gdevenyi
commented
9 years ago I believe autocrop+ is one of our special programs and hasn't made it into a quarantine.
Closed raihaan closed 9 years ago
gdevenyi
commented
9 years ago I believe autocrop+ is one of our special programs and hasn't made it into a quarantine.
gdevenyi
commented
9 years ago I think you had it loaded from matt's homedir or someplace, we'll have to find it.
raihaan
commented
9 years ago Got it, I will poke around and see if I can find it.
pipitone
commented
9 years ago Correct. autocrop+ is just autocrop with two added options to make it possible to autocrop label volumes. I've put the source here: https://gist.github.com/pipitone/b8bea7ee287e9de50a5c
raihaan
commented
9 years ago I see. Stole a copy from your scinet :)
Test currently running
gdevenyi
commented
9 years ago autocrop+ now packaged in minc-toolkit-extra
In using mincmontage_test to create QC images for MAGeT, autocrop+ can't be found. Had this same issue on scinet.
Locally: patrai@cicws25:/data/chamal/projects/raihaan$ ./mincmontage_test -isostep 1 -slices 16 Shaw-3T-data-September8/1201_t1.mnc Shaw-3T-data-September8/MAGeT-output/labels/1201_t1_extracted_labels.mnc Shawtest.png autocrop+ -byte -keep_real_range -nearest_neighbour -isostep 1 Shaw-3T-data-September8/MAGeT-output/labels/1201_t1_extracted_labels.mnc /tmp/mincmontage_test-2VNOzEJMIGp/isostep_labels.mnc Can't exec "autocrop+": No such file or directory at ./mincmontage_test line 222. Died at ./mincmontage_test line 222.
On scinet: autocrop+ -byte -keep_real_range -nearest_neighbour -isostep 1 ../scratch/Lepage/output/fusion/majority_vote/2001_labels.mnc /tmp/mincmontage_test-IbKzTn903kg/isostep_labels.mnc [autocrop+] [patelmo6@gpc-f102n084-ib0:/home/m/mchakrav/patelmo6/scripts] [2014-09-20 18:35:55] /project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/bin/mincreshape -byte -keep_real_range -nearest_neighbour ../scratch/Lepage/output/fusion/majority_vote/2001_labels.mnc /tmp/mincmontage_test-IbKzTn903kg/isostep_labels.mnc -start 0,180,235 -count 182,-182,-236
Usage: /project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/bin/mincreshape []
/project/m/mchakrav/quarantine/minc-toolkit/1.0.01/build/bin/mincreshape [-help]
autocrop+: crashed while running mincreshape (termination status=256) Died at ./mincmontage_test line 222.
Not sure if this is of any importance, but I successfully ran mincmontage_test ~2 weeks ago (locally)