AC/PC Or Normalization 1 Mandatory argument write of None has no value

[ansleymartin04]

Hello,

Here is the breakdown of the issue to the most useful detail I can provide. I am new to Morphologist and BrainVISA, but have done my due diligence to the best of my ability by consulting this discussion board, all of the tutorials I can find, the manuals, and Claude. Please help, thank you.

Environment (running on my local Neurodesk environment because I use Mac Silicon):

• BrainVISA 6.0.36 running inside Neurodesk (Docker, Linux)
• Morphologist 2025 pipeline
• Database ontology: morphologist-bids-2.0

Data:

• HCP T1w_acpc_dc_restore.nii.gz — native space, AC-PC aligned, bias-corrected, 0.7mm isotropic, float32,
  shape (260, 311, 260)
• Staged to morpho_raw/.nii.gz, imported via Import T1 MRI (multiple) into a morphologist-bids-2.0
  database
• Results in: sub-/ses-morpho_raw/run-0/sub-_ses-morpho_raw_run-0_desc-conform_T1w.nii.gz
• Note: when imported, the terminal said BrainVisa converted the files into SBIT16, hence the "_desc_conform." This becomes important, I think, because the first few trials I successfully ran with the morphologist did not have the autopopulated output name include the "_desc_conform" part when imported.

Error (consistent across subjects):
RuntimeError: Mandatory argument write of None has no value
in Normalization pipeline
in AC/PC Or Normalization
in Morphologist 2025

Partial outputs present before failure:

• sub-_ses-morpho_raw_run-0_normalized_SPM.nii — SPM normalisation output exists
• sub-_ses-morpho_raw_run-0_sn.mat — SPM deformation matrix exists
• No segmentation, meshes, or sulcal graphs produced

Observation:
One subject processed successfully in an earlier test using an identical T1 file placed directly in the database root folder (named T1w_acpc_dc_restore.nii.gz), which produced a ses-HCP session and completed through to sulcal graphs and a morphologist report PDF. Additionally, last week I ran a few more files through Morphologist in a database identical to my current structure, and they worked, so I iterated through multiple files. In the morning, it crashed. Then everything went downhill, and I have received this error ever since. The difference between that run and the current failing batch is unclear.

Here are the solutions I have tried:

• inspected ontology (several times)

• completely rebuilt my directory from the zipped download from HCP to a clean input with the .nii.gz files, made a new database, reimported all of the files, and attempted again. Same error.

• I tried running the tester file on my Neurodesk.play (different instance) and got oddly a different error, which I included as "Error 2" at the bottom.

• I have tried doing the AC/PC registration manually, still did not process through. Which really confused me.

• I double-checked SPM in preferences, and it appears to be correct.

• Claude seems to think that the difference in resolution between HCP data and SPM is the issue.
  Claude's comments below:
  "Suspected cause (from community posts): The SPM normalization FOV quality check compares voxel count of the
  normalised output (~4.6M at 1mm) against the conform input. At 0.7mm (~21M voxels), the ratio is ~0.35, below
  the 0.6 threshold. This may trigger a retry that corrupts the MNI referential, leaving the write output
  unresolvable.

  Questions:

  1. Is 0.7mm HCP data supported as direct input to Morphologist 2025, or does it require resampling to 1mm
     before import?
  2. If resampling is required, should it be done before import (on the staged files) or after import (on the
     desc-conform files)?
  3. Is there a configuration parameter to adjust the FOV check threshold for higher-resolution data?"

Error 1 (main error):
?Process Morphologist 2025 started on 2026/06/29 14:02
?Process Aims Converter started on 2026/06/29 14:02
?Process Aims Converter finished on 2026/06/29 14:02 (1 seconds)
Trying 1st pass of normalization...
?Process Anatomy Normalization (using SPM12) started on 2026/06/29 14:02
?Process spm12 - Old normalise: Estimate & Write - generic started on 2026/06/29 14:02
?Process spm12 - Old normalise: Estimate & Write - generic finished on 2026/06/29 14:03 (29 seconds)
?Process Anatomy Normalization (using SPM12) finished on 2026/06/29 14:03 (29 seconds)
the normalization has probably failed and the field of view is wrong
1st pass failed, changing internal transformation initialization
?Process Reset internal image transformation started on 2026/06/29 14:03
?Process Reset internal image transformation finished on 2026/06/29 14:03 (0 seconds)
Retrying normalization after changing initialization...
?Process Anatomy Normalization (using SPM12) started on 2026/06/29 14:03
?Process spm12 - Old normalise: Estimate & Write - generic started on 2026/06/29 14:03
?Process spm12 - Old normalise: Estimate & Write - generic finished on 2026/06/29 14:03 (23 seconds)
?Process Anatomy Normalization (using SPM12) finished on 2026/06/29 14:03 (23 seconds)
? in SPM Normalization Pipeline 1 Mandatory argument write of None has no value
RuntimeError
RuntimeError: Mandatory argument write of None has no value
? in Normalization pipeline 1 Mandatory argument write of None has no value
RuntimeError
RuntimeError: Mandatory argument write of None has no value
? in AC/PC Or Normalization 1 Mandatory argument write of None has no value
RuntimeError
RuntimeError: Mandatory argument write of None has no value
? in Morphologist 2025 1 Mandatory argument write of None has no value
RuntimeError
RuntimeError: Mandatory argument write of None has no value

