Ha! I understand that sharing the images may be tricky, but do you think you
could send me the segmentations
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii
And
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz
?
Cheers,
/E
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of r04458...@ntu.edu.tw
<r04458...@ntu.edu.tw>
Date: Monday, April 1, 2024 at 10:24 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
with --parc option ?
External Email - Use Caution
Hello Eugenio
Thanks for the reply!
After I follow your instruction, the command works for a while for the
segmentation part and some errors come up as following.
Any hints?
Thanks in advance for your help.
Best,
Edward
mri_easyreg --ref
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip.nii
--flo
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_0000.nii.gz
--ref_seg
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii
--flo_seg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz
--ref_reg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_ref_reg.nii.gz
--flo_reg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_flo_reg.nii.gz
--fwd_field
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_FWF.nii.gz
--bak_field
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_BWF.nii.gz
2024-04-01 22:08:39.479784: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not
find cuda drivers on your machine, GPU will not be used.
2024-04-01 22:08:39.500470: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not
find cuda drivers on your machine, GPU will not be used.
2024-04-01 22:08:39.500724: I
tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is
optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations,
rebuild TensorFlow with the appropriate compiler flags.
2024-04-01 22:08:39.793976: W
tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not
find TensorRT
using 1 thread
Segmenting reference image
Reading reference image
Setting up segmentation net
2024-04-01 22:08:41.454567: E
tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to
cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2024-04-01 22:08:41.454592: I
tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168]
retrieving CUDA diagnostic information for host: chang-System-Product-Name
2024-04-01 22:08:41.454595: I
tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname:
chang-System-Product-Name
2024-04-01 22:08:41.454678: I
tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda
reported version is: 545.23.8
2024-04-01 22:08:41.454689: I
tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel
reported version is: 545.23.8
2024-04-01 22:08:41.454691: I
tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel
version seems to match DSO: 545.23.8
Inference / segmentation
2024-04-01 22:08:42.569555: W
tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 471859200
exceeds 10% of free system memory.
2024-04-01 22:08:43.290274: W
tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 471859200
exceeds 10% of free system memory.
2024-04-01 22:08:45.227286: W
tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 471859200
exceeds 10% of free system memory.
2024-04-01 22:08:49.154534: W
tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 353894400
exceeds 10% of free system memory.
2024-04-01 22:08:51.720818: W
tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 471859200
exceeds 10% of free system memory.
1/1 [==============================] - 85s 85s/step
Postprocessing
Saving result
Segmenting floating image
Reading floating image
Inference / segmentation
1/1 [==============================] - 190s 190s/step
Postprocessing
Saving result
Linear registration
Computing centroids and estimating affine transform
Traceback (most recent call last):
File "/usr/local/freesurfer/python/scripts/mri_easyreg", line 1809, in
<module>
main()
File "/usr/local/freesurfer/python/scripts/mri_easyreg", line 180, in main
Mref = getM(atlasCOG[:, ok > 0], refCOG[:, ok > 0])
File "/usr/local/freesurfer/python/scripts/mri_easyreg", line 1198, in getM
x = np.matmul(np.linalg.inv(np.matmul(np.transpose(A), A)),
np.matmul(np.transpose(A), b))
File "<__array_function__ internals>", line 180, in inv
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py",
line 552, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py",
line 89, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Monday, April 1, 2024 8:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
with --parc option ?
Dear Edward,
Try deleting:
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii
and
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz
And then run the same command. Easy_reg will create the right segmentations for
you.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
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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 r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>
<r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>>
Date: Sunday, March 31, 2024 at 3:55 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with
--parc option ?
External Email - Use Caution
Hello Freesurfer Developpers,
I attempted to run mri_easyreg (Freesurfer 7.4) between two images.
After I ran mri-easyreg adding these images (--ref_seg
--flo_reg), I get again the > no cortical parcels.
The following is the command I used and the error code.
What did I do wong?
Any hints?
Thanks in advance for your help.
Best,
Edward
mri_easyreg --ref
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip.nii
--flo
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_0000.nii.gz
--ref_seg
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii
--flo_seg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz
--ref_reg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_ref_reg.nii.gz
--flo_reg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_flo_reg.nii.gz
--fwd_field
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_FWF.nii.gz
--bak_field
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_BWF.nii.gz
2024-03-31 15:50:23.731218: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not
find cuda drivers on your machine, GPU will not be used.
2024-03-31 15:50:23.752531: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not
find cuda drivers on your machine, GPU will not be used.
2024-03-31 15:50:23.752807: I
tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is
optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations,
rebuild TensorFlow with the appropriate compiler flags.
2024-03-31 15:50:24.041622: W
tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not
find TensorRT
using 1 thread
Segmentation of reference image already exists; reading from disk
Error: No cortical labels found; does the segmentation include cortical parcels?
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