Fmriprep 1.1.1 anat-only: troubleshooting talairach_afd error

Hi there,

First post here on Neurostars.org. Should have joined this a long time ago but better late than never.

I am running an analysis on a subset of the original OASIS database (anatomical only). I’ve been using fmriprep 1.1.1 on a subset of 30 subjects using the following command on a slurm cluster:

singularity run -B /localscratch:/localscratch -e -B /cvmfs:/cvmfs -B /project:/project -B /scratch:/scratch /opt/singularity/bids-apps/poldracklab_fmriprep_1.1.1.img /home/user/study/PHASE2/input_data/OAS1_bids /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1 participant --participant_label $subj --nthreads 8 --n_cpus 8 --omp-nthreads 8 --mem_mb 32000 --debug -w /scratch/${USER}/${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID} --fs-license-file /opt/freesurfer/.license --resource-monitor --notrack --anat-only

29 out of 30 completed successfully but one subject (sub-0180) failed (see bottom of message for the full output log).

Here’s a screenshot of sub-0180. Ventricles large (not so unusual in this cohort) and the head/neck is perhaps more extended than most.

It appears to be failing on one of the freesurfer steps encapsulated in fmriprep. If I was running freesurfer on its own I would likely try out some of the strategies suggested in the output log. However, just wanted to ask here about whether there are some best practices, guidelines, or suggestions on how to successfully get an output without deviating too much from the bids-app workflow.

Appreciate your time, and thanks to @ChrisGorgolewski and colleagues for making this tool available!

Let me know if you need any more clarification.

Best regards,
jon

The error message is the following:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 68, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 644, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1044, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 981, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /scratch/user/6427737_9/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-0180_T1w_ras.nii.gz -noskullstrip -openmp 8 -subjid sub-0180 -sd /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/scripts/recon-all.local-copy'
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180

 mri_convert /scratch/user/6427737_9/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-0180_T1w_ras.nii.gz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig/001.mgz 

mri_convert.bin /scratch/user/6427737_9/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-0180_T1w_ras.nii.gz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /scratch/user/6427737_9/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-0180_T1w_ras.nii.gz...
TR=1000.00, 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 /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Wed Jul 18 00:08:16 UTC 2018
Found 1 runs
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig/001.mgz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/rawavg.mgz 

/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180

 mri_convert /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/rawavg.mgz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig.mgz --conform 

mri_convert.bin /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/rawavg.mgz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/rawavg.mgz...
TR=1000.00, 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 
Reslicing using trilinear interpolation 
writing to /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig.mgz...

 mri_add_xform_to_header -c /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/transforms/talairach.xfm /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig.mgz /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Wed Jul 18 00:08:23 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

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

/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Wed Jul 18 00:08:23 UTC 2018
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.29315
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29315/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29315/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=1000.00, 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)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.29315/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jul 18 00:08:25 UTC 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.29315/nu0.mnc ./tmp.mri_nu_correct.mni.29315/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29315/0/ -iterations 1000 -distance 50
[user@node643:/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/] [2018-07-18 00:08:25] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29315/0/ ./tmp.mri_nu_correct.mni.29315/nu0.mnc ./tmp.mri_nu_correct.mni.29315/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 76 
CV of field change: 0.000995587
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.29315/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.29315/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.29315/nu1.mnc...
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
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Jul 18 00:09:57 UTC 2018
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...
Started at Wed Jul 18 00:09:57 UTC 2018
Ended   at Wed Jul 18 00:10:21 UTC 2018
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Wed Jul 18 00:10:23 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0697, pval=0.0034 < threshold=0.0050)

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 Jul 18 00:10:24 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

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

/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Wed Jul 18 00:10:24 UTC 2018
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.32667
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.32667/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.32667/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=1000.00, 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)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.32667/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jul 18 00:10:25 UTC 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.32667/nu0.mnc ./tmp.mri_nu_correct.mni.32667/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.32667/0/ -iterations 1000 -distance 50
[user@node643:/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/] [2018-07-18 00:10:25] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.32667/0/ ./tmp.mri_nu_correct.mni.32667/nu0.mnc ./tmp.mri_nu_correct.mni.32667/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 76 
CV of field change: 0.000995587
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.32667/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.32667/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.32667/nu1.mnc...
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
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Jul 18 00:11:58 UTC 2018
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...
Started at Wed Jul 18 00:11:58 UTC 2018
Ended   at Wed Jul 18 00:12:22 UTC 2018
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Wed Jul 18 00:12:24 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0614, pval=0.0034 < threshold=0.0050)

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: Trying MINC mritotal to perform Talairach align...