Error 2:
" t1mri = /home/jovyan/Desktop/HCP/T1w_acpc_dc_restore.nii.gz
perform_normalization = True
anterior_commissure = [90.0002670288086, 92.11294555664062, 114.27655029296875]
posterior_commissure = [89.79739159811288, 120.67088449001312, 112.43509008735418]
interhemispheric_point = [90.31357981264591, 126.47017651796341, 61.65425541996956]
left_hemisphere_point = None
t1mri_nobias = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/segmentation/sub-T1w_acpc_dc_restore_ses-HCP_run-0_nobias.nii.gz
histo_analysis = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/segmentation/sub-T1w_acpc_dc_restore_ses-HCP_run-0_nobias.han
split_brain = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/segmentation/sub-T1w_acpc_dc_restore_ses-HCP_run-0_voronoi.nii.gz
left_graph = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/folds/3.1/sub-T1w_acpc_dc_restore_ses-HCP_run-0_hemi-L.arg
right_graph = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/folds/3.1/sub-T1w_acpc_dc_restore_ses-HCP_run-0_hemi-R.arg
perform_sulci_recognition = True
left_labelled_graph = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/folds/3.1/sul-0_auto/sub-T1w_acpc_dc_restore_ses-HCP_run-0_sul-0_hemi-L_auto.arg
right_labelled_graph = /home/jovyan/Desktop/HCP/sub-T1w_acpc_dc_restore/ses-HCP/run-0/ana-0/folds/3.1/sul-0_auto/sub-T1w_acpc_dc_restore_ses-HCP_run-0_sul-0_hemi-R_auto.arg
allow_multithreading = True
Output
?Process Morphologist 2025 started on 2026/06/29 11:28
? in Morphologist 2025 1
RuntimeError: System command exited with non null value : 111"

I am happy to provide any additional information that may be of help. Thank you for your time. Have a good day.

[denisri]

Hi,
It seems that a parameter in the process "SPM sn3d to Aims transformation converter" has not been automatically filled (as it should have been) and has been left empty.
However the first suspicious thing I see in the log you send is that the imported T1 MRI is named sub-_ses-morpho_raw_run-0_desc-conform_T1w.nii.gz, see the sub-_ses...: the subject part is empty, which is not normal and possibly causes problems.
You say you have used the "Import T1 MRI (multiple)" process for importation.
This process should look like this (for just 1 subject here):

here I have selected files (one in my case) in inputs, selected a valid output_database (/tmp/bv in this example), then parameters completion should work, outputs and subjects fields should contain something. subjects is the list of subjects IDs (100206 etc for HCP), you can edit and change them if you wish, and those subjects IDs should appear in outputs filenames as sub-100206 etc. You see here that there is this subject ID after the sub- prefix of the BIDS filenames.
I guess this part has failed, and then later problems arise from this one (I hope).

[ansleymartin04]

Hello, thank you for your quick response.

Error two was from a single-subject text, so it did not have a subject number to start. It also ran successfully at first, but then when I tried again, it did not. The main issue is error one, this is an example of the path to an imported T1: `/home/jovyan/neurodesktop-storage/BV_import/sub-102614/ses-morpho_raw/run-0/sub-102614_ses-morpho_raw_run-0_desc-conform_T1w.nii.gz'

My primary issue is with this error here "in SPM Normalization Pipeline 1 Mandatory argument write of None has no value
RuntimeError" How can I fix the parameter in the process "SPM sn3d to Aims transformation converter"?

[ansleymartin04]

This is the full error for Error one: ? in Morphologist 2025 1 Mandatory argument write of None has no value

RuntimeError
Traceback (most recent call last):
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3443, in _processExecution
result = process.execution(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 1668, in execution
return self._executionNode.run(context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2760, in _run
result.append(node.run(context))
^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2634, in _run
return context.runProcess(self._process)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3129, in runProcess
result = self._processExecution(_process, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3443, in _processExecution
result = process.execution(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 1668, in execution
return self._executionNode.run(context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2867, in _run
res = node.run(context)
^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2760, in _run
result.append(node.run(context))
^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2634, in _run
return context.runProcess(self._process)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3129, in runProcess
result = self._processExecution(_process, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3443, in _processExecution
result = process.execution(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 1668, in execution
return self._executionNode.run(context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2867, in _run
res = node.run(context)
^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2634, in _run
return context.runProcess(self._process)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3129, in runProcess
result = self._processExecution(_process, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3443, in _processExecution
result = process.execution(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 1668, in execution
return self._executionNode.run(context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2760, in _run
result.append(node.run(context))
^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2316, in run
return self._run(context)
^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 2634, in _run
return context.runProcess(self._process)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3128, in runProcess
self._setArguments(_process, *args, **kwargs)
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 3089, in _setArguments
_process.checkArguments()
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/processes.py", line 947, in checkArguments
o.checkValue(p, getattr(self, p, None))
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/data/writediskitem.py", line 71, in checkValue
Parameter.checkValue(self, name, value)
File "/opt/miniconda/envs/brainvisa/lib/python3.11/site-packages/brainvisa/data/neuroData.py", line 220, in checkValue
raise RuntimeError(
RuntimeError: Mandatory argument write of None has no value

[ansleymartin04]

Here is also the information for a file that failed (and resulted in Error 1): Type: Raw T1 MRI
Format: gz compressed NIFTI-1 image
Uuid: 205e1e61-3a33-0c8a-1709-967c5a71555a
Files: [ /home/jovyan/neurodesktop-storage/BV_import/sub-102109/ses-morpho_raw/run-0/sub-102109_ses-morpho_raw_run-0_desc-conform_T1w.nii.gz ]
Hierarchy attributes:

_ontology = morphologist-bids-2.0
subject = 102109
session = morpho_raw
bids = run-0
normalized = no
_database = /home/jovyan/neurodesktop-storage/BV_import

Minf attributes:

disk_data_type = S16
bits_allocated = 32
data_type = S16
scale_factor_applied = 0
possible_data_types = ['FLOAT', 'DOUBLE']
cal_min = 0
cal_max = 0
freq_dim = 0
phase_dim = 0
slice_dim = 0
slice_code = 0
slice_start = 0
slice_end = 0
slice_duration = 0
storage_to_memory = [1, 0, 0, 0, 0, -1, 0, 310, 0, 0, -1, 259, 0, 0, 0, 1]
sizeX = 260
sizeY = 311
sizeZ = 260
sizeT = 1
volume_dimension = [260, 311, 260, 1]
voxel_size = [0.699999988079071, 0.70001220703125, 0.70001220703125, 1]
tr = 2.40000009536743
referentials = ['Talairach-MNI template-SPM', 'Talairach-MNI template-SPM']
transformations = [[-1, 0, 0, 90, 0, -0.999982595443726, 0, 91, 0, 0, -0.999982595443726, 109.300003051758, 0, 0, 0, 1], [-1, 0, 0, 90, 0, -0.999982595443726, 0, 91, 0, 0, -0.999982595443726, 109.300003051758, 0, 0, 0, 1]]
toffset = 0
xyz_units = 2
time_units = 8
descrip = FSL5.0
aux_file =
nifti_type = 1
object_type = Volume
file_type = NIFTI-1
referential = 1af66c79-1bb0-8abd-88c8-f3b4e4939d18

Special attributes:

Minf file name = sub-102109_ses-morpho_raw_run-0_desc-conform_T1w.nii.gz.minf
priority = 1
identified = False

[denisri]

It's strange and not normal that this parameter is not automatically filled.
Have you tried if it's the same using the latest brainvisa version ?
When I try it on my side, the write parameter of the process "SPM sn3d to AIMS transformation converter" correctly fills, see image here.

[ansleymartin04]

No, mine definitely does not look like that. I will contact Neurodesk and see if we can get the most recent version or try it on our cluster instead. It may be an issue with how SPM and BrainVISA are containerized on Neurodesk. Thank you so much for your time. I was actually able to get it running but using AimsMIRegister, i know your documentation suggests SPM (as I would also like to use it) but given the error, i figured i would try. I have been manually checking the AC/PC alignments, and it seems properly aligned and oriented. Oddly, SPM still runs and normalizes for the skull-stripping brain normalization, so I am really not sure at this point. Thank you again for the help.

[denisri]

That's intriguing. I don't thing it could be related to the containerized installation, since everything is self-contained in pixi, and as you say it, SPM does work at some point. I more suspect a nomenclature bug in this specific version (which is pretty recent, but not the latest), that would have been fixed (I have done slight modifs in this part recently).
AimsMIRegister is actually a workaround, but it is both not as robust as SPM and performs rigid-only registration, which is more limited (it doesn't allow anisotropic scaling factors, for instance, and I even don't remember if a global scaling is included).

[ansleymartin04]

Greetings, it must have been a bug with the older version. I now have the newer version up and running, and it is working smoothly! Thank you!

[denisri]

Very good news ! Thanks for the feedback...