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_1.0 mm_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://secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.com 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_1.0 mm_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_1.0 mm_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/linal g.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/linal g.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_1.0 mm_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 <http://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ _5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3 ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F 80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaS lF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.c om> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.com 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_1.0 mm_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_1.0 mm_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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