acpc alignment of labels generated by recon-all
Asa Borzabadi
Glasser, Matt
What is the error when running inside the HCP Pipelines results?
Matt.
From: Asa Borzabadi <asa.bo...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, September 27, 2022 at 1:13 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: [hcp-users] acpc alignment of labels generated by recon-all
Dear experts,
My aim is to use MRI data which has been minimally-processed via the HCPpipeline and I want to identify subject-specific labels coming from the Benson,2014 method in which the visual areas are estimated based on subject-specific results of the recon-all. My analysis needs to be done in native subject space ( as T1w_acpc_dc_restore_brain.nii.gz), which means I want the areas' labels in the native subject space as well.
For some reason when I use ${StudyFolder}/${SubjectID}/T1w/${SubjectID}/ as the output of recon-all ( after prefreesurfer, freesurfer, and postfreesurfer bash files being compiled) the benson14_retinotopy code faces errors. However, when I used the unprocessed data and simply ran the recon-all command ( independent of the pipeline), and used those outputs, the benson14_retinotopy code worked and I got the labels; the labels (.mgz) are aligned with the brain.mgz file which has been generated by the freesurfer recon-all command.
(brain.mgz after simple recon-all (no pipeline) & Visual_areas_benson_aligned_with_brain_mgz_recon_all.nii.gz)
However, I want the labels to be aligned with the T1w_acpc_dc_restore_brain.nii.gz, hence I first used convert-xmf to get the inverse of acpc.mat file and then tried the following command:
applywarp -i Visual_areas_benson_aligned_with_brain_mgz_recon_all.nii.gz -o Visual_areas_aligned_with_brain_HCP_T1w_acpc_dc_restore_brain.nii.gz -r T1w_acpc_dc_restore_brain.nii.gz -w acpc_inverse.mat
The results would be ( T1w_acpc_dc_restore-brain.nii.gz &Visual_areas_aligned_with_brain_HCP_T1w_acpc_dc_restore_brain.nii.gz) :
Could you please let me know what is the correct way to achieve this goal?
Thank you so much for your help.
Regards,
Asa Farahani
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Asa Borzabadi
Processing subject 031:
- Interpolating template...
Traceback (most recent call last):
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/__main__.py", line 19, in <module>
sys.exit(main(sys.argv[1:]))
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/__main__.py", line 16, in main
return commands[argv[0]](argv[1:])
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/commands/benson14_retinotopy.py", line 157, in main
(lhdat, rhdat) = predict_retinotopy(sub,
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/vision/retinotopy.py", line 1678, in predict_retinotopy
subj_hems = (sub.lh, sub.rh)
File "/home/asa/.local/lib/python3.8/site-packages/pimms/immutable.py", line 135, in _imm_getattribute
value = memfn(*[getattr(self, arg) for arg in args])
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/mri/core.py", line 154, in lh
return hemis.get('lh', None)
File "/usr/lib/python3.8/_collections_abc.py", line 660, in get
return self[key]
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 856, in __getitem__
return self._examine_val(k, ps.PMap.__getitem__(self, k))
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 852, in _examine_val
val = val()
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 756, in curried_f
return f(*(args0 + args), **merge(kwargs0, kwargs))
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/freesurfer/core.py", line 562, in cortex_from_filemap
tris = hdat.tess['white']
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 856, in __getitem__
return self._examine_val(k, ps.PMap.__getitem__(self, k))
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 852, in _examine_val
val = val()
File "/home/asa/.local/lib/python3.8/site-packages/pimms/util.py", line 756, in curried_f
return f(*(args0 + args), **merge(kwargs0, kwargs))
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/util/filemap.py", line 980, in lookup
if 'filt' in inst: val = inst['filt'](val)
File "/home/asa/.local/lib/python3.8/site-packages/neuropythy/freesurfer/core.py", line 318, in <lambda>
'load':_load_geo, 'filt':lambda u:u[1]}),
TypeError: 'NoneType' object is not subscriptable
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Asa Borzabadi
Glasser, Matt
They should have that file. Are you sure the HCP Pipelines ran without error? Are you running FreeSurfer version 6.0?
Matt.
From: Asa Borzabadi <asa.bo...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, September 27, 2022 at 3:30 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] acpc alignment of labels generated by recon-all
Could it be due to the fact that in the outputs from HCPpipeline, we don't have a file named "rh.white" in the surf directory?
- if so, should I rename lh.white.deformed to lh.white?
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Asa Borzabadi
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CC4FE80C-D83C-4AE3-AD54-AA5B5EF87B73%40wustl.edu.