xr-x 1 7959 999 1160 2003-02-21 16:48 makehtmeqns
-rwxr-xr-x 1 7959 999 1794844 2007-11-14 14:42 makerot
-rwxr-xr-x 1 7959 999 3732 2007-11-14 14:23 maskdyads
-rwxr-xr-x 1 7959 999 227 2007-07-23 17:16 mccutup
-rwxr-xr-x 1 7959 999 1952344 2007-11-14 14:43 mcflirt
-rwxr-xr-x 1 7959 999 895646 2007-11-14 14:34 mean
-rwxr-xr-x 1 7959 999 1756573 2007-11-14 14:38 medianfilter
-rwxr-xr-x 1 7959 999 2828048 2007-11-14 14:44 melodic
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Melodic -> Runtcl
-rwxr-xr-x 1 7959 999 1550 2007-07-27 07:56 mfast
-rwxr-xr-x 1 7959 999 1163965 2007-11-14 14:38 mfast_exe
-rwxr-xr-x 1 7959 999 725081 2007-11-14 14:42 midtrans
-rwxr-xr-x 1 7959 999 2621989 2007-11-14 14:45 mm
-rwxr-xr-x 1 7959 999 8470 2007-11-14 14:44 morph_kernel
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Nudge -> Runtcl
-rwxr-xr-x 1 7959 999 4266 2007-11-14 14:23 old_betall
-rwxr-xr-x 1 7959 999 2083537 2007-11-14 14:45 overlay
-rwxr-xr-x 1 7959 999 4358 2007-11-14 14:24 pairreg
-rwxr-xr-x 1 7959 999 5788 2007-11-14 14:23 perfusion_subtract
-rwxr-xr-x 1 7959 999 356284 2007-11-14 14:45 pngappend
-rwxr-xr-x 1 7959 999 1794825 2007-11-14 14:42 pointflirt
-rwxr-xr-x 1 7959 999 1994053 2007-11-14 14:47 possum
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Possum -> Runtcl
-rwxr-xr-x 1 7959 999 720125 2007-11-14 14:47 possum_sum
-rwxr-xr-x 1 7959 999 7648 2007-11-14 14:24 possumX
-rwxr-xr-x 1 7959 999 2040 2008-01-21 16:40 possumX_postproc.sh
-rwxr-xr-x 1 7959 999 1867669 2007-11-14 14:43 prelude
-rwxr-xr-x 1 7959 999 1774281 2007-11-14 14:40 prewhiten
-rwxr-xr-x 1 7959 999 3520 2007-11-14 14:23 probtrack
-rwxr-xr-x 1 7959 999 2538317 2007-11-14 14:39 probtrackx
-rwxr-xr-x 1 7959 999 1761004 2007-11-14 14:39 proj_thresh
-rwxr-xr-x 1 7959 999 11861 2007-11-14 14:44 ptoz
-rwxr-xr-x 1 7959 999 1850641 2007-11-14 14:47 pulse
-rwxr-xr-x 1 7959 999 1886073 2007-11-14 14:45 randomise
-rwxr-xr-x 1 7959 999 4137 2007-11-14 14:24 remove_ext
-rwxr-xr-x 1 7959 999 5221 2007-11-14 14:23 renderhighres
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Renderhighres -> Runtcl
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Renderstats -> Runtcl
-rwxr-xr-x 1 7959 999 1756659 2007-11-14 14:42 rmsdiff
-rwxr-xr-x 1 7959 999 5513 2007-11-14 14:23 run_first
-rwxr-xr-x 1 7959 999 5900 2008-03-20 13:53 run_first_all
-rwxr-xr-x 1 7959 999 5369 2007-11-14 14:24 runfsl
-rwxr-xr-x 1 7959 999 1105 2007-07-19 17:12 Runtcl
-rwxr-xr-x 1 7959 999 680217 2007-11-14 14:33 selfintersection
-rwxr-xr-x 1 7959 999 20428 2007-11-14 14:24 siena
-rwxr-xr-x 1 7959 999 6045 2007-11-14 14:24 siena_cal
-rwxr-xr-x 1 7959 999 1805431 2007-11-14 14:45 siena_diff
-rwxr-xr-x 1 7959 999 6493 2007-11-14 14:24 siena_flirt
-rwxr-xr-x 1 7959 999 6092 2007-11-14 14:24 siena_flow2std
-rwxr-xr-x 1 7959 999 18759 2007-11-14 14:24 sienax
-rwxr-xr-x 1 7959 999 1871936 2007-11-14 14:43 sigloss
-rwxr-xr-x 1 7959 999 1818051 2007-11-14 14:47 signal2image
-rwxr-xr-x 1 7959 999 4267 2007-11-14 14:23 sliceanimate
-rwxr-xr-x 1 7959 999 2065659 2007-11-14 14:44 slicer
-rwxr-xr-x 1 7959 999 5836 2007-11-14 14:24 slices
-rwxr-xr-x 1 7959 999 5591 2007-11-14 14:24 slicesdir
-rwxr-xr-x 1 7959 999 4325 2007-11-14 14:24 slicesmask
-rwxr-xr-x 1 7959 999 1804609 2007-11-14 14:46 slicetimer
-rwxr-xr-x 1 7959 999 1812789 2007-11-14 14:36 smoothest
-rwxr-xr-x 1 7959 999 1801501 2007-11-14 14:47 spharm_rm
-rwxr-xr-x 1 7959 999 8514 2007-11-14 14:24 standard_space_roi
-rwxr-xr-x 1 7959 999 1768738 2007-11-14 14:42 std2imgcoord
-rwxr-xr-x 1 7959 999 1805905 2007-11-14 14:45 surface_norm
-rwxr-xr-x 1 7959 999 1870589 2007-11-14 14:46 susan
lrwxrwxrwx 1 7959 999 6 2008-07-01 12:22 Susan -> Runtcl
-rwxr-xr-x 1 7959 999 739424 2007-11-14 14:47 systemnoise
-rwxr-xr-x 1 7959 999 5054 2007-11-14 14:24 tbss_1_preproc
