Hi all, I have installed MRtrix3Tissue and set the path to it in my my .zsh startup file.
The path to the MRtrix3Tissue directory is /Users/myusername/MRtrix3Tissue.
The path to the python3 directory is /usr/local/bin/python3.
I have created a directory named python and linked it to python3 using sudo ln -s /usr/local/bin/python3 /usr/local/bin/python (otherwise I would get env: python: no such file or directory every time I tried to run a command.
When I run the command mrinfo I indeed get:
~ % mrinfo
MRtrix 3Tissue_v5.2.9 mrinfo Oct 31 2024
mrinfo: part of the MRtrix3 package
SYNOPSIS
Display image header information, or extract specific information from the
header
USAGE
mrinfo [ options ] image [ image ... ]
image the input image(s).
DESCRIPTION
By default, all information contained in each image header will be printed
to the console in a reader-friendly format.
Alternatively, command-line options may be used to extract specific
details from the header(s); these are printed to the console in a format
Despite this if I try to run ss3t_csd_beta1 I get: env: python: Permission denied.
If I check the ownership of the files in the bin directory of MRtrix3Tissue I get:
ls -l ~/MRtrix3Tissue/bin
total 105448
-rwxr-xr-x 1 root staff 258400 31 Ott 01:49 5tt2gmwmi
-rwxr-xr-x 1 root staff 239584 31 Ott 01:42 5tt2vis
-rwxr-xr-x 1 root staff 253488 31 Ott 01:50 5ttcheck
-rwxr-xr-x 1 root staff 256496 31 Ott 01:48 5ttedit
-rwxr-xr-x 1 myusername staff 3026 18 Ago 23:33 5ttgen
drwxr-xr-x 3 myusername staff 96 31 Ott 18:46 __pycache__
-rwxr-xr-x 1 root staff 1185144 31 Ott 01:57 afdconnectivity
-rwxr-xr-x 1 root staff 425176 31 Ott 01:59 amp2response
-rwxr-xr-x 1 root staff 497072 31 Ott 01:53 amp2sh
-rwxr-xr-x 1 myusername staff 1619 18 Ago 23:33 blend
-rwxr-xr-x 1 root staff 599096 31 Ott 01:58 connectome2tck
-rwxr-xr-x 1 root staff 359608 31 Ott 01:49 connectomestats
-rwxr-xr-x 1 myusername staff 3689 18 Ago 23:33 convert_bruker
-rwxr-xr-x 1 root staff 75088 31 Ott 01:45 dcmedit
-rwxr-xr-x 1 root staff 75976 31 Ott 01:59 dcminfo
-rwxr-xr-x 1 root staff 129152 31 Ott 01:45 dirflip
-rwxr-xr-x 1 root staff 148680 31 Ott 01:51 dirgen
-rwxr-xr-x 1 root staff 103296 31 Ott 01:58 dirmerge
-rwxr-xr-x 1 root staff 113512 31 Ott 01:50 dirorder
-rwxr-xr-x 1 root staff 130392 31 Ott 01:53 dirsplit
-rwxr-xr-x 1 root staff 304800 31 Ott 01:47 dirstat
-rwxr-xr-x 1 root staff 279088 31 Ott 01:50 dwi2adc
-rwxr-xr-x 1 root staff 689800 31 Ott 01:48 dwi2fod
-rwxr-xr-x 1 root staff 540072 31 Ott 01:54 dwi2mask
-rwxr-xr-x 1 myusername staff 5351 18 Ago 23:33 dwi2response
-rwxr-xr-x 1 root staff 323032 31 Ott 01:54 dwi2tensor
-rwxr-xr-x 1 myusername staff 2749 18 Ago 23:33 dwibiascorrect
