Closed BWIEDOR closed 11 months ago
Hi @BWIEDOR Brian, Too bad that you do not have support, it can be frustrating to deal with these cases indeed. From the message you have posted it seems that FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) is either not installed, or installed but not setup correctly for pydeface.
whereis fsl5.0-fsl
in the terminal?echo $FSLDIR
in the terminal?Certainly, below are the results for each command.
- Can you post what returns when you execute
whereis fsl5.0-fsl
in the terminal?whereis fsl5.0-fsl fsl5: /usr/bin/fsl5.0-fsl_sub /usr/bin/fsl5.0-Possum /usr/bin/fsl5.0-convertwarp /usr/bin/fsl5.0-first /usr/bin/fsl5.0-pnm_stage1 /usr/bin/fsl5.0-new_invwarp /usr/bin/fsl5.0-applytopup /usr/bin/fsl5.0-tbss_3_postreg /usr/bin/fsl5.0-imrm /usr/bin/fsl5.0-fslecho /usr/bin/fsl5.0-ttoz /usr/bin/fsl5.0-old_betall /usr/bin/fsl5.0-fast /usr/bin/fsl5.0-fslanimate /usr/bin/fsl5.0-fslascii2img /usr/bin/fsl5.0-randomise /usr/bin/fsl5.0-mm /usr/bin/fsl5.0-applyxfm4D /usr/bin/fsl5.0-swap_subjectwise /usr/bin/fsl5.0-invwarp_exe /usr/bin/fsl5.0-feat /usr/bin/fsl5.0-flirt_average /usr/bin/fsl5.0-applywarp /usr/bin/fsl5.0-filmbabescript /usr/bin/fsl5.0-fsl_abspath /usr/bin/fsl5.0-ftoz /usr/bin/fsl5.0-cutoffcalc /usr/bin/fsl5.0-quasil /usr/bin/fsl5.0-fsl_gui /usr/bin/fsl5.0-fsl_boxplot /usr/bin/fsl5.0-gps /usr/bin/fsl5.0-possum_matrix /usr/bin/fsl5.0-Fsl_prepare_fieldmap /usr/bin/fsl5.0-signal2image /usr/bin/fsl5.0-betsurf /usr/bin/fsl5.0-viena_createpng /usr/bin/fsl5.0-bet /usr/bin/fsl5.0-fsl_anat /usr/bin/fsl5.0-Melodic /usr/bin/fsl5.0-fslcpgeom /usr/bin/fsl5.0-fslcorrecthd /usr/bin/fsl5.0-Vest2Text /usr/bin/fsl5.0-fslroi /usr/bin/fsl5.0-fslsize /usr/bin/fsl5.0-lesion_filling /usr/bin/fsl5.0-fslreorient2std /usr/bin/fsl5.0-fsl_glm /usr/bin/fsl5.0-midtrans /usr/bin/fsl5.0-perfusion_subtract /usr/bin/fsl5.0-create_lut /usr/bin/fsl5.0-siena /usr/bin/fsl5.0-ztop /usr/bin/fsl5.0-run_first /usr/bin/fsl5.0-drawmesh /usr/bin/fsl5.0-fslval /usr/bin/fsl5.0-updatefeatreg /usr/bin/fsl5.0-setFEAT /usr/bin/fsl5.0-feat_model /usr/bin/fsl5.0-fsl_reg /usr/bin/fsl5.0-fslvbm_3_proc /usr/bin/fsl5.0-tcalc /usr/bin/fsl5.0-first_boundary_corr /usr/bin/fsl5.0-fslvbm_2_template /usr/bin/fsl5.0-convert_xfm /usr/bin/fsl5.0-maskdyads /usr/bin/fsl5.0-slicer /usr/bin/fsl5.0-aff2rigid /usr/bin/fsl5.0-tsplot /usr/bin/fsl5.0-invfeatreg /usr/bin/fsl5.0-first_mult_bcorr /usr/bin/fsl5.0-tbss_4_prestats /usr/bin/fsl5.0-pvmfit /usr/bin/fsl5.0-wpng /usr/bin/fsl5.0-prelude /usr/bin/fsl5.0-xfibres /usr/bin/fsl5.0-fugue /usr/bin/fsl5.0-whirlgif /usr/bin/fsl5.0-sliceanimate /usr/bin/fsl5.0-morph_kernel /usr/bin/fsl5.0-eddy /usr/bin/fsl5.0-pnm_evs /usr/bin/fsl5.0-viena_quant /usr/bin/fsl5.0-extracttxt /usr/bin/fsl5.0-oxford_asl /usr/bin/fsl5.0-tbss_non_FA /usr/bin/fsl5.0-pointflirt /usr/bin/fsl5.0-fsl_mvlm /usr/bin/fsl5.0-imcp /usr/bin/fsl5.0-imln /usr/bin/fsl5.0-fslswapdim /usr/bin/fsl5.0-fslFixText /usr/bin/fsl5.0-label2surf /usr/bin/fsl5.0-prewhiten /usr/bin/fsl5.0-setup_masks /usr/bin/fsl5.0-fdr /usr/bin/fsl5.0-sigloss /usr/bin/fsl5.0-Featquery /usr/bin/fsl5.0-ConcatXFM /usr/bin/fsl5.0-basil_var /usr/bin/fsl5.0-checkFEAT /usr/bin/fsl5.0-avscale /usr/bin/fsl5.0-siena_diff /usr/bin/fsl5.0-bedpostx /usr/bin/fsl5.0-ccops /usr/bin/fsl5.0-fslfft /usr/bin/fsl5.0-mvntool /usr/bin/fsl5.0-InvertXFM /usr/bin/fsl5.0-ApplyXFM /usr/bin/fsl5.0-match_smoothing /usr/bin/fsl5.0-Renderhighres /usr/bin/fsl5.0-first_roi_slicesdir /usr/bin/fsl5.0-melodic /usr/bin/fsl5.0-generate_b0 /usr/bin/fsl5.0-run_first_all /usr/bin/fsl5.0-concat_bvars /usr/bin/fsl5.0-distancemap /usr/bin/fsl5.0-dtifit /usr/bin/fsl5.0-fslpspec /usr/bin/fsl5.0-topup /usr/bin/fsl5.0-slicesdir /usr/bin/fsl5.0-asl_calib /usr/bin/fsl5.0-Glm /usr/bin/fsl5.0-imtest /usr/bin/fsl5.0-Asl /usr/bin/fsl5.0-vecreg /usr/bin/fsl5.0-AnatomicalAverage /usr/bin/fsl5.0-flameo /usr/bin/fsl5.0-tbss_deproject /usr/bin/fsl5.0-susan /usr/bin/fsl5.0-fsladd /usr/bin/fsl5.0-generateConfounds /usr/bin/fsl5.0-generate_brain /usr/bin/fsl5.0-imglob /usr/bin/fsl5.0-filmbabe /usr/bin/fsl5.0-zeropad /usr/bin/fsl5.0-Flirt /usr/bin/fsl5.0-fnirt /usr/bin/fsl5.0-fsl_histogram /usr/bin/fsl5.0-fslmerge /usr/bin/fsl5.0-makerot /usr/bin/fsl5.0-dual_regression /usr/bin/fsl5.0-asl_mfree /usr/bin/fsl5.0-fsl2ascii /usr/bin/fsl5.0-fsl /usr/bin/fsl5.0-tmpnam /usr/bin/fsl5.0-rmsdiff /usr/bin/fsl5.0-fslerrorreport /usr/bin/fsl5.0-mainfeatreg /usr/bin/fsl5.0-contrast_mgr /usr/bin/fsl5.0-medianfilter /usr/bin/fsl5.0-halfcosbasis /usr/bin/fsl5.0-Nudge /usr/bin/fsl5.0-fslmodhd /usr/bin/fsl5.0-extractfidparams /usr/bin/fsl5.0-calc_grad_perc_dev /usr/bin/fsl5.0-fslinfo /usr/bin/fsl5.0-autoaq /usr/bin/fsl5.0-cluster /usr/bin/fsl5.0-design_ttest2 /usr/bin/fsl5.0-sienax /usr/bin/fsl5.0-fslcomplex /usr/bin/fsl5.0-proj_thresh /usr/bin/fsl5.0-img2imgcoord /usr/bin/fsl5.0-unconfound /usr/bin/fsl5.0-Susan /usr/bin/fsl5.0-Text2Vest /usr/bin/fsl5.0-fslnvols /usr/bin/fsl5.0-remove_ext /usr/bin/fsl5.0-fsledithd /usr/bin/fsl5.0-first_utils /usr/bin/fsl5.0-fabber /usr/bin/fsl5.0-pulse /usr/bin/fsl5.0-fslchfiletype /usr/bin/fsl5.0-fslslice /usr/bin/fsl5.0-film_gls /usr/bin/fsl5.0-qboot /usr/bin/fsl5.0-asl_reg /usr/bin/fsl5.0-fdt_rotate_bvecs /usr/bin/fsl5.0-easythresh /usr/bin/fsl5.0-b0calc /usr/bin/fsl5.0-find_the_biggest /usr/bin/fsl5.0-fnirtfileutils /usr/bin/fsl5.0-flirt /usr/bin/fsl5.0-eddy_correct /usr/bin/fsl5.0-probtrackx /usr/bin/fsl5.0-fsl_sbca /usr/bin/fsl5.0-fslstats /usr/bin/fsl5.0-fsl_schurprod /usr/bin/fsl5.0-bet2 /usr/bin/fsl5.0-fslinterleave /usr/bin/fsl5.0-Fast /usr/bin/fsl5.0-Fdt /usr/bin/fsl5.0-avw2fsl /usr/bin/fsl5.0-fslmeants /usr/bin/fsl5.0-run_mesh_utils /usr/bin/fsl5.0-systemnoise /usr/bin/fsl5.0-fslsmoothfill /usr/bin/fsl5.0-Make_flobs /usr/bin/fsl5.0-tbss_skeleton /usr/bin/fsl5.0-bedpost /usr/bin/fsl5.0-make_dyadic_vectors /usr/bin/fsl5.0-fslchfiletype_exe /usr/bin/fsl5.0-mccutup /usr/bin/fsl5.0-Bet /usr/bin/fsl5.0-mcflirt /usr/bin/fsl5.0-fsl_tsplot /usr/bin/fsl5.0-img2stdcoord /usr/bin/fsl5.0-slices_summary /usr/bin/fsl5.0-Renderstats /usr/bin/fsl5.0-cluster2html /usr/bin/fsl5.0-tbss_sym /usr/bin/fsl5.0-tbss_fill /usr/bin/fsl5.0-slicesmask /usr/bin/fsl5.0-possumX /usr/bin/fsl5.0-probtrackx2 /usr/bin/fsl5.0-randomise_parallel /usr/bin/fsl5.0-siena_flow2std /usr/bin/fsl5.0-surface_fdr /usr/bin/fsl5.0-first3Dview /usr/bin/fsl5.0-fslselectvols /usr/bin/fsl5.0-bedpostx_datacheck /usr/bin/fsl5.0-surf2volume /usr/bin/fsl5.0-immv /usr/bin/fsl5.0-epi_reg /usr/bin/fsl5.0-possum_sum /usr/bin/fsl5.0-baycest /usr/bin/fsl5.0-first_flirt /usr/bin/fsl5.0-standard_space_roi /usr/bin/fsl5.0-fsl_motion_outliers /usr/bin/fsl5.0-fabber_var /usr/bin/fsl5.0-popp /usr/bin/fsl5.0-pngappend /usr/bin/fsl5.0-connectedcomp /usr/bin/fsl5.0-std2imgcoord /usr/bin/fsl5.0-possum /usr/bin/fsl5.0-siena_cal /usr/bin/fsl5.0-generate_b0calc /usr/bin/fsl5.0-fslsplit /usr/bin/fsl5.0-basil /usr/bin/fsl5.0-tbss_x /usr/bin/fsl5.0-ttologp /usr/bin/fsl5.0-probtrack /usr/bin/fsl5.0-fslchpixdim /usr/bin/fsl5.0-spharm_rm /usr/bin/fsl5.0-fslmaths /usr/bin/fsl5.0-surf2surf /usr/bin/fsl5.0-renderhighres /usr/bin/fsl5.0-ptoz /usr/bin/fsl5.0-fslcreatehd /usr/bin/fsl5.0-fslvbm_1_bet /usr/bin/fsl5.0-featquery /usr/bin/fsl5.0-surf_proj /usr/bin/fsl5.0-pairreg /usr/bin/fsl5.0-selfintersection /usr/bin/fsl5.0-dtigen /usr/bin/fsl5.0-asl_file /usr/bin/fsl5.0-fslhd /usr/bin/fsl5.0-eddy_combine /usr/bin/fsl5.0-overlay /usr/bin/fsl5.0-feat_gm_prepare /usr/bin/fsl5.0-fsl_regfilt /usr/bin/fsl5.0-tbss_1_preproc /usr/bin/fsl5.0-swap_voxelwise /usr/bin/fsl5.0-invwarp /usr/bin/fsl5.0-slicetimer /usr/bin/fsl5.0-siena_flirt /usr/bin/fsl5.0-qboot_parallel /usr/bin/fsl5.0-fsl_prepare_fieldmap /usr/bin/fsl5.0-tbss_2_reg /usr/bin/fsl5.0-hist2prob /usr/bin/fsl5.0-robustfov /usr/bin/fsl5.0-fslswapdim_exe /usr/bin/fsl5.0-fslcc /usr/bin/fsl5.0-Pnm /usr/bin/fsl5.0-smoothest /usr/bin/fsl5.0-featregapply /usr/bin/fsl5.0-fslsurfacemaths /usr/bin/fsl5.0-mean /usr/bin/fsl5.0-slices /usr/bin/fsl5.0-estnoise /usr/bin/fsl5.0-fslorient /usr/bin/fsl5.0-Feat
- Can you post what returns when you execute
echo $FSLDIR
in the terminal?
For my own login I am getting no return on the echo command. I have also reached out to the user to ask them to run these commands on their own login, as they insisted they can run FSL normally on its own.
I also wanted to add: The person who installed FSL did so directly from the Ubuntu 20.04 repo, via the apt-get install fsl command. So far as they can remember, they did not make any adjustments or changes, just ran that command as it was.
Thanks. Now, can you try executing lines below within the same terminal, and post what you get:
FSLDIR=/usr/bin
If these does not work can you try again with below, and post the results:
alias fsl="fsl5.0-fsl"
A user in my building has requested help with this issue. I must preface this by saying I have no experience in this matter and minimal Linux experience, however due to departmental downsizing and limitation, I am the one who was given this to investigate. Please be understanding.
This was their exact message to me:
I will provide whatever information is helpful or needed if anyone has some ideas what is going on here. The person in my department who had experience with these installations is no longer available for me to call upon.
Best, Brian