#--------------------------------------------
#@# Talairach Wed Jul 18 00:12:24 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

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

/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Wed Jul 18 00:12:24 UTC 2018
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.3455
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3455/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3455/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=1000.00, 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)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.3455/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jul 18 00:12:26 UTC 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.3455/nu0.mnc ./tmp.mri_nu_correct.mni.3455/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3455/0/ -iterations 1000 -distance 50
[user@node643:/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri/] [2018-07-18 00:12:26] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3455/0/ ./tmp.mri_nu_correct.mni.3455/nu0.mnc ./tmp.mri_nu_correct.mni.3455/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 76 
CV of field change: 0.000995587
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.3455/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.3455/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.3455/nu1.mnc...
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
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Jul 18 00:13:56 UTC 2018
mri_nu_correct.mni done

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

/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
/opt/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $
Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Wed Jul 18 00:13:56 UTC 2018
tmpdir is transforms/tmp.talairach.4800
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.4800/src.mnc
mri_convert.bin orig_nu.mgz transforms/tmp.talairach.4800/src.mnc 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig_nu.mgz...
TR=1000.00, 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 transforms/tmp.talairach.4800/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.4800/src.mnc transforms/talairach.auto.xfm
Transforming slices:................................................................................................................................Done
Copying chunks:......................................................................................................................................................Done.
Copying chunks:..........................................................................................................Done.
Transforming slices:......................................................................................................................................................Done
Copying chunks:....................................................................................................................Done.
Copying chunks:....................................................................................................................Done.
Source volume size:  74  by 106  by 106 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =   -0.000  187.807
Source min/max voxel=   -0.000  187.807

Target volume size:  58  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=    0.970  123.710
Target min/max voxel =   -0.000  123.710


AFTER init_params()
Transform matrix    =    1.0000    0.0000    0.0000  106.0939 
                         0.0000    1.0000    0.0000 -143.6382 
                         0.0000    0.0000    1.0000  -98.6123 

Transform center   = -105.766  126.047  108.067
Transform rotations  =    0.000    0.000    0.000
Transform trans    =  106.094 -143.638  -98.612
Transform scale    =    1.000    1.000    1.000
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -85.095 -125.510  -47.250
Lattice count      =       43       55       29

Source volume size:  84  by 116  by 116 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =   -0.000  228.534
Source min/max voxel=   -0.000  228.534

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=   -0.000  144.070
Target min/max voxel =   -0.000  144.070


AFTER init_params()
Transform matrix    =    0.7569   -0.1210    0.2308   73.0487 
                        -0.0273    0.6683    0.4399 -124.7935 
                        -0.2592   -0.4238    0.6277  -39.4539 

Transform center   = -105.766  126.047  108.067
Transform rotations  =   -0.594    0.330   -0.036
Transform trans    =  108.453 -116.173 -105.694
Transform scale    =    0.801    0.801    0.801
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -85.095 -125.510  -57.250
Lattice count      =       43       55       34

Source volume size:  84  by 116  by 116 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.018   22.809
Source min/max voxel=    0.018   22.809

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=    0.037   11.652
Target min/max voxel =    0.037   11.652


AFTER init_params()
Transform matrix    =    0.8808   -0.0365   -0.0515  102.0183 
                         0.0573    0.7643    0.4387 -135.3286 
                         0.0264   -0.4409    0.7647  -22.4860 

Transform center   = -105.766  126.047  108.067
Transform rotations  =   -0.523   -0.030    0.065
Transform trans    =  104.455 -123.700 -106.280
Transform scale    =    0.883    0.883    0.883
Transform shear    =    0.000   -0.000   -0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

