[Freesurfer] freesurfer-7.1.1-centos8.rpm :: problems
External Email - Use Caution Hello, I installed freesurfer-7.11 from centos8 rpm on stock docker centos8 image: there is some problems // misses with this installation 1) some scripts are python and uses /usr/bin/env python which is not available by default on centos8 currently freesurfer rpm specfile should have a dependency to python2, and associated python required modules, ie: dipy graph_tools holoviews plotly statsmodels pyyaml in that case, following files sheebang should be modified slicedelay dsh mcparams2reg rca-config2csh shebang should be /usr/bin/env python2 instead of /usr/bin/env python other solution will be to port those scripts to python3 and use fspython 2) some scripts are tclsh ones but no tclsh installed. eg unpackimadir2, unpacksdcmdir. fsgfget please add tcl rpm dependency to rpm specfile 3) tools depending on MRC matlab runtime segmentSubjectT2_autoEstimateAlveusML segmentSubjectT1_autoEstimateAlveusML segmentSubject segmentSubjectT1T2_autoEstimateAlveusML SegmentThalamicNuclei SegmentSubfieldsT1Longitudinal irepifitvol.glnx64 and fs_spmreg.glnxa64 are linked versus libmwmclmcrrt.so.8.3 which is not provided by mcr runtime R2014b but version 8.4 is. and by the way libncurses-devel is required as rpm dependency 4) some tools uses commands that are not available show_tal, tal_compare uses mri_show which is not avaialble 5) qdec tcl have invalid environement configuration Singularity> qdec Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/lib/tcl8.4 /usr/local/freesurfer/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/library /usr/local/freesurfer/library /usr/local/freesurfer/tcl8.4.6/library /usr/local/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 you may want to add $FREESURFER_HOME/lib/tktools/tcl8.4 to TCL_LIBRARY regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script
External Email - Use Caution Le 03/06/2021 à 15:53, Eric Deveaud a écrit : > External Email - Use Caution > > Le 03/06/2021 à 13:46, Eric Deveaud a écrit : >> External Email - Use Caution >> >> Hello, >> >> >> While installing freesurfer-7.1.1 for centos via rpm >> (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: >> >> /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that >> use /usr/bin/env python, not fspython which is 3.6.8 >> >> either python2 should added as rpm requirement, either mcparams2reg >> should ported to python3 > > same problem with slicedelay > same problem with dsh Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer-7.1.1 "" anatomiCutsUtils :: missing lzma python module
External Email - Use Caution Hello, freesurfer-centos8-7.1.1 rpm installa in singularity container Singularity> anatomiCutsUtils -h /usr/local/freesurfer/7.1.1-1/python/packages/pandas/compat/__init__.py:117: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. warnings.warn(msg) Traceback (most recent call last): File "/usr/local/freesurfer/7.1.1-1/python/scripts/anatomiCutsUtils", line 19, in import graph_tools as gt ModuleNotFoundError: No module named 'graph_tools' regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script
External Email - Use Caution Le 03/06/2021 à 13:46, Eric Deveaud a écrit : > External Email - Use Caution > > Hello, > > > While installing freesurfer-7.1.1 for centos via rpm > (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: > > /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that > use /usr/bin/env python, not fspython which is 3.6.8 > > either python2 should added as rpm requirement, either mcparams2reg > should ported to python3 same problem with slicedelay Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found
External Email - Use Caution Le 03/06/2021 à 14:54, Eric Deveaud a écrit : > External Email - Use Caution > > Hello freesurfer-7.1.1 installed from rpm on centos8 > > show_tal tries to call mri_shown a non existing program in > /usr/local/freesurfer/7.1.1/bin tal_compare, same problem regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer-7.1.1 :: rebuild_gca_atlas.csh :: missing subjects.csh
External Email - Use Caution subjects.csh is not installed but rebuild_gca_atlas.csh requires it best regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found
External Email - Use Caution Hello freesurfer-7.1.1 installed from rpm on centos8 show_tal tries to call mri_shown a non existing program in /usr/local/freesurfer/7.1.1/bin regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script
External Email - Use Caution Hello, While installing freesurfer-7.1.1 for centos via rpm (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that use /usr/bin/env python, not fspython which is 3.6.8 either python2 should added as rpm requirement, either mcparams2reg should ported to python3 regards Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
