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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 http://www.jeiglesias.comhttp://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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?

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Monday, April 1, 2024 at 10:24 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 http://www.jeiglesias.comhttp://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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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Hello Malte

Thank you for your response. I am writing to express my interest in utilizing the easy_reg tool for the purpose of normalizing patient data, specifically those diagnosed with Gliomas, to MNI space.

A particular concern of mine is the potential impact of the tumor region on the loss function during the registration process.

It is my hope that the loss function attributed to the tumor region could be excluded or minimized to ensure the accuracy of the normalization.

Furthermore, I am keen to know whether easy_reg supports the application of cost function masking, or if there exists an alternative approach within FreeSurfer that you might recommend for achieving this objective.

Thanks in advance!

Best regards, Edward

Sent from my iPad

On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:

What are you trying to achieve?

---

From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, April 4, 2024 09:02 To: Freesurfer support list Cc: Hoffmann, Malte,PhD Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@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 ?

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Monday, April 1, 2024 at 10:24 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...http://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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?

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1yHEkeBnbAAzb8GXeE9RJC5tvBqLBv6ecNOIKAr7wnWNuqV... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzy... https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzyrvMmBCQCY35Pg28byQDOvYEpcmgqtgfk9PV8BwpYzE0uNrf2UKDiB0zDuCkhnoMcTxLeh7Nrz6mlvpFvXI0jlaupScnsdaDk-Ht_vMfBjOtF3bXeXKwIeSvzOPCnhmPhcrmqyUqwYE2lm8kNZTKvZI-Fwv6mi7nMWLVamAHFGJAi75EJ-J8nkhu2l3NEZdXBHIGPsDVTuAcnCceQ5Pmrm5rCKVwy92Z4QZZ7-M2-RYfZyV8g1MAhlRbsjsHP2VWrLfmIOfWXYsJdexePxZTO3KoL_IrCJ-9dRdUzKzPw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Dear Malte,

Thank you for your reply.

Upon implementing the methodologies you described on my dataset, I observed an unusual, lumpy artifact in the registered images. Could you possibly shed light on the nature of this anomaly?

Thanks in advance.

Warm regards, Edward -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Hoffmann, Malte,PhD Sent: Saturday, April 6, 2024 1:04 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

Thanks for clarifying, Edward. I'm afraid this is not currently implemented and would likely require retraining with a specifically labeled dataset and/or a new architecture that could take in masks at test time.

That being said, these methods don't optimize at registration time and have been trained on very diverse data, so they might produce reasonable results for glioma patients out of the box - as we found SynthMorph does in this paper: https://secure-web.cisco.com/1kE_bDAbkt12NU_kEzYQ7uTItDfPtktuoWiyahNJ9_wRqrd... (see top right of Figures 1 and 13, for example).

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Edward Su r04458005@ntu.edu.tw Sent: Thursday, April 4, 2024 23:49 To: Freesurfer support list Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

External Email - Use Caution

Hello Malte

Thank you for your response. I am writing to express my interest in utilizing the easy_reg tool for the purpose of normalizing patient data, specifically those diagnosed with Gliomas, to MNI space.

A particular concern of mine is the potential impact of the tumor region on the loss function during the registration process.

It is my hope that the loss function attributed to the tumor region could be excluded or minimized to ensure the accuracy of the normalization.

Furthermore, I am keen to know whether easy_reg supports the application of cost function masking, or if there exists an alternative approach within FreeSurfer that you might recommend for achieving this objective.

Thanks in advance!

Best regards, Edward

Sent from my iPad

On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:

What are you trying to achieve?

---

From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, April 4, 2024 09:02 To: Freesurfer support list Cc: Hoffmann, Malte,PhD Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i _ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9 oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw 5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3K XDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/ http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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_ti rq_1.0mm_T1_scalp_trip_synthseg.nii And /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_0000_synthseg.nii.gz ? Cheers, /E -- Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i _ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9 oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw 5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3K XDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/ http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1cT1MaLk1h UpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SM IOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2 783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBD KEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHu omZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.m gh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr. mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Monday, April 1, 2024 at 10:24 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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_ti rq_1.0mm_T1_scalp_trip.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_04 2_0000.nii.gz --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_ti rq_1.0mm_T1_scalp_trip_synthseg.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_0000_synthseg.nii.gz --ref_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_ref_reg.nii.gz --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_flo_reg.nii.gz --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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_ti rq_1.0mm_T1_scalp_trip_synthseg.nii and /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/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 http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i _ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9 oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw 5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3K XDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/ http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1-q3mT9vTd AapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2Quivsdva RRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdc b01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC -pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Q a1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.m gh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr. mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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_ti rq_1.0mm_T1_scalp_trip.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_04 2_0000.nii.gz --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_ti rq_1.0mm_T1_scalp_trip_synthseg.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_0000_synthseg.nii.gz --ref_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_ref_reg.nii.gz --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_flo_reg.nii.gz --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/042/pre_042_FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synths eg/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?

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1yHEkeBnbAAzb8GXeE9RJC5tvBqLBv6ecNOIKAr7w nWNuqVrmb5unTEKaiMDcNFZ59DXHnJ3I7gn1kn3hrvcJkpFEAiAXuJ2ORtR4qY61oYz65I g7aUYzFJhlGg6IYbXngt0G95mguTMxc4jIcP_eBbY8deRllIsAArj4opPBe23rqitVoK8x MJ60rwOVeY3KGmvfpRxwErl35INeGbDmdJxXVofqy1sjutC5T8B0-UFaUnhjcv9qYQZC10 w_TSyunT0sGsNzