Error at infant_recon_all stage

[sb8498]

participants.json
dataset_description.json

What happened?

I am trying to run Nibabies with derivatives from BIBSNet. I get an error log that infant_recon_all couldn't be performed because it couldn't access "brain.nii.gz".

sub-06_ses-1_infant_recon_all.2502281351.log
summary.sub-06_ses-1_infant_recon_all.2502281351.log

What command did you use?

`sudo docker run --rm -it -v /media/devcogpsy/EXTERNAL_US/MOTOSO:/input -v /media/devcogpsy/EXTERNAL_US/MOTOSO:/output -v /home/devcogpsy/freesurfer:/fs-subjects-dir -v /media/devcogpsy/EXTERNAL_US/MOTOSO/bibsnet:/derivatives --entrypoint /bin/bash nipreps/nibabies:latest

nibabies /input /output participant --participant-label 06 --fs-license-file /fs-subjects-dir/license.txt --anat-only --derivatives derivatives=/input/bibsnet --nprocs 20 --nthreads 2`

What version of NiBabies are you using?

24.1.0

Relevant log output

`Cmdline:
infant_recon_all --age 13 --segfile /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz --masked /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/apply_t1w_mask/clipped_masked.nii.gz --outdir /output/sourcedata/freesurfer/sub-06_ses-1 --subject sub-06_ses-1
Stdout:
InfantReconAll scripts DIR /opt/freesurfer/bin
PWD /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/infantfs_surface_recon_wf/reconall

Log file is /output/sourcedata/freesurfer/sub-06_ses-1/work/sub-06_ses-1_infant_recon_all.2502281351.log

Fri Feb 28 13:51:15 UTC 2025
--age 13 --segfile /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz --masked /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/apply_t1w_mask/clipped_masked.nii.gz --outdir /output/sourcedata/freesurfer/sub-06_ses-1 --subject sub-06_ses-1
infant_recon_all infant-dev-4a14499
b41660d545c9
Linux b41660d545c9 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
Processing the following subject: sub-06_ses-1
mri_convert --conform-dc /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/apply_t1w_mask/clipped_masked.nii.gz /output/sourcedata/freesurfer/sub-06_ses-1/work/mprage.nu.conf.masked.nii.gz 
reading from /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/apply_t1w_mask/clipped_masked.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.995006, 0.0998159, -9.07845e-08)
j_ras = (-0.0998159, 0.995006, -2.52974e-08)
k_ras = (8.7806e-08, 3.42328e-08, 1)
keeping DC 0 2 1
ostr RAS, width 256, size 1
K ---------------
-0.80000   0.00000   0.00000   211.00000;
 0.00000   0.00000  -0.80000   256.00000;
 0.00000   0.80000   0.00000   8.00000;
 0.00000   0.00000   0.00000   1.00000;
Kinv ---------------
-1.25000  -0.00000  -0.00000   263.75000;
-0.00000  -0.00000   1.25000  -10.00000;
-0.00000  -1.25000  -0.00000   320.00000;
-0.00000  -0.00000  -0.00000   1.00000;
Smri ---------------
 0.79600  -0.07985   0.00000  -73.54336;
 0.07985   0.79600   0.00000  -106.09596;
-0.00000  -0.00000   0.80000  -125.97798;
 0.00000   0.00000   0.00000   1.00000;
Stemp ---------------
-0.99501  -0.00000  -0.09982   137.20143;
-0.09982  -0.00000   0.99501  -92.99484;
 0.00000  -1.00000  -0.00000   130.02200;
 0.00000   0.00000   0.00000   1.00000;
----------------------
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 223 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation 
writing to /output/sourcedata/freesurfer/sub-06_ses-1/work/mprage.nu.conf.masked.nii.gz...
MASKED FILE /output/sourcedata/freesurfer/sub-06_ses-1/work/mprage.nu.conf.masked.nii.gz
WORKING WITH EXISTING SEGMENTATION FILE /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz
mri_convert --conform-dc /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz /output/sourcedata/freesurfer/sub-06_ses-1/work/finalaseg.nii.gz -rt nearest --no_scale 1 
INFO: using NIfTI-1 qform 
reading from /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.995006, 0.0998159, -9.07845e-08)
j_ras = (-0.0998159, 0.995006, -2.52974e-08)
k_ras = (8.7806e-08, 3.42328e-08, 1)
keeping DC 0 2 1
ostr RAS, width 256, size 1
K ---------------
-0.80000   0.00000   0.00000   211.00000;
 0.00000   0.00000  -0.80000   256.00000;
 0.00000   0.80000   0.00000   8.00000;
 0.00000   0.00000   0.00000   1.00000;
Kinv ---------------
-1.25000  -0.00000  -0.00000   263.75000;
-0.00000  -0.00000   1.25000  -10.00000;
-0.00000  -1.25000  -0.00000   320.00000;
-0.00000  -0.00000  -0.00000   1.00000;
Smri ---------------
 0.79600  -0.07985   0.00000  -73.54336;
 0.07985   0.79600   0.00000  -106.09596;
-0.00000  -0.00000   0.80000  -125.97798;
 0.00000   0.00000   0.00000   1.00000;
Stemp ---------------
-0.99501  -0.00000  -0.09982   137.20143;
-0.09982  -0.00000   0.99501  -92.99485;
 0.00000  -1.00000  -0.00000   130.02199;
 0.00000   0.00000   0.00000   1.00000;
----------------------
Reslicing using nearest 
writing to /output/sourcedata/freesurfer/sub-06_ses-1/work/finalaseg.nii.gz...
/output/sourcedata/freesurfer/sub-06_ses-1/work/sub-06_ses-1/mri /tmp/work/nibabies_24_1_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/infantfs_surface_recon_wf/reconall 
mri_convert norm.nii.gz norm.mgz 
reading from norm.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.995006, -0.0998159, 9.07845e-08)
j_ras = (-8.7806e-08, -3.42328e-08, -1)
k_ras = (-0.0998159, 0.995006, -2.52974e-08)
writing to norm.mgz...
ln: failed to create symbolic link 'brain.nii.gz': Operation not permitted

Stderr:

Traceback:
RuntimeError: subprocess exited with code 1.
`

Add any additional information or context about the problem here.

This issue does not occur when I try to run Nibabies without the --derivatives flag.

[mgxd]

Sounds like you don't have sufficient permission for your --derivatives directory or files - can you expand permissions to ensure they can be accessed/copied?

[sb8498]

Since posting the issue, I have run the same commands with proper permissions and I have been able to solve the error. However, the reconall runs smoothly but in the log it shows that BIBSNet derivatives were not used. I have attached the summary and log file of the recon all process from /sourcedata/freesurfer/sub-06_ses-1/log

sub-06_ses-1_infant_recon_all.2502201554.log
summary.sub-06_ses-1_infant_recon_all.2502201554.log

[mgxd]

@sb8498 infant FS will used the already masked t1w, as well as the precomputed aseg if available, so the mask is not needed.

[sb8498]

Is there a way to force infant FS (within Nibabies) to use the segmentation and masks obtained from BIBSNet instead?

[mgxd]

If precomputed mask / segmentation are found, they will be used - do you have any indication the seg was found in your log prior to infant recon all? I added #452 to simplify this for future versions

[sb8498]

[environment]
cpu_count = 24
exec_env = "singularity"
free_mem = 56.7
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "24.2.2"
version = "24.1.0"

[execution]
bids_dir = "/input"
bids_database_dir = "/tmp/work/20250228-113719_7198d0c5-bbe1-4ad1-9097-b0061c8b40db/bids_db"
bids_description_hash = "910d47240f374feb04ecca2e7b7069178c02c5eaba2ae2b2c286ac265238a578"
boilerplate_only = false
copy_derivatives = false
sloppy = false
debug = []
fs_license_file = "/fs-subjects-dir/license.txt"
fs_subjects_dir = "/output/sourcedata/freesurfer"
layout = "BIDS Layout: .../input | Subjects: 1 | Sessions: 1 | Runs: 0"
log_dir = "/output/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
nibabies_dir = "/output"
notrack = false
output_dir = "/output"
me_output_echos = false
output_layout = "bids"
reports_only = false
run_uuid = "20250228-113719_7198d0c5-bbe1-4ad1-9097-b0061c8b40db"
participant_label = [ "06",]
templateflow_home = "/home/nibabies/.cache/templateflow"
unique_labels = [ [ "06", "1",],]
work_dir = "/tmp/work"
write_graph = false

[workflow]
analysis_level = "participant"
anat_only = true
bold2anat_dof = 6
bold2anat_init = "auto"
cifti_output = false
fd_radius = 45
fmap_bspline = false
force_syn = false
hires = true
hmc_bold_frame = 16
ignore = []
level = "full"
longitudinal = false
medial_surface_nan = false
project_goodvoxels = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "UNCInfant:cohort-1"
skull_strip_anat = "force"
slice_time_ref = 0.5
surface_recon_method = "auto"
use_bbr = false
use_syn_sdc = false
me_t2s_fit_method = "curvefit"

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 2
omp_nthreads = 1
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 44053
ants = 40229
numpy = 2459

[execution.dataset_links]
raw = "/input"
templateflow = "/home/nibabies/.cache/templateflow"
derivatives = "/input/bibsnet"

[execution.derivatives]
derivatives = "/input/bibsnet"

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

This was the content of the file nibabies.toml.

[execution.dataset_links]
raw = "/input"
templateflow = "/home/nibabies/.cache/templateflow"
derivatives = "/input/bibsnet"

[execution.derivatives]
derivatives = "/input/bibsnet" 

----I assumed this must mean that derivatives are being recognized?

[mgxd]

That just means you have passed in a derivatives folder.

Can you try running with the latest unstable version? It should be more clear on what data has been found. Here is a sample log using verbose

[sb8498]

sub-06_ses-1_infant_recon_all.2503061726.log
nibabies_sub06.log

Here are the logs from nibabies and specifically infant_recon_all - run with 25.0.1.

[mgxd]

Looks like the bibsnet segmentations are being used, along with the masked T1w file, from the infant_recon_all log:

Logfile for infant_recon_all
Thu Mar 6 17:26:26 UTC 2025
--age 13 --segfile /input/bibsnet/sub-06/ses-1/anat/sub-06_ses-1_space-T1w_desc-aseg_dseg.nii.gz --masked /tmp/work/nibabies_25_0_wf/single_subject_sub-06_ses-1_wf/infant_anat_fit_wf/apply_t1w_mask/clipped_masked.nii.gz --outdir /output/sourcedata/freesurfer/sub-06_ses-1 --subject sub-06_ses-1

[mgxd]

Closing, please reopen if still having problems