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Hi Paul,shouldn’t it be../../bin/?Cheers,AndreasVon: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von paul mccarthy <[log in to unmask]>Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>Datum: Montag, 13. April 2020 um 11:03An: <[log in to unmask]>Betreff: Re: [FSL] FSL installation and python environmentHi Renxi,It turns out that there is a problem with MSM in fsl 6.0.3 - the executable files have not been moved intothe$FSLDIR/bin/directory. You can fix this by running the following commands:cd $FSLDIR/src/MSM/sudo cp estimate_metric_distortion msm msmapplywarp msm_metric_sim msmresample surfconvert ../bin/PaulOn Apr 12 2020, at 5:43 pm, RENXI LI <[log in to unmask]> wrote:Hi Paul:Here is what I got from terminal after entering these commands:(base) Renxis-Mac-mini:~ renxili$ envTERM_PROGRAM=Apple_TerminalSHELL=/bin/bashTERM=xterm-256colorTMPDIR=/var/folders/43/fx4rgnhx4cd13w99xxqms0mc0000gn/T/CONDA_SHLVL=1FSLMULTIFILEQUIT=TRUECONDA_PROMPT_MODIFIER=(base)TERM_PROGRAM_VERSION=433TERM_SESSION_ID=15EA6C46-D10E-40C5-919A-FB2CC6C7AC33USER=renxiliFSLGECUDAQ=cuda.qCONDA_EXE=/Users/renxili/opt/anaconda3/bin/condaSSH_AUTH_SOCK=/private/tmp/com.apple.launchd.8WnEt0fKfE/Listeners_CE_CONDA=PATH=/Library/Frameworks/Python.framework/Versions/3.8/bin:/Users/renxili/opt/anaconda3/bin:/Users/renxili/opt/anaconda3/condabin:/usr/local/fsl/bin:/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/binLaunchInstanceID=D27358A7-9FFB-4C44-B78B-0D6823A24D1ACONDA_PREFIX=/Users/renxili/opt/anaconda3PWD=/Users/renxiliLANG=en_US.UTF-8FSLTCLSH=/usr/local/fsl/bin/fsltclshFSLMACHINELIST=XPC_FLAGS=0x0FSLREMOTECALL=FSLWISH=/usr/local/fsl/bin/fslwish_CE_M=XPC_SERVICE_NAME=0SHLVL=1HOME=/Users/renxiliCONDA_PYTHON_EXE=/Users/renxili/opt/anaconda3/bin/pythonLOGNAME=renxiliFSLDIR=/usr/local/fslCONDA_DEFAULT_ENV=baseDISPLAY=/private/tmp/com.apple.launchd.kcmCn05h1U/org.macosforge.xquartz:0FSLLOCKDIR=FSLOUTPUTTYPE=NIFTI_GZSECURITYSESSIONID=186a6_=/usr/bin/env(base) Renxis-Mac-mini:~ renxili$ ls $FSLDIR/bin/AnatomicalAverage fslroiApplyXFM_gui fslselectvolsBet_gui fslsizeConcatXFM_gui fslsliceFSLeyes.app fslsmoothfillFast_gui fslsplitFdt_gui fslstatsFeat_gui fslsurfacemathsFeatquery_gui fslswapdimFlirt_gui fslswapdim_exeFsl_prepare_fieldmap_gui fsltclshGlm_gui fslvalInvertXFM_gui fslvbm_1_betMake_flobs_gui fslvbm_2_templateMelodic_gui fslvbm_3_procNudge_gui fslviewPnm_gui fslview.appPossum_gui fslview_deprecatedRenderhighres_gui fslwishRenderstats_gui ftozRuntcl fugueSusan_gui funpackText2Vest funpack_demoVest2Text generateConfoundsaff2rigid generate_b0applytopup generate_b0calcapplywarp generate_brainapplyxfm4D gpsasl_calib halfcosbasisasl_file hist2probasl_gui imcpasl_mfree img2imgcoordasl_reg img2stdcoordassistant.app imglobatlasq imlnatlasquery immvatlasquery_bin imrmautoaq imtestavscale invfeatregavw2fsl invwarpb0calc invwarp_exebasil label2surfbasil_var lesion_fillingbaycest mainfeatregbedpost