Source volume size:  84  by 116  by 116 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.018   22.809
Source min/max voxel=    0.018   22.809

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=    0.037   11.652
Target min/max voxel =    0.037   11.652


AFTER init_params()
Transform matrix    =    0.6988   -0.0762   -0.0240   81.7916 
                         0.0782    0.6093    0.3425  -94.6126 
                        -0.0163   -0.3430    0.6139  -25.0363 

Transform center   = -105.766  126.047  108.067
Transform rotations  =   -0.510    0.023    0.111
Transform trans    =  101.446 -115.115 -108.267
Transform scale    =    0.703    0.703    0.703
Transform shear    =   -0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

Source volume size:  84  by 116  by 116 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.018   22.809
Source min/max voxel=    0.018   22.809

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=    0.037   11.652
Target min/max voxel =    0.037   11.652


AFTER init_params()
Transform matrix    =    0.6734   -0.1473   -0.0791   91.8724 
                         0.2231    0.7243    0.5505 -124.0833 
                        -0.0299   -0.4871    0.6531  -28.8442 

Transform center   = -105.766  126.047  108.067
Transform rotations  =   -0.641    0.037    0.241
Transform trans    =   99.303 -122.938 -124.582
Transform scale    =    0.694    0.937    0.815
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

Source volume size:  84  by 116  by 116 
Source voxel size =    2.000    2.000    2.000
Source min/max real range =    0.018   22.809
Source min/max voxel=    0.018   22.809

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
Target min/max real range=    0.037   11.652
Target min/max voxel =    0.037   11.652


AFTER init_params()
Transform matrix    =    0.6697   -0.1395   -0.1210   94.6509 
                         0.2435    0.6481    0.6006 -116.7125 
                        -0.0078   -0.6267    0.6795   -6.0976 

Transform center   = -105.766  126.047  108.067
Transform rotations  =   -0.745    0.008    0.269
Transform trans    =   98.919 -121.927 -118.908
Transform scale    =    0.695    0.917    0.924
Transform shear    =   -0.000    0.000   -0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

 
 
Wed Jul 18 00:14:06 UTC 2018
talairach done

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

#--------------------------------------------
#@# Talairach Failure Detection Wed Jul 18 00:14:08 UTC 2018
/home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0455, pval=0.0034 < threshold=0.0050)

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


ERROR: Talairach failed!

Linux node643 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-0180 exited with ERRORS at Wed Jul 18 00:14:08 UTC 2018

For more details, see the log file /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1/freesurfer/sub-0180/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

In case the singularity call to fmriprep isn’ t clear here is the command as listed in the generated html file:

/usr/local/miniconda/bin/fmriprep /home/user/study/PHASE2/input_data/OAS1_bids /home/user/study/PHASE2/input_data/OAS1_bids/derivatives/fmriprep_1.1.1 participant --participant_label 0180 --nthreads 8 --n_cpus 8 --omp-nthreads 8 --mem_mb 32000 --debug -w /scratch/user/6427737_9 --fs-license-file /opt/freesurfer/.license --resource-monitor --notrack --anat-only

  1. This error has been reported previously in different contexts. Please have a look: https://github.com/poldracklab/fmriprep/issues/562 and https://github.com/poldracklab/fmriprep/issues/656
  2. This could be an issue with nifti headers. If you have access to DICOMs could you try to convert them to nifti using the latest release of dcm2niix https://github.com/rordenlab/dcm2niix/releases

Thanks for the links!

For issue 562, there was some discussion around the problem being related to FreeSurfer’s intensity nonuniformity correction. The images available from OAS1 are already nonuniformity corrected and defaced (original file name on download: OAS1_0180_MR1_mpr_n4_anon_sbj_111.nii.gz). Is there a way to bypass the FreeSurfer nonuniformity correction when running fmriprep?

All subjects were downloaded directly from https://central.xnat.org so I unfortunately don’t have access to the DICOMs.

