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nipreps / smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

Home Page:https://nipreps.github.io/smriprep

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Include 3T18yoSchwartzReactN32 in Docker

psadil opened this issue · comments

commented

Describe the bug

When Talairach registration fails a QA check, FreeSurfer will attempt to retry the registration with target=3T18yoSchwartzReactN32_as_orig. To allow for this, fMRIPrep includes that atlas. But sMRIPrep does not.

Exact command line executed

singularity run \
  -e \
  --bind ${base}:/ds \
  --bind $MYSCRATCH:/scratch \
  code/smriprep_0.12.1.sif \
  --nprocs 16 \
  --omp-nthreads 8 \
  --mem-gb 24 \
  --output-spaces T1w MNI152NLin2009cAsym \
  --fs-license-file  /ds/code/license  \
  -w /scratch/work  \
  --no-submm-recon \
  /ds/inputs/rawdata /ds/derivatives/smriprep participant

Are you positive that the input dataset is BIDS-compliant?

  • I have used the online BIDS-Validator
  • I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
  • I let sMRIPrep check it for me (in other words, I didn't set the --skip-bids-validation argument).
  • No, I haven't checked myself AND used the --skip-bids-validation argument.

sMRIPrep feedback information

crash log for example participant 
Node: smriprep_wf.single_subject_SCN9747_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Working directory: /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/surface_recon_wf/autorecon1

Node inputs:

FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon1
environ = {}
expert = <undefined>
flags = <undefined>
hemi = <undefined>
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
steps = <undefined>
subject_id = recon_all
subjects_dir = <undefined>
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1.

Cmdline:
	recon-all -autorecon1 -i /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/anat_validate/sub-SCN9747_ses-phase1pretx_T1w_noise_corrected_valid.nii.gz -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-SCN9747 -sd /ds/derivatives/smriprep/freesurfer
Stdout:
	fs-check-version --s sub-SCN9747 --o /tmp/tmp.1HXzfW
	Wed Aug 16 01:58:26 EDT 2023

	setenv SUBJECTS_DIR /ds/derivatives/smriprep/freesurfer
	cd /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/surface_recon_wf/autorecon1
	/opt/freesurfer/bin/fs-check-version --s sub-SCN9747 --o /tmp/tmp.1HXzfW
	-rwxrwxr-x 1 root root 18565 Aug  4  2022 /opt/freesurfer/bin/fs-check-version

	freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	$Id$
	Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	pid 32078
	Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	Subject does not have a bstampfile, copying /opt/freesurfer/build-stamp.txt
	Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	No constraints on version because REQ=UnSet and FsVerFile=NotThere
	#@#% fs-check-version match = 1
	fs-check-version Done
	INFO: SUBJECTS_DIR is /ds/derivatives/smriprep/freesurfer
	Actual FREESURFER_HOME /opt/freesurfer
	Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747

	 mri_convert /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/anat_validate/sub-SCN9747_ses-phase1pretx_T1w_noise_corrected_valid.nii.gz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig/001.mgz 

	mri_convert /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/anat_validate/sub-SCN9747_ses-phase1pretx_T1w_noise_corrected_valid.nii.gz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig/001.mgz 
	reading from /scratch/work/smriprep_wf/single_subject_SCN9747_wf/anat_preproc_wf/anat_validate/sub-SCN9747_ses-phase1pretx_T1w_noise_corrected_valid.nii.gz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (1, 0, 0)
	j_ras = (0, 1, 0)
	k_ras = (0, 0, 1)
	writing to /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig/001.mgz...
	#--------------------------------------------
	#@# MotionCor Wed Aug 16 01:58:28 EDT 2023
	Found 1 runs
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig/001.mgz
	Checking for (invalid) multi-frame inputs...
	Only one run found so motion
	correction will not be performed. I'll
	copy the run to rawavg and continue.