make_bianca_maskbedpostx make_dyadic_vectorsbedpostx_datacheck makerotbedpostx_postproc.sh maskdyadsbedpostx_preproc.sh match_smoothingbedpostx_single_slice.sh mccutupbet mcflirtbet2 meanbetsurf medianfilterbianca melodicbianca_cluster_stats midtransbianca_overlap_measures mistcalc_grad_perc_dev mist_1_trainccops mist_2_fitcheckFEAT mist_FA_regcluster mist_displaycluster2html mist_mesh_utilsconcat_bvars mmconnectedcomp morph_kernelcontrast_mgr mp_diffpow.shconvert_xfm mvntoolconvertwarp new_invwarpcreate_lut old_betallcutoffcalc overlaydesign_ttest2 oxford_asldistancemap pairregdrawmesh perfusion_subtractdtifit pngappenddtigen pnm_evsdual_regression pnm_stage1easythresh pointflirteddy poppeddy_combine possumeddy_correct possumXeddy_cuda7.5 possumX_postproc.sheddy_quad possum_interpmot.pyeddy_squad possum_matrixepi_reg possum_plot.pyestnoise possum_sumextractfidparams preludeextracttxt prewhitenfabber probtrackfabber_asl probtrackxfabber_cest probtrackx2fabber_dce proj_threshfabber_dsc ptozfabber_dualecho pulsefabber_dwi pvmfitfabber_qbold pyfeedsfabber_t1 qbootfabber_var qboot_parallelfast qboot_postproc.shfdr qboot_preproc.shfdt_matrix_merge quasilfdt_rotate_bvecs randomisefeat randomise_parallelfeat_gm_prepare remove_extfeat_model renderfeatquery renderhighresfeatregapply rmsdifffilm_cifti robustfovfilm_gls run_firstfilmbabe run_first_allfilmbabescript run_mesh_utilsfind_the_biggest select_dwi_volsfirst selfintersectionfirst3Dview setFEATfirst_boundary_corr setup_masksfirst_flirt sienafirst_mult_bcorr siena_calfirst_roi_slicesdir siena_difffirst_utils siena_flirtflameo siena_flow2stdflirt sienaxflirt_average siglossfnirt signal2imagefnirtfileutils sliceanimatefsl slicerfsl2ascii slicesfslFixText slices_summaryfsl_abspath slicesdirfsl_anat slicesmaskfsl_boxplot slicetimerfsl_deface smoothestfsl_ents spharm_rmfsl_gen_3D standard_space_roifsl_glm std2imgcoordfsl_gui surf2surffsl_histogram surf2volumefsl_motion_outliers surf_projfsl_mvlm surface_fdrfsl_prepare_fieldmap surfmathsfsl_reg susanfsl_regfilt swap_subjectwisefsl_sbca swap_voxelwisefsl_schurprod swefsl_sub systemnoisefsl_tsplot tbss_1_preprocfsladd tbss_2_regfslanimate tbss_3_postregfslascii2img tbss_4_prestatsfslcc tbss_deprojectfslchfiletype tbss_fillfslchfiletype_exe tbss_non_FAfslchpixdim tbss_skeletonfslcomplex tbss_symfslcpgeom tbss_xfslcreatehd tcalcfslecho tmpnamfsledithd toastfslerrorreport topupfsleyes tsplotfslfft ttologpfslhd ttozfslinfo unconfoundfslinterleave updatefeatregfslipython vecregfslmaths verbenafslmeants viena_createpngfslmerge viena_quantfslmodhd whirlgiffslnvols wpngfslorient xfibresfslpspec xtractfslpython xtract_viewerfslpythonw zeropadfslreorient2std ztop(base) Renxis-Mac-mini:~ renxili$Best,RenxiTo unsubscribe from the FSL list, click the following link:To unsubscribe from the FSL list, click the following link:To unsubscribe from the FSL list, click the following link:
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