I will also provide a better initialization for talairach alignment by preprocessing sub-0180 with an AC-PC transformation before running fmriprep. Will report back with my results.

I had a closer look at the image you posted and it looks like an average of at least two images. Might be worth contacting OASIS about this.

Thanks. If this works we should do it automatically in FMRIPREP.

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Yes, the OAS1 data have all been preprocessed. They are averages of 3-4 MPRAGE scans in a single session after rigid registration. Figure 1 from Marcus, JCN, 2007:


Update: I have fmriprep running on a roughly talairach aligned version of sub-0180 as input. Just started autorecon1. Will let you know how it goes.

I see - thanks for clarifying. Are the individual scans (before averaging) available? FMRIPREP cand deal with them and create a new average internally that might work better.

Reading from the OASIS-1 fact sheet:

For each subject, a number of images are provided, including: 1) 3-4 images corresponding to multiple
repetitions of the same structural protocol within a single session to increase signal-to-noise, 2) an average
image that is a motion-corrected coregistered average of all available data

I would recommend using the 3-4 images instead of the average (sub-0180_run-1_T1w.nii.gz, sub-0180_run-2_T1w.nii.gz etc.). FMRIPREP has a built-in robust everage procedure, which hopefully will yield results that don’t cause freesurfer errors.

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For my purposes so far I’ve just been using the “recon” (i.e. average) for the signal bump. fmriprep has worked out of the box on 29/30 of them! Now just need to figure out this last one so happy to try that next.

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Following up here. fmriprep completed successfully after I preprocessed the data with the following rigid registration to MNI305. I used the output from flirt as input to the bids-app:

flirt -dof 6 -in OAS1_bids/sub-0180/anat/sub-0180_T1w.nii.gz -ref average_305.nii.gz -omat rigid.xfm -out OAS1_bids_sub-0180_fixed/sub-0180/anat/sub-0180_T1w.nii.gz

My plan is to document this in my write-up and the project README.md. Any suggestions or links to best practices for reporting these sort of deviations from “standard” workflows would be welcome.

The XNAT server seems to be having some issues with downloads, so I haven’t been able to try @ChrisGorgolewski’s suggestion with inputting multiple anatomical runs for the same subject yet. However, the solution with pre-alignment may be more generalizable in cases where there is only one run available.

Side note: freesurfer reconstruction looks good, but the template registration is pretty poor; appreciating that this is a difficult case (large ventricles, atrophy). Doesn’t appear like the forum supports SVG files so I’ve provided a link to them here.

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This looks as if the nonlinear template normalization did not run at all. Could you share the full report (html + the figures folder, zipped)?

Thanks for looking into this. Should I start a new thread?

As requested, here’s the zipped folder. I’ve removed output files that I’ve deemed unlikely to be relevant (e.g. the freesurfer output) to save space, but let me know if you need any of it.

The log for the singularity call can be found at ./fmriprep_1.1.1/jobs/fmriprep_1.1.1.participant.6507493_1.out. Trying to familiarize myself with the output, but below is the one call to antsRegistration which doesn’t seem to include any nonlinear parameters:

antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /scratch/jclau/6507493_1/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/t1_2_mni/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /scratch/jclau/6507493_1/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /scratch/jclau/6507493_1/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /scratch/jclau/6507493_1/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /scratch/jclau/6507493_1/fmriprep_wf/single_subject_0180_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ] --write-composite-transform 1

Let me know if you need anything else!

Could you start a new thread?

PS I got the answer.

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Thanks Chris! Looking forward to hearing what you found. A new thread has been started to resolve the nonlinear registration problem that we’ve since found: Fmriprep 1.1.1 anat-only: T1 to MNI poor quality nonlinear registration

The original problem related to this thread has been solved. I’ll summarize here with two possible solutions if someone runs into this problem in the future:

  1. Perform a rigid body pre-alignment with “talairach” MNI305 space and use that as input to fmriprep. [what I ended up doing]
  2. If you have multiple input structural scans, fmriprep can handle them as separate inputs (just label as different runs as per BIDS protocol), which may improve the freesurfer talairach registration step.

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