ASLprep error freesurfer subjects directory in NeurodeskApp

Software Support
,
1

Summary of what happened:

Hello!

I am running aslprep through Neurodesk.
And we are getting back the same error, what we believe does not make sense…

Any help would be appreciated.

Thanks in advance!

Version:

0.7.2

Environment (Docker, Singularity / Apptainer, custom installation):

Neurodesk

I have used the following command (which I have been using for long at it previously worked perfectly):

Command used

aslprep \
neurodesktop-storage/Agueda/BIDS \
neurodesktop-storage/Agueda/BIDS/derivatives/aslprep \
participant \
--participant-label sub-388 \
--force-bbr \
--basil \
 --ignore t2w \
--fs-subjects-dir neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/sourcedata/freesurfer_pre/sourcedata \
--bids-filter-file neurodesktop-storage/Agueda/BIDS/BIDS_filter_file.json \
--fs-license-file neurodesktop-storage/Agueda/BIDS/license.txt \
--skip_bids_validation \
-vv \
-w \
neurodesktop-storage/Agueda/BIDS

We have tried to run without freesurfer pre-existing directory and with --fs-no-reconall command. We also tried using previous version on aslprep (0.6.0 and 0.7.0) and we are receiving the same error all the times.

aslprep \
neurodesktop-storage/Agueda/BIDS \
neurodesktop-storage/Agueda/BIDS/derivatives/aslprep \
participant \
--participant-label sub-388 \
--force-bbr \
--basil \
--ignore t2w \
--fs-no-reconall \
--bids-filter-file neurodesktop-storage/Agueda/BIDS/BIDS_filter_file.json \
--fs-license-file neurodesktop-storage/Agueda/BIDS/license.txt \
--skip_bids_validation \
-vv \
-w neurodesktop-storage/Agueda/BIDS

Relevant Log Outputs

> Traceback (most recent call last):
  File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/cli/workflow.py", line 95, in build_workflow
    retval["workflow"] = init_aslprep_wf()
                         ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 68, in init_aslprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 273, in init_single_subject_wf
    anat_fit_wf = init_anat_fit_wf(
                  ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/smriprep/workflows/anatomical.py", line 749, in init_anat_fit_wf
    anat_template_wf = init_anat_template_wf(
                       ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/smriprep/workflows/anatomical.py", line 1483, in init_anat_template_wf
    StructuralReference(
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/freesurfer/base.py", line 244, in __init__
    super(FSCommandOpenMP, self).__init__(**inputs)
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/freesurfer/base.py", line 134, in __init__
    self.inputs.subjects_dir = self._subjects_dir
    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'subjects_dir' trait of a RobustTemplateInputSpec instance must be a pathlike object or string representing an existing directory, but a value of '/home/jovyan/freesurfer-subjects-dir' <class 'str'> was specified.
2

Just to make sure I understand, when you set --fd-subjects-dirs to that path, you still get the error saying that the subjects dir is /home/jovyan/freesurfer-subjects-dir?

3

Yes, and the thing is we are getting the same error even with --fs-no-reconall and trying to run freesurfer

4

I’m not sure what could be causing that. Can you share the config.toml file and full log files?

5

It stops before generating any log file. config.toml shows this:

[environment]
cpu_count = 20
exec_env = "singularity"
free_mem = 45.6
overcommit_policy = "always"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "24.2.0"
version = "0.7.2"

[execution]
bids_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS"
derivatives = []
bids_database_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/20240916-115054_e08873f6-91db-4804-9846-5236a18ea43c/bids_db"
boilerplate_only = false
sloppy = false
debug = []
aslprep_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep"
fs_license_file = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/license.txt"
fs_subjects_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/sourcedata/freesurfer_pre/sourcedata"
layout = "BIDS Layout: ...urodesktop-storage/Agueda/BIDS | Subjects: 91 | Sessions: 170 | Runs: 0"
log_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep/logs"
log_level = 15
low_mem = false
md_only_boilerplate = false
notrack = false
output_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep"
output_spaces = "MNI152NLin2009cAsym:res-native"
reports_only = false
run_uuid = "20240916-115054_e08873f6-91db-4804-9846-5236a18ea43c"
participant_label = [ "319", "320",]
templateflow_home = "/home/jovyan/.cache/templateflow"
work_dir = "/home/jovyan/neurodesktop-storage/Agueda/BIDS"
write_graph = false

[workflow]
anat_only = false
asl2t1w_dof = 6
asl2t1w_init = "register"
m0_scale = 1
cifti_output = false
dummy_scans = 0
fmap_bspline = false
force_syn = false
hires = true
ignore = [ "t2w",]
level = "full"
longitudinal = false
run_msmsulc = false
medial_surface_nan = false
project_goodvoxels = false
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
use_bbr = true
use_syn_sdc = false
smooth_kernel = 5
scorescrub = false
basil = true

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 20
omp_nthreads = 8
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 13810
ants = 64169
numpy = 28357

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

[execution.bids_filters.t1w]
datatype = "anat"
session = "1"
acquisition = "<Query.NONE: 1>"
suffix = "T1w"

[execution.bids_filters.asl]
datatype = "perf"
session = "1"
suffix = "asl"
6

That is very confusing. I will try to reproduce the error on my end, but it may take a couple of days.

Just on the off chance this is a known issue with recent versions of sMRIPrep (since ASLPrep’s anatomical processing is mostly copied from fMRIPrep and relies on sMRIPrep), @effigies does this error look familiar? No worries if not.

7

Also tagging @stebo85 as this could be a neurodesk hard coding variables thing.

1 Like
8

I haven’t seen this before.

1 Like
9

It seems to be an issue with Neurodesk

1 Like
10

It could be an issue on our side. I have a look.

11

I had a quick look: We set a Freesurfer SUBJECTS_DIR globally in Neurodesk so users don’t have to specify this. Somehow this now interferes with aslprep, but I am not sure why yet.

For now, can you try to unset this variable before running your pipeline?

image
image846×294 59.8 KB

12

Hi @stebo85!
Apologize for the late reply. The thing is that we have precomputed freesurfer outputs and we want to use them. I have tried again and that did not solve our issue.

13

Dear @lucia_sanchez_aranda,

That makes sense! If you want to use precomputed freesurfer outputs can you try to set the Freesurfer variable to this location as well?

export SUBJECTS_DIR=$PWD/freesurfer_pre_computed_output
aslprep ds000240 \
   aslprep-output-with-freesurfer-precomputed \
   participant \
   --participant-label 01 \
   --fs-license-file ~/.license \
   --fs-subjects-dir $SUBJECTS_DIR
   -w aslprep-work-with-freesurfer-precomputed