Hi AFNI gurus and enthusiasts,
I'm running into a few puzzling, related problems with uber_subject.py.
After filling out the fields in the GUI, I click on the upper left document icon, which sets up the familiar folder structure and creates "cmd.ap.subj" in the subj folder. However, clicking on the right upper document icon produces an error message: "cmd.ap.subj: No such file or directory.". An error log ("output.cmd.ap.test" stating "cmd.ap.test: No such file or directory.") is created in the $top_dir (bc it looks for cmd.ap.subj there, instead of the subj folder). The $top_dir is always the shell login directory, i.e., it doesn't matter from which directory I call the uber_subject.py GUI, it always sets the login directory as $top_dir.
Executing cmd.ap.test in the subj folder (the only file created) generates the expected proc script - in the $top_dir, not in the subj folder as usual. Making some minor changes to the proc script (e.g., adding full paths to input/result directories; same changes I've made to other proc scripts on other systems that worked without problems) and executing it results in early termination as stats.REML_cmd looks for X.xmat.1D in the $top_dir, not the subj folder. The proc script cds into the subj folder and executes stats.REML_cmd from there...so I don't know why/how stats.REML_cmd looks in the $top_dir?! (There are problems with generating some of the review scripts/outputs down the line, too.)
Could this be related to using ~/.cshrc.local and ~/.cshrc pointing to some .cshrc.master (but I can't see how anything in that file would lead to my problems)? I'm working on a remote server that is shared among many users.
Thank you very much for your help in advance!
Nic
#########
######### uber_subject.py output (cmd.ap.test) #########
#########
#!/usr/bin/env tcsh
# created by uber_subject.py: version 0.41 (October 10, 2017)
# creation date: Wed Nov 29 19:22:40 2017
# set subject and group identifiers
set subj = subj
set gname = bh.9457
# set data directories
set top_dir = /data1/nschwarz
set anat_dir = $top_dir/data/subj
set epi_dir = $top_dir/data/subj
set stim_dir = $top_dir/projects/cvr/analyses/bh/glm/scripts
# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_dir/subj_T1w+orig \
-dsets $epi_dir/subj_BOLD_air_breathhold_mag+orig.HEAD \
-tcat_remove_first_trs 0 \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 3.0 \
-regress_stim_times $stim_dir/stimtimes.txt \
-regress_stim_labels \
bh \
-regress_basis 'TENT(9,45,7)' \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts
#########
######### System information #########
#########
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-358.el6.x86_64
version: #1 SMP Tue Jan 29 11:47:41 EST 2013
distribution: Red Hat Enterprise Linux Server 6.4 Santiago
number of CPUs: 20
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /cm/shared/abin/afni
afni version : Precompiled binary linux_openmp_64: Oct 12 2017
: AFNI_17.3.00
AFNI_version.txt : AFNI_17.3.00, linux_openmp_64, Oct 12 2017
which python : /cm/shared/anaconda/bin/python
python version : 2.7.14
which R : /cm/shared/anaconda/bin/R
R version : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/cm/shared/abin/afni)
R : 3
/cm/shared/anaconda2/bin/R
/usr/local/bin/R
/cm/shared/anaconda3/bin/R
python : 3
/cm/shared/anaconda2/bin/python2.7
/usr/bin/python
/cm/shared/anaconda3/bin/python3.6
python2 : 2
/cm/shared/anaconda2/bin/python2.7
/usr/bin/python
python3 : 1 (/cm/shared/anaconda3/bin/python3.6)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE <--- Will be updated soon :)
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lme4!
These packages are not installed on the computer: psych!
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /cm/shared/anaconda/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /cm/shared/PALM:/cm/shared/micutil:/home/nschwarz/.local/bin:/cm/shared/mypytools:/cm/shared/bxh_xcede_tools-1.11.1-lsb30.x86_64/bin:/cm/shared/freesurfer-6.0.0/bin:/cm/shared/freesurfer-6.0.0/fsfast/bin:/cm/shared/freesurfer-6.0.0/tktools:/cm/shared/fsl-5.0.10/bin:/cm/shared/freesurfer-6.0.0/mni/bin:/cm/shared/fsl-5.0.10/bin:.:/home/nschwarz/bin:/home/nschwarz/bin/fsl:/cm/shared/fix:/cm/shared/ICA-AROMA:/cm/shared/workbench1.2.3/bin_rh_linux64:/cm/shared/ants-2.1.0:/cm/shared/spm12-standalone:/cm/shared/mricrogl:/cm/shared/mricron:/cm/shared/freesurfer/bin:/cm/shared/freesurfer/fsfast/bin:/cm/shared/freesurfer/tktools:/cm/shared/fsl/bin:/cm/shared/freesurfer/mni/bin:.:/cm/shared/anaconda/bin:/cm/shared/apps/sge/current/bin/UNSUPPORTED-lx-amd64:/cm/shared/fsl/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/opt/ibutils/bin:/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/cm/shared/apps:/cm/shared/apps/sge/current/bin/lx-amd64:/cm/shared/apps/sge/current/utilbin/lx-amd64:/cm/shared/apps/MATLAB/R2014a/bin:/cm/shared/apps/SublimeText2:/cm/shared/abin:/cm/shared/anaconda2/bin:/cm/shared/anaconda3/bin:/cm/shared/abin/afni
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /cm/shared/abin
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.2.29
========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
