(1) I cleared my working directory and ran the workflow cleanly, and I realized that the fixedfx directory doesn’t exist anymore because I changed the workflow a bit. (I build my own fixedfx workflow from scratch, rather than loading the pre-made workflow.) The FLAMEO command is now:
flameo --copefile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/copemerge/mapflow/_copemerge0/cope1_merged.nii.gz --covsplitfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.grp --designfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.mat --ld=stats --maskfile=/scratch/groups/hyo/SwiSt/BIDS_data/derivatives/fmriprep/sub-06/func/sub-06_task-tomloc_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz --runmode=fe --tcontrastsfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.con --varcopefile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/varcopemerge/mapflow/_varcopemerge0/varcope1_merged.nii.gz
I checked each of the files in this new command—I can ls
all of them. I tried running this new command inside the Singularity image and got a different error:
flameo --copefile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/copemerge/mapflow/_copemerge0/cope1_merged.nii.gz --covsplitfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.grp --designfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.mat --ld=stats --maskfile=/scratch/groups/hyo/SwiSt/BIDS_data/derivatives/fmriprep/sub-06/func/sub-06_task-tomloc_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz --runmode=fe --tcontrastsfile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/l2model/design.con --varcopefile=/scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/varcopemerge/mapflow/_varcopemerge0/varcope1_merged.nii.gz
Log directory is: stats
Setting up:
ntptsing=2.000000
evs_group=1.000000
Aborted
The command does generate a new stats
directory, but the directory only includes a logfile with a single line (the FSL command).
(2) 5.0.10! Here’s the output when I run the same command on the Terminal:
Log directory is: stats+
Setting up:
ntptsing=2.000000
evs_group=1.000000
No f contrasts
WARNING: The passed in varcope file, /scratch/groups/hyo/swist_cache/l1_model/task-tomloc_model-localizer_sub-06/l1/varcopemerge/mapflow/_varcopemerge0/varcope1_merged.nii.gz, contains voxels inside the mask with zero (or negative) values. These voxels will be excluded from the analysis.
nevs=1
ntpts=2
ngs=1
nvoxels=74434
Running:
nmaskvoxels=74434
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Saving results
Log directory was: stats+
The stats+
directory contains the following files:
[nvelez@sh-06-36 /home/groups/hyo/singularity]$ ls stats+
cope1.nii.gz res4d.nii.gz zflame1lowertstat1.nii.gz
logfile tdof_t1.nii.gz zflame1uppertstat1.nii.gz
mask.nii.gz tstat1.nii.gz zstat1.nii.gz
mean_random_effects_var1.nii.gz varcope1.nii.gz
pe1.nii.gz weights1.nii.gz