	 cp /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig/001.mgz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz 


	 mri_info /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz 

	rawavg.mgz ========================================
	Volume information for /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz
	          type: MGH
	    dimensions: 224 x 224 x 150
	   voxel sizes: 0.946000, 0.946000, 1.000000
	          type: FLOAT (3)
	           fov: 211.904
	           dof: 1
	        xstart: -106.0, xend: 106.0
	        ystart: -106.0, yend: 106.0
	        zstart: -75.0, zend: 75.0
	            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
	       nframes: 1
	       PhEncDir: UNKNOWN
	       FieldStrength: 0.000000
	ras xform present
	    xform info: x_r =   1.0000, y_r =   0.0000, z_r =   0.0000, c_r =   105.9520
	              : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =   105.9520
	              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =    75.0000

	talairach xfm : 
	Orientation   : RAS
	Primary Slice Direction: axial

	voxel to ras transform:
	                0.9460   0.0000   0.0000     0.0000
	                0.0000   0.9460   0.0000     0.0000
	                0.0000   0.0000   1.0000     0.0000
	                0.0000   0.0000   0.0000     1.0000

	voxel-to-ras determinant 0.894916

	ras to voxel transform:
	                1.0571   0.0000   0.0000     0.0000
	                0.0000   1.0571   0.0000     0.0000
	                0.0000   0.0000   1.0000     0.0000
	                0.0000   0.0000   0.0000     1.0000
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747

	 mri_convert /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz --conform 

	mri_convert /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz --conform 
	reading from /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/rawavg.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (1, 0, 0)
	j_ras = (0, 1, 0)
	k_ras = (0, 0, 1)
	changing data type from float to uchar (noscale = 0)...
	MRIchangeType: Building histogram -1.64746 800745 1000, flo=0, fhi=0.999, dest_type=0
	Reslicing using trilinear interpolation 
	writing to /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz...

	 mri_add_xform_to_header -c /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talairach.xfm /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz 

	INFO: extension is mgz

	 mri_info /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz 

	orig.mgz ========================================
	Volume information for /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/orig.mgz
	          type: MGH
	    dimensions: 256 x 256 x 256
	   voxel sizes: 1.000000, 1.000000, 1.000000
	          type: UCHAR (0)
	           fov: 256.000
	           dof: 1
	        xstart: -128.0, xend: 128.0
	        ystart: -128.0, yend: 128.0
	        zstart: -128.0, zend: 128.0
	            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
	       nframes: 1
	       PhEncDir: UNKNOWN
	       FieldStrength: 0.000000
	ras xform present
	    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =   105.9520
	              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =   105.9520
	              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =    75.0000

	talairach xfm : /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talairach.xfm
	Orientation   : LIA
	Primary Slice Direction: coronal

	voxel to ras transform:
	               -1.0000   0.0000   0.0000   233.9520
	                0.0000   0.0000   1.0000   -22.0480
	                0.0000  -1.0000   0.0000   203.0000
	                0.0000   0.0000   0.0000     1.0000

	voxel-to-ras determinant -1

	ras to voxel transform:
	               -1.0000  -0.0000  -0.0000   233.9520
	               -0.0000  -0.0000  -1.0000   203.0000
	               -0.0000   1.0000  -0.0000    22.0480
	               -0.0000  -0.0000  -0.0000     1.0000
	#--------------------------------------------
	#@# Talairach Wed Aug 16 01:58:36 EDT 2023
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri

	 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 

	/usr/bin/bc
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri
	/opt/freesurfer/bin/mri_nu_correct.mni
	--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
	nIters 1
	mri_nu_correct.mni 7.3.2
	Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Wed Aug 16 01:58:36 EDT 2023
	tmpdir is ./tmp.mri_nu_correct.mni.32430
	cd /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri
	AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.32430/nu0.mgz --dtype uchar
	AntsN4BiasFieldCorrectionFs done
	mri_convert ./tmp.mri_nu_correct.mni.32430/nu0.mgz orig_nu.mgz --like orig.mgz --conform
	mri_convert ./tmp.mri_nu_correct.mni.32430/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
	reading from ./tmp.mri_nu_correct.mni.32430/nu0.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	INFO: transform src into the like-volume: orig.mgz
	writing to orig_nu.mgz...
 