-rwxr-xr-x 1 7959 999 5063 2007-11-14 14:24 tbss_2_reg
-rwxr-xr-x 1 7959 999 7026 2007-11-14 14:24 tbss_3_postreg
-rwxr-xr-x 1 7959 999 4552 2007-11-14 14:24 tbss_4_prestats
-rwxr-xr-x 1 7959 999 6626 2007-11-14 14:24 tbss_deproject
-rwxr-xr-x 1 7959 999 4990 2007-11-14 14:24 tbss_fill
-rwxr-xr-x 1 7959 999 4998 2007-11-14 14:24 tbss_non_FA
-rwxr-xr-x 1 7959 999 5491 2007-11-14 14:24 tbss_reg
-rwxr-xr-x 1 7959 999 1829012 2007-11-14 14:46 tbss_skeleton
-rwxr-xr-x 1 7959 999 6995 2007-11-14 14:44 tmpnam
-rwxr-xr-x 1 7959 999 2342360 2007-11-14 14:40 tsplot
-rwxr-xr-x 1 7959 999 1940340 2007-11-14 14:41 ttologp
-rwxr-xr-x 1 7959 999 1942385 2007-11-14 14:41 ttoz
-rwxr-xr-x 1 7959 999 1760681 2007-11-14 14:45 unconfound
-rwxr-xr-x 1 7959 999 6101 2007-11-14 14:23 updatefeatreg
-rwxr-xr-x 1 7959 999 1818525 2007-11-14 14:39 vecreg
-rwxr-xr-x 1 7959 999 1783143 2007-11-14 14:43 vmapper
-rwxr-xr-x 1 7959 999 29406 2007-11-14 14:44 whirlgif
-rwxr-xr-x 1 7959 999 186399 2007-11-14 14:45 wpng
-rwxr-xr-x 1 7959 999 1896961 2007-11-14 14:39 xfibres
-rwxr-xr-x 1 7959 999 3776 2007-11-14 14:23 zeropad
-rwxr-xr-x 1 7959 999 12486 2007-11-14 14:44 ztop
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Matthew Webster [[log in to unmask]]
Sent: Tuesday, July 01, 2008 3:28 PM
To: [log in to unmask]
Subject: Re: [FSL] FSL installation on FSL_vm5_32
This message usually means that the binary does not match the OS.
Can you send me the results of the following ( in a terminal)
echo $FSLMACHTYPE
ls -al /usr/local/fsl/bin
Regards
Matthew
> This is what I get if I do that:
>
> emma@clinicalneuro-desktop:~$ Melodic
> /usr/local/fsl/bin/fslwish: line 17: /usr/local/fsl/extras/bin/
> fslwish8.4: cannot execute binary file
> /usr/local/fsl/bin/fslwish: line 17: /usr/local/fsl/extras/bin/
> fslwish8.4: Success
>
> Any suggestions?
>
> Emma
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
> Of Matthew Webster [[log in to unmask]]
> Sent: Tuesday, July 01, 2008 3:15 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FSL installation on FSL_vm5_32
>
> Hi,
> If the install script has completed successfully you should be
> able to open a terminal and type (.e.g)
>
> Flirt
>
> to bring up a GUI. It shouldn't matter which directory you are in...
>
> Matthew
>> Hi again,
>>
>> I was having a look on the website on the installation/running
>> section. It writes this:
>>
>> "To run the FSL tools from the command line, you can find the tools
>> in $FSLDIR/bin. In general command-line programs are lower case
>> (e.g. 'bet'). In general the GUI version is capitalised (e.g.
>> 'Bet'), except on Mac, where '_gui' is appended because those file
>> systems can't tell the difference between upper and lower case (e.g.
>> 'Bet_gui').
>>
>> To bring up a simple GUI which is just a menu of the main individual
>> FSL GUI tools, just type fsl."
>>
>> I want to be able to use a GUI, but where do i type fsl to bring up
>> this list of tools, and if it's in the terminal, what directory do I
>> need to be in?
>>
>> Sorry to keep asking so many questions
>>
>> Emma
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Matthew Webster [[log in to unmask]]
>> Sent: Tuesday, July 01, 2008 2:07 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FSL installation on FSL_vm5_32
>>
>> Hi,
>> Is your PATH variable set up correctly - does it contain /usr/
>> local/fsl/bin? what happens if you run /usr/local/fsl/bin/melodic? Do
>> any of the GUI's launch ( e.g. Feat Flirt etc)?
>>
>> Matthew
>>
>>> Dear Matthew,
>>>
>>> The usr/local/fsl folder contains all fsl files and subdirectories
>>> (as far
>>> as I know)
>>> I tried your commands (for bash), but nothing appeared to happen. I
>>> believe
>>> I'd tried that before, as that is also a suggestion somewhere on the
>>> website.
>>>
>>> Emma
>>>
>>
>
|