shaymaadarawshy
commented
3 years ago @effigies Dear Chris, can you help with this error? Thank you, Shaymaa
Open shaymaadarawshy opened 3 years ago
shaymaadarawshy
commented
3 years ago @effigies Dear Chris, can you help with this error? Thank you, Shaymaa
effigies
commented
3 years ago Hi, thanks for the nudge. Could you share a screenshot of the subject's T1w image? If Talairach registration fails, there's often a visible issue with the image.
shaymaadarawshy
commented
3 years ago Dear Chris,
Attached are the T1 of both subject who failed the Talariach alignment.
effigies
commented
3 years ago Sorry for letting this one fall by the wayside. I'm not an expert in FreeSurfer, so I would recommend working with the FreeSurfer team to process subjects with such severe lesions. You can then provide the pre-computed FreeSurfer directory to fMRIPrep.
You will also probably want to have a lesion mask in your dataset to improve spatial normalization.
Hi, I'm running Fmriprep on patients with huge brain lesions, and I got this error for two of my patients. This is the code I'm running: fmriprep-docker /home/shymaa/Desktop/my_dataset/Participant /home/shymaa/Desktop/my_dataset/Participant/derivative participant --participant-label 07 --fs-license-file /home/shymaa/Desktop/license.txt --use-aroma --cifti-outputs
Error: Node: fmriprep_wf.single_subject_07_wf.anat_preproc_wf.surface_recon_wf.autorecon1 Working directory: /tmp/work/fmriprep_wf/single_subject_07_wf/anat_preproc_wf/surface_recon_wf/autorecon1
Node inputs:
FLAIR_file =
T1_files =
T2_file =
args =
big_ventricles =
brainstem =
directive = autorecon1
environ = {}
expert =
flags =
hemi =
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires =
mprage =
mri_aparc2aseg =
mri_ca_label =
mri_ca_normalize =
mri_ca_register =
mri_edit_wm_with_aseg =
mri_em_register =
mri_fill =
mri_mask =
mri_normalize =
mri_pretess =
mri_remove_neck =
mri_segment =
mri_segstats =
mri_tessellate =
mri_watershed =
mris_anatomical_stats =
mris_ca_label =
mris_fix_topology =
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 8
parallel =
steps =
subject_id = recon_all
subjects_dir =
talairach =
use_FLAIR =
use_T2 =
xopts =
Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception ).format(**runtime.dictcopy()) RuntimeError: Command: recon-all -autorecon1 -i /data/sub-07/anat/sub-07_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-07 -sd /out/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 /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-07/scripts/recon-all.local-copy' /out/freesurfer/sub-07
mri_convert /data/sub-07/anat/sub-07_T1w.nii.gz /out/freesurfer/sub-07/mri/orig/001.mgz
mri_convert.bin /data/sub-07/anat/sub-07_T1w.nii.gz /out/freesurfer/sub-07/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-07/anat/sub-07_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.990846, 0.00867391, -0.134721) j_ras = (-0.0205356, 0.996005, -0.086908) k_ras = (0.133429, 0.088879, 0.987065) writing to /out/freesurfer/sub-07/mri/orig/001.mgz...
--------------------------------------------
@# MotionCor Mon Apr 5 09:47:52 UTC 2021
Found 1 runs /out/freesurfer/sub-07/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 /out/freesurfer/sub-07/mri/orig/001.mgz /out/freesurfer/sub-07/mri/rawavg.mgz
/out/freesurfer/sub-07
mri_convert /out/freesurfer/sub-07/mri/rawavg.mgz /out/freesurfer/sub-07/mri/orig.mgz --conform
mri_convert.bin /out/freesurfer/sub-07/mri/rawavg.mgz /out/freesurfer/sub-07/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-07/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.990846, 0.00867391, -0.134721) j_ras = (-0.0205356, 0.996005, -0.086908) k_ras = (0.133429, 0.088879, 0.987065) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-07/mri/orig.mgz...
mri_add_xform_to_header -c /out/freesurfer/sub-07/mri/transforms/talairach.xfm /out/freesurfer/sub-07/mri/orig.mgz /out/freesurfer/sub-07/mri/orig.mgz
INFO: extension is mgz
--------------------------------------------
@# Talairach Mon Apr 5 09:48:04 UTC 2021
/out/freesurfer/sub-07/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/out/freesurfer/sub-07/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 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:48:04 UTC 2021 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.548 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.548/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.548/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.548/nu0.mnc...
Iteration 1 Mon Apr 5 09:48:07 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.548/nu0.mnc ./tmp.mri_nu_correct.mni.548/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.548/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:48:07] 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.548/0/ ./tmp.mri_nu_correct.mni.548/nu0.mnc ./tmp.mri_nu_correct.mni.548/nu1.imp
Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835
mri_convert ./tmp.mri_nu_correct.mni.548/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.548/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.548/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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...
Mon Apr 5 09:50:29 UTC 2021 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 Mon Apr 5 09:50:29 UTC 2021 Ended at Mon Apr 5 09:51:17 UTC 2021 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
--------------------------------------------
@# Talairach Failure Detection Mon Apr 5 09:51:19 UTC 2021
/out/freesurfer/sub-07/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED (p=0.0000, pval=0.0000 < 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 Mon Apr 5 09:51:19 UTC 2021
/out/freesurfer/sub-07/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/out/freesurfer/sub-07/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 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:51:19 UTC 2021 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.4743 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4743/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4743/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4743/nu0.mnc...