 
	Wed Aug 16 02:02:16 EDT 2023
	mri_nu_correct.mni done

	 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

	talairach_avi log file is transforms/talairach_avi.log...
	mv -f /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
	Started at Wed Aug 16 02:02:17 EDT 2023
	Ended   at Wed Aug 16 02:02:39 EDT 2023
	talairach_avi done

	 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

	lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
	7.3.2

	--src: orig.mgz src image (geometry).
	--trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
	--inmni: transforms/talairach.xfm input MNI/XFM transform.
	--outlta: transforms/talairach.xfm.lta output LTA.
	--s: fsaverage subject name
	--ltavox2vox: output LTA as VOX_TO_VOX transform.
	 LTA read, type : 1
	 0.99308  -0.04203  -0.01786  -99.60434;
	-0.02070   1.01954   0.34062  -143.46477;
	 0.00457  -0.31989   1.04014  -40.56763;
	 0.00000   0.00000   0.00000   1.00000;
	setting subject to fsaverage
	Writing  LTA to file transforms/talairach.xfm.lta...
	lta_convert successful.
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri 
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri 
	#--------------------------------------------
	#@# Talairach Failure Detection Wed Aug 16 02:02:41 EDT 2023
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri

	 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

	talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6574, pval=0.3663 >= threshold=0.0050)

	 awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talairach_avi.log 


	 tal_QC_AZS /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talairach_avi.log 

	TalAviQA: 0.92288
	z-score: -12
	WARNING: Talairach QA check failed!
	z-score of -12 is <= threshold of -9


	Manual Talairach alignment may be necessary, or
	include the -notal-check flag to skip this test,
	making sure the -notal-check flag follows -all
	or -autorecon1 in the command string.
	See:

	http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

	INFO: Retrying Talairach align using 3T-based atlas...

	#--------------------------------------------
	#@# Talairach Wed Aug 16 02:02:41 EDT 2023
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri

	 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 

	/usr/bin/bc
	/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri
	/opt/freesurfer/bin/mri_nu_correct.mni
	--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
	nIters 1
	mri_nu_correct.mni 7.3.2
	Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Wed Aug 16 02:02:41 EDT 2023
	tmpdir is ./tmp.mri_nu_correct.mni.1135
	cd /ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri
	AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1135/nu0.mgz --dtype uchar
	AntsN4BiasFieldCorrectionFs done
	mri_convert ./tmp.mri_nu_correct.mni.1135/nu0.mgz orig_nu.mgz --like orig.mgz --conform
	mri_convert ./tmp.mri_nu_correct.mni.1135/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
	reading from ./tmp.mri_nu_correct.mni.1135/nu0.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	INFO: transform src into the like-volume: orig.mgz
	writing to orig_nu.mgz...
 
 
	Wed Aug 16 02:06:15 EDT 2023
	mri_nu_correct.mni done

	 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 

	talairach_avi log file is transforms/talairach_avi.log...
	ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
	Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s sub-SCN9747 exited with ERRORS at Wed Aug 16 02:06:15 EDT 2023

	For more details, see the log file /ds/derivatives/smriprep/freesurfer/sub-SCN9747/scripts/recon-all.log
	To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Stderr:

Traceback:
	RuntimeError: subprocess exited with code 1.

With relevant log from FreeSurfer

$ cat derivatives/smriprep/freesurfer/sub-SCN9747/mri/transforms/talairach_avi.log
/ds/derivatives/smriprep/freesurfer/sub-SCN9747/mri
/opt/freesurfer/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig
talairach_avi 7.3.2
Linux compute-110.cm.cluster 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Wed Aug 16 02:06:15 EDT 2023
mri_convert orig_nu.mgz talsrcimg.img 
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to talsrcimg.img...
Analyze Output Matrix
-1.00000   0.00000   0.00000   234.95200;
 0.00000   0.00000   1.00000  -23.04800;
 0.00000  -1.00000   0.00000   204.00000;
 0.00000   0.00000   0.00000   1.00000;
--------------------
INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Wed Aug 16 02:06:15 EDT 2023
/opt/freesurfer/bin/mpr2mni305 talsrcimg
mpr2mni305 7.3.2
target=3T18yoSchwartzReactN32_as_orig
ERROR: /opt/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

Visual reports of sMRIPrep

Not Applicable

Installation type (please complete the following information):

  • "Bare-metal"
  • Singularity
  • Docker

Additional context

I'm working with a dataset that I expect to have difficulties with registration (the dataset comprises participants that have lesions).

commented

Good catch. Would you be up for submitting a PR?

commented

Will do