I am trying to install an older version (18.2.15) of AFNI on my computer (MacOS 10.14.5) but I have been unsuccessful so far… From what I understand it seems like the only way to install an older version of AFNI is to recompile it from source with the command @get.afni.version 18.2.15.
After doing that I figured one needs to copy the right Makefile (in my case Makefile.macos_10.12_local) which does not work at all, specifically because it looks for some files that are simply not there. Specifically all the files in the /sw directory. I don’t know when or by what this directory is supposed to be created but it wasn’t in my case.
I then tried using Makefile.macosx_10.10_Intel_64 as there was no /sw involved, but here I get this output :
10 warnings generated.
/bin/rm -f to3d
/usr/bin/gcc -O2 -DDARWIN -m64 -Wall -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -o to3d to3d.o -L. -L/usr/X11R6/lib -L/usr/lib -L/usr/local/lib -L/usr/X11R6/lib -L/usr/local/lib -lpython2.7 -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load -Wl,-no_compact_unwind -lmrix -lcoxplot -lmri -lf2c /usr/local/lib/libXm.a -lXt -lXft -lfontconfig /usr/local/lib/libpng.a -liconv -lXmu -lXp -lXpm -lXext -lX11 -lz /usr/local/opt/expat/lib/libexpat.a -lm -lc
Undefined symbols for architecture x86_64:
“_jpeg_CreateDecompress”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_calc_output_dimensions”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_destroy_decompress”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_finish_decompress”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_read_header”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_read_scanlines”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_start_decompress”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_std_error”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
“_jpeg_stdio_src”, referenced from:
_load_jpeg in libXm.a(Jpeg.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [to3d] Error 1
Any advice on how to install am older version as I was not able to find that answer on the board?
Best regards,
Augustin
I’ll also add that if you wanted to, you could build any version of AFNI using the github pull and an updated Makefile that I wrote specifically for 10.14 (probably 10.13 too) that uses homebrew for dependencies and Anaconda for Python. It’s part of the distribution and a solid starting point. Let me know if you have questions should you decide to build other iterations.
Hi Rick,
“Not trivial” to say the least indeed ^^" Thank you very much for the binaries! I’m running the script and it seems to be working like a charm.
Is there any conflict to expect if I want to switch back to the new version (the way I would do it is to rename the abin directory abin_18.2.15 and the abin_19.6 directory abin).
Thanks again,
Augustin
I am working on data analyses of resting-state fMRI with children on a MacOs Mojave 10.14.6 In October 2018 I installed AFNI v18.3.01 and C-PAC v1.3.0 (https://fcp-indi.github.io/docs/user/index.html) as I was working at the Child Mind Institute with the C-PAC developers. The software worked well for me until I updated AFNI last July to v19.2.00, when C-PAC started crashing due to a bug that miscommunicated the pipeline with the upgraded AFNI.
I would like to try downgrading AFNI to that specific version and see if I could make the pipeline work again. Do you happen to have a compilation of that version for my Mac?
Thank you very much for the quick response and the compilation, Rick!
I am not sure of what is exactly the problem but had to do with the seed-based correlation analyses. However, C-PAC was updated as well and I had a merge of versions of AFNI and C-PAC that were not working. I am trying now to use the same software that worked for me in October, let’s see if it works.
I am having the same issue with 3dTcorr1d in CPAC after updating afni in July. Error is below. I am in Ubuntu 16.04.
I need to get an older version of afni (pre June 2019) for Ubuntu 16.04. Is this possible? Otherwise I am quite stuck.
error:
3dTcorr1D main
** Command line was:
3dTcorr1D -pearson -prefix scrubbed_preprocessed_correlation.nii.gz /home/jlee38/RS/wrk/resting_preproc_113051-100/sca_roi_0/_scan_funcf/_threshold_0.25/_compcor_ncomponents_5_selector_pc10.linear1.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_tt_mask_pad/3dTCorr1D/scrubbed_preprocessed.nii.gz /home/jlee38/RS/wrk/resting_preproc_113051-100/roi_timeseries_for_sca_0/_scan_funcf/_threshold_0.25/_compcor_ncomponents_5_selector_pc10.linear1.wm1.global1.motion1.quadratic0.gm0.compcor0.csf1/_bandpass_freqs_0.008.0.08/_mask_tt_mask_pad/3dROIstats/roi_stats.csv
** AFNI compile date = Jun 25 2019
** [[Precompiled binary linux_openmp_64: Jun 25 2019]]
** Program Crash **
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=452) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
THD_datablock_apply_atr – brick statistics {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=452) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
+++++++THD_find_atr [7]: {ENTRY (file=thd_atr.c line=408) from THD_datablock_apply_atr {500 ms}
-------THD_find_atr [7]: EXIT} (file=thd_atr.c line=448) to THD_datablock_apply_atr {500 ms}
------THD_datablock_apply_atr [6]: EXIT} (file=thd_initdblk.c line=1178) to THD_open_nifti {500 ms}
-----THD_open_nifti [5]: EXIT} (file=thd_niftiread.c line=800) to THD_open_one_dataset {500 ms}
+++++THD_patch_brickim [5]: {ENTRY (file=thd_loaddblk.c line=1274) from THD_open_one_dataset {500 ms}
-----THD_patch_brickim [5]: EXIT} (file=thd_loaddblk.c line=1313) to THD_open_one_dataset {500 ms}
+++++THD_report_obliquity [5]: {ENTRY (file=thd_coords.c line=704) from THD_open_one_dataset {500 ms}
++++++AFNI_process_environ [6]: {ENTRY (file=afni_environ.c line=112) from THD_report_obliquity {500 ms}
+++++++AFNI_suck_file [7]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ {500 ms}
-------AFNI_suck_file [7]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ {500 ms}
------AFNI_process_environ [6]: EXIT} (file=afni_environ.c line=132) to THD_report_obliquity {500 ms}
-----THD_report_obliquity [5]: EXIT} (file=thd_coords.c line=711) to THD_open_one_dataset {500 ms}
----THD_open_one_dataset [4]: EXIT} (file=thd_opendset.c line=252) to THD_open_dataset {500 ms}
++++THD_patch_brickim [4]: {ENTRY (file=thd_loaddblk.c line=1274) from THD_open_dataset {500 ms}
----THD_patch_brickim [4]: EXIT} (file=thd_loaddblk.c line=1313) to THD_open_dataset {500 ms}
—THD_open_dataset [3]: EXIT} (file=thd_mastery.c line=171) to 3dTcorr1D main {500 ms}
+++mri_read_1D [3]: {ENTRY (file=mri_read.c line=2997) from 3dTcorr1D main {500 ms}
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