-rwxr-xr-x 1 myusername staff 6515 18 Ago 23:33 dwicat
-rwxr-xr-x 1 root staff 835992 31 Ott 01:47 dwidenoise
-rwxr-xr-x 1 root staff 226448 31 Ott 01:59 dwiextract
-rwxr-xr-x 1 myusername staff 71898 18 Ago 23:33 dwifslpreproc
-rwxr-xr-x 1 myusername staff 7883 18 Ago 23:33 dwigradcheck
-rwxr-xr-x 1 myusername staff 1419 18 Ago 23:33 dwinormalise
-rwxr-xr-x 1 myusername staff 2732 18 Ago 23:33 dwishellmath
-rwxr-xr-x 1 root staff 232504 31 Ott 01:53 fixel2sh
-rwxr-xr-x 1 root staff 875872 31 Ott 01:51 fixel2tsf
-rwxr-xr-x 1 root staff 589176 31 Ott 01:51 fixel2voxel
-rwxr-xr-x 1 root staff 1212960 31 Ott 01:59 fixelcfestats
-rwxr-xr-x 1 root staff 350976 31 Ott 01:59 fixelconvert
-rwxr-xr-x 1 root staff 292392 31 Ott 01:51 fixelcorrespondence
-rwxr-xr-x 1 root staff 276960 31 Ott 01:54 fixelcrop
-rwxr-xr-x 1 root staff 297112 31 Ott 01:49 fixelreorient
-rwxr-xr-x 1 root staff 446528 31 Ott 01:44 fod2dec
-rwxr-xr-x 1 root staff 602352 31 Ott 01:45 fod2fixel
-rwxr-xr-x 1 myusername staff 15726 18 Ago 23:33 foreach
-rwxr-xr-x 1 myusername staff 4457 18 Ago 23:33 gen_scheme
-rwxr-xr-x 1 root staff 282968 31 Ott 01:44 label2colour
-rwxr-xr-x 1 root staff 515544 31 Ott 01:46 label2mesh
-rwxr-xr-x 1 root staff 298424 31 Ott 01:58 labelconvert
-rwxr-xr-x 1 myusername staff 8784 18 Ago 23:33 labelsgmfix
-rwxr-xr-x 1 root staff 132088 31 Ott 01:53 maskdump
-rwxr-xr-x 1 root staff 316416 31 Ott 01:58 maskfilter
-rwxr-xr-x 1 root staff 556216 31 Ott 01:47 mesh2voxel
-rwxr-xr-x 1 root staff 413376 31 Ott 01:59 meshconvert
-rwxr-xr-x 1 root staff 430528 31 Ott 01:51 meshfilter
-rwxr-xr-x 1 root staff 643928 31 Ott 01:53 mraverageheader
-rwxr-xr-x 1 root staff 443440 31 Ott 01:45 mrcalc
-rwxr-xr-x 1 root staff 499344 31 Ott 01:46 mrcat
-rwxr-xr-x 1 root staff 127728 31 Ott 01:54 mrcheckerboardmask
-rwxr-xr-x 1 root staff 511752 31 Ott 01:45 mrclusterstats
-rwxr-xr-x 1 root staff 352432 31 Ott 01:52 mrcolour
-rwxr-xr-x 1 root staff 877096 31 Ott 01:45 mrconvert
-rwxr-xr-x 1 root staff 188800 31 Ott 01:50 mrdegibbs
-rwxr-xr-x 1 root staff 496280 31 Ott 01:46 mrdump
-rwxr-xr-x 1 root staff 145392 31 Ott 01:52 mredit
-rwxr-xr-x 1 root staff 457512 31 Ott 01:50 mrfilter
-rwxr-xr-x 1 root staff 439680 31 Ott 01:44 mrgrid
-rwxr-xr-x 1 root staff 226080 31 Ott 01:45 mrhistmatch
-rwxr-xr-x 1 root staff 157288 31 Ott 01:58 mrhistogram
-rwxr-xr-x 1 root staff 212992 31 Ott 01:49 mrinfo
-rwxr-xr-x 1 root staff 1425712 31 Ott 02:00 mrmath
-rwxr-xr-x 1 root staff 929624 31 Ott 01:52 mrmetric
-rwxr-xr-x 1 root staff 3884544 31 Ott 01:52 mrregister
-rwxr-xr-x 1 root staff 172152 31 Ott 01:45 mrstats
-rwxr-xr-x 1 root staff 596408 31 Ott 01:58 mrthreshold
-rwxr-xr-x 1 root staff 1361072 31 Ott 02:00 mrtransform
