Glad to hear, Edward!
The cost masking feature is not available.
To provide such a functionality, one would have to retrain with (possibly
random) masks? I don’t know if Malte (CCed) plans to incorporate this into
SynthMorph (or maybe he’s done already and I’m unaware of it?).
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: Wednesday, April 3, 2024 at 7:43 PM
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
I just wanted you to know that the issue with the command has been resolved
successfully after employing an alternative MNI template.
The modification appears to have rectified the problem, and the command is now
functioning as expected.
However, I would like to inquire about the capabilities of Easyreg pertaining
to registration processes. Specifically, does Easyreg facilitate the
implementation of cost function masking during registration?
Thanks in advance for your help.
Best,
Edward
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Wednesday, April 3, 2024 4:16 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
with --parc option ?
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
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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: Monday, April 1, 2024 at 10:24 AM
To: 'Freesurfer support list'
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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"
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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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