Iteration 1 Mon Apr 5 09:51:22 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.4743/nu0.mnc ./tmp.mri_nu_correct.mni.4743/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4743/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:51:23] 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.4743/0/ ./tmp.mri_nu_correct.mni.4743/nu0.mnc ./tmp.mri_nu_correct.mni.4743/nu1.imp
Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835
mri_convert ./tmp.mri_nu_correct.mni.4743/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4743/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.4743/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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...
Mon Apr 5 09:54:03 UTC 2021 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 Mon Apr 5 09:54:04 UTC 2021 Ended at Mon Apr 5 09:54:49 UTC 2021 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
--------------------------------------------
@# Talairach Failure Detection Mon Apr 5 09:54:52 UTC 2021
/out/freesurfer/sub-07/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4905, pval=0.1531 >= threshold=0.0050)
awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-07/mri/transforms/talairach_avi.log
tal_QC_AZS /out/freesurfer/sub-07/mri/transforms/talairach_avi.log
TalAviQA: 0.85645 z-score: -27 WARNING: Talairach QA check failed! z-score of -27 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: Trying MINC mritotal to perform Talairach align...
--------------------------------------------
@# Talairach Mon Apr 5 09:54:52 UTC 2021
/out/freesurfer/sub-07/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/out/freesurfer/sub-07/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 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:54:52 UTC 2021 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.6926 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6926/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6926/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6926/nu0.mnc...
Iteration 1 Mon Apr 5 09:54:55 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.6926/nu0.mnc ./tmp.mri_nu_correct.mni.6926/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6926/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:54:55] 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.6926/0/ ./tmp.mri_nu_correct.mni.6926/nu0.mnc ./tmp.mri_nu_correct.mni.6926/nu1.imp
Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835
mri_convert ./tmp.mri_nu_correct.mni.6926/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.6926/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.6926/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) 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...
Mon Apr 5 09:57:40 UTC 2021 mri_nu_correct.mni done
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/out/freesurfer/sub-07/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 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:57:40 UTC 2021 tmpdir is transforms/tmp.talairach.7643 /out/freesurfer/sub-07/mri mri_convert orig_nu.mgz transforms/tmp.talairach.7643/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.7643/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ 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, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) writing to transforms/tmp.talairach.7643/src.mnc...
mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7643/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 = -0.000 157.547 Source min/max voxel= -0.000 157.547
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 4.1908 0.0000 1.0000 0.0000 -10.2661 0.0000 0.0000 1.0000 33.3827
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.000 0.000 0.000 Transform trans = 4.191 -10.266 33.383 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 = -0.000 214.907 Source min/max voxel= -0.000 214.907
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 = 0.8973 -0.2092 -0.1398 -1.3581 0.1477 0.8571 -0.3348 -11.7152 0.2037 0.3002 0.8584 46.4240
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.336 -0.220 0.163 Transform trans = 3.916 -3.227 46.826 Transform scale = 0.932 0.932 0.932 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 = 0.023 24.915 Source min/max voxel= 0.023 24.915
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 = 0.8493 -0.3524 -0.1329 -1.8151 0.2467 0.7682 -0.4605 -13.8695 0.2846 0.3857 0.7959 37.7361
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.451 -0.311 0.283 Transform trans = 4.529 -2.106 38.697 Transform scale = 0.929 0.929 0.929 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 = 0.023 24.915 Source min/max voxel= 0.023 24.915
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 = 0.8413 -0.3229 0.1654 -19.8003 0.3494 0.8335 -0.1501 23.9121 -0.0976 0.2009 0.8885 10.4402
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.222 0.107 0.394 Transform trans = -20.779 27.373 12.013 Transform scale = 0.916 0.916 0.916 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 = 0.023 24.915 Source min/max voxel= 0.023 24.915
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 = 0.7832 -0.3616 0.0905 -12.9926 0.5471 1.1481 -0.1464 21.9242 -0.0406 0.1307 0.8739 2.7341
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.149 0.046 0.442 Transform trans = -11.671 22.228 4.950 Transform scale = 0.867 1.280 0.885 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 = 0.023 24.915 Source min/max voxel= 0.023 24.915
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 = 0.7722 -0.3700 0.0882 -13.1052 0.5643 1.1383 -0.1659 21.3297 -0.0313 0.1427 0.8723 3.0791
Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.162 0.035 0.456 Transform trans = -11.625 22.108 5.209 Transform scale = 0.861 1.281 0.884 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
Mon Apr 5 09:57:52 UTC 2021 talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
--------------------------------------------
@# Talairach Failure Detection Mon Apr 5 09:57:54 UTC 2021
/out/freesurfer/sub-07/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED (p=0.0442, 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 1f98b6a77b48 5.8.0-45-generic #51~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-07 exited with ERRORS at Mon Apr 5 09:57:55 UTC 2021
For more details, see the log file /out/freesurfer/sub-07/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
How can I fix this error?
thank you, Shaymaa