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Hi Dr. Greve,
Thanks for your explanation! I will go back to the fmriprep then
Best,
Tengwen
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Wednesday, July 31, 2024 2:33 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer in fmriprep
The log file says that recon-all finished without error. The command (robust
register) was not called during recon-all. It must be called by fmriprep at
some point. I don't understand what they are trying to do. It looks like they
are registering the FS-conformed anatomical volume back to the native space,
which would not make sense. Sorry, I'm going to have to send you back to the
fmriprep folks.
On 7/29/2024 6:00 PM, Tengwen Fan wrote:
External Email - Use Caution
Hi Dr. Greve,
Thanks for your reply! Attached is the recon-all.log file.
Please let me know if more information is needed! Thanks so much!
Best,
Tengwen
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Monday, July 29, 2024 12:26 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer in fmriprep
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please send the recon-all.log file in the scripts folder
On 7/23/2024 2:14 PM, Tengwen Fan wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I hope this email finds you well!
I am using fMRIprep to do pre-processing. The fMRIprep combines methodology
from AFNI, ANTs, Freesurfer, FSL, and Mindboggle to do preprocessing.
An error was reported while running the fMRIprep. It seems that it was due to
the structural data and it was about the registration by FreeSurfer. But I am
new in the neuroimaging area and not very sure about what the error actually is
about.
I asked the fmriprep team in neurostars
(https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5)
and they are also not sure about this and recommended to ask the FreeSurfer.
Although I am not sure if the FreeSurfer in fmriprep is what you also work
with, I would like to ask and would really appreciate it if you could help
explain what error it is. Thanks you so much!
The error is attached below. Please let me know if you have any questions or if
more information is needed!
[https://neurostars.org/uploads/default/original/2X/1/1898e24a8821a606fad2dd418e9bd1f472e78ded.png]<https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5>
Fmriprep error: makeIsotropic WARNING: not different enough, won't
reslice!<https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5>
Summary of what happened: Hi, I am running fmriprep and getting the following
error. I would really appreciate any help! Please let me know if more
information should be provided! Thanks so much, tengwen Command used (and if a
helper script was used, a link to the helper script or the command generated):
fmriprep-docker /Users/Desktop/WL_fMRI/data/BIDS
/Users/Desktop/WL_fMRI/data/derivatives/fmriprep participant
--participant-label sub-WLfMRI035 --fs-license-file
/Users/Desktop/WL_fMRI/licen...
neurostars.org
The Error is:
Cmdline:
mri_robust_register --satit --iscale --lta
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta
--mov /out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz --dst
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz
Stdout:
7.3.2
--satit: Will iterate with different SAT to ensure outliers below
wlimit!
--iscale: Enabling intensity scaling!
--lta: Output transform as
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta
.
--mov: Using /out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz as
movable/source volume.
--dst: Using
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz
as target volume.
reading source '/out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz'...
reading target
'/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz'...
Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
Type Source : 0 Type Target : 3 ensure both FLOAT (3)
Reordering axes in mov to better fit dst... ( -1 -3 2 )
Determinant after swap : 1
Mov: (0.5, 0.5, 0.5)mm and dim (512, 512, 512)
Dst: (0.5, 0.5, 0.5)mm and dim (360, 512, 512)
Asserting both images: 0.5mm isotropic
- reslicing Mov ...
-- changing data type from 0 to 3 (noscale = 0)...
- reslicing Dst ...
-- Original : (0.5, 0.5, 0.5)mm and (360, 512, 512) voxels.