-rw-r--r-- 1 myusername staff 1730 18 Ago 23:33 mrtrix3.py
-rwxr-xr-x 1 root staff 3140696 31 Ott 01:57 mrview
-rwxr-xr-x 1 root staff 466712 31 Ott 01:51 mtnormalise
-rwxr-xr-x 1 myusername staff 835 18 Ago 23:33 notfound
-rwxr-xr-x 1 root staff 109184 31 Ott 01:50 peaks2amp
-rwxr-xr-x 1 myusername staff 40007 18 Ago 23:33 population_template
-rwxr-xr-x 1 myusername staff 4482 18 Ago 23:33 responsemean
-rwxr-xr-x 1 root staff 320224 31 Ott 01:42 sh2amp
-rwxr-xr-x 1 root staff 277504 31 Ott 01:57 sh2peaks
-rwxr-xr-x 1 root staff 153800 31 Ott 01:59 sh2power
-rwxr-xr-x 1 root staff 269816 31 Ott 01:43 sh2response
-rwxr-xr-x 1 root staff 302024 31 Ott 01:53 shbasis
-rwxr-xr-x 1 root staff 241040 31 Ott 01:50 shconv
-rwxr-xr-x 1 root staff 617872 31 Ott 01:47 shview
-rwxr-xr-x@ 1 root group 15030 18 Ago 23:33 ss3t_csd_beta1
-rwxr-xr-x 1 root staff 607936 31 Ott 01:46 tck2connectome
-rwxr-xr-x 1 root staff 1008200 31 Ott 01:51 tck2fixel
-rwxr-xr-x 1 root staff 432272 31 Ott 01:45 tckconvert
-rwxr-xr-x 1 root staff 989120 31 Ott 01:59 tckdfc
-rwxr-xr-x 1 root staff 347984 31 Ott 01:50 tckedit
-rwxr-xr-x 1 root staff 2020976 31 Ott 01:53 tckgen
-rwxr-xr-x 1 root staff 674592 31 Ott 01:48 tckglobal
-rwxr-xr-x 1 root staff 220624 31 Ott 01:53 tckinfo
-rwxr-xr-x 1 root staff 1663232 31 Ott 01:45 tckmap
-rwxr-xr-x 1 root staff 371640 31 Ott 01:43 tckresample
-rwxr-xr-x 1 root staff 919112 31 Ott 01:59 tcksample
-rwxr-xr-x 1 root staff 1553920 31 Ott 01:43 tcksift
-rwxr-xr-x 1 root staff 1534936 31 Ott 01:52 tcksift2
-rwxr-xr-x 1 root staff 242520 31 Ott 01:43 tckstats
-rwxr-xr-x 1 root staff 358176 31 Ott 01:42 tcktransform
-rwxr-xr-x 1 root staff 282224 31 Ott 01:50 tensor2metric
-rwxr-xr-x 1 root staff 359552 31 Ott 01:44 transformcalc
-rwxr-xr-x 1 root staff 216648 31 Ott 01:58 transformcompose
-rwxr-xr-x 1 root staff 123928 31 Ott 01:42 transformconvert
-rwxr-xr-x 1 root staff 223048 31 Ott 01:51 tsfdivide
-rwxr-xr-x 1 root staff 201656 31 Ott 01:51 tsfinfo
-rwxr-xr-x 1 root staff 223048 31 Ott 01:47 tsfmult
-rwxr-xr-x 1 root staff 205624 31 Ott 01:45 tsfsmooth
-rwxr-xr-x 1 root staff 205424 31 Ott 01:53 tsfthreshold
-rwxr-xr-x 1 root staff 221312 31 Ott 01:45 tsfvalidate
-rwxr-xr-x 1 root staff 177784 31 Ott 01:43 vectorstats
-rwxr-xr-x 1 root staff 234528 31 Ott 01:59 voxel2fixel
-rwxr-xr-x 1 root staff 548920 31 Ott 01:57 voxel2mesh
-rwxr-xr-x 1 root staff 310728 31 Ott 01:44 warp2metric
-rwxr-xr-x 1 root staff 300744 31 Ott 01:58 warpconvert
-rwxr-xr-x 1 root staff 190440 31 Ott 01:45 warpcorrect
-rwxr-xr-x 1 root staff 148552 31 Ott 01:52 warpinit
-rwxr-xr-x 1 root staff 196032 31 Ott 01:44 warpinvert
Do you have any suggestion to solve this problem?
Thank you.