Hi, Thanks for the data - are you sure you are running in our supplied VM - the FSLMACHTYPE looks like it could just be the ubuntu OS? If you still have an OSX machine available there is a 4.0.4 OSX version available on our download page. Regards Matthew > 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 >>>> >>> >> >