-- Resampled: (0.5, 0.5, 0.5)mm and (512, 512, 512) voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
- WARNING: trg mri outside_val = 0 but suspected background:
-0.00687514
If background is black or darkgray, ignore this. If
white, pass --whitebgdst
Registration::findSaturation
- computing centroids
- computing initial transform
-- using translation info
- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
- Max Resolution used: 3
-- gpS ( 64 , 64 , 64 )
-- gpT ( 64 , 64 , 64 )
- running loop to estimate saturation parameter:
-- Iteration: 1 trying sat: 16
min sat: 0 ( -1 ), max sat: 16 ( 0.12101 ), sat diff: 16,
(wlimit=0.16)
-- Iteration: 2 trying sat: 8
min sat: 8 ( 0.324589 ), max sat: 16 ( 0.12101 ), sat diff: 8,
(wlimit=0.16)
-- Iteration: 3 trying sat: 12
min sat: 12 ( 0.193726 ), max sat: 16 ( 0.12101 ), sat diff: 4,
(wlimit=0.16)
-- Iteration: 4 trying sat: 14
min sat: 12 ( 0.193726 ), max sat: 14 ( 0.15173 ), sat diff: 2,
(wlimit=0.16)
-- Iteration: 5 trying sat: 13
min sat: 13 ( 0.17074 ), max sat: 14 ( 0.15173 ), sat diff: 1,
(wlimit=0.16)
-- Iteration: 6 trying sat: 13.5
- final SAT: 14 ( it: 6 , weight check 0.15173 <= 0.16 )
Registration::computeMultiresRegistration
- computing centroids
- computing initial transform
-- using translation info
- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
- initial transform:
Ti = [ ...
1.0000000000000 0 0 1.6982521922295
0 1.0000000000000 0 -1.1595074345649
0 0 1.0000000000000 -1.1415599519338
0 0 0 1.0000000000000 ]
- initial iscale: Ii =1
Resolution: 4 S( 32 32 32 ) T( 32 32 32 )
Iteration(f): 1
-- intensity log diff: abs(-0.85599)
-- diff. to prev. transform: 1.62699
Iteration(f): 2
-- intensity log diff: abs(-0.0720915)
-- diff. to prev. transform: 0.761125
Iteration(f): 3
-- intensity log diff: abs(-0.00194135)
-- diff. to prev. transform: 0.0383579
Iteration(f): 4
-- intensity log diff: abs(-0.00123869)
-- diff. to prev. transform: 0.0128975
Iteration(f): 5
-- intensity log diff: abs(-0.000750416) <= 0.001 :-)
-- diff. to prev. transform: 0.00518321 <= 0.01 :-)
Resolution: 3 S( 64 64 64 ) T( 64 64 64 )
Iteration(f): 1
-- intensity log diff: abs(0.00702447)
-- diff. to prev. transform: 0.977321
Iteration(f): 2
-- intensity log diff: abs(9.94659e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.0258922
Iteration(f): 3
-- intensity log diff: abs(1.21569e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.00163623 <= 0.01 :-)
Resolution: 2 S( 128 128 128 ) T( 128 128 128 )
Iteration(f): 1
-- intensity log diff: abs(-0.000545933) <= 0.001 :-)
-- diff. to prev. transform: 0.356881
Iteration(f): 2
-- intensity log diff: abs(-7.53945e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.0881187
Iteration(f): 3
-- intensity log diff: abs(-5.00529e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.0253314
Iteration(f): 4
-- intensity log diff: abs(-2.0764e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.00744419 <= 0.01 :-)
Resolution: 1 S( 256 256 256 ) T( 256 256 256 )
Iteration(f): 1
-- intensity log diff: abs(0.00127177)
-- diff. to prev. transform: 0.268975
Iteration(f): 2
-- intensity log diff: abs(0.000348898) <= 0.001 :-)
-- diff. to prev. transform: 0.0666025
Iteration(f): 3
-- intensity log diff: abs(8.4156e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.016444
Iteration(f): 4
-- intensity log diff: abs(2.77798e-05) <= 0.001 :-)
-- diff. to prev. transform: 0.00492133 <= 0.01 :-)
Resolution: 0 S( 512 512 512 ) T( 512 512 512 )
Iteration(f): 1
-- WARNING: mem usage large: 4668.08Mb mem + 6 MRI
Maybe use --subsample <int>
Stderr:
makeIsotropic WARNING: not different enough, won't reslice!
Killed
Traceback:
Traceback (most recent call last):
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py",
line 398, in run
runtime = self._post_run_hook(runtime)
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/freesurfer.py",
line 248, in _post_run_hook
fix_lta_length(lta_file)
File
"/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/freesurfer.py",
line 399, in fix_lta_length
lines = Path(lta_file).read_text().splitlines(keepends=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1134,
in read_text
with self.open(mode='r', encoding=encoding, errors=errors) as f:
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1119,
in open
return self._accessor.open(self, mode, buffering, encoding, errors,
FileNotFoundError: [Errno 2] No such file or directory:
'/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta'
Best,
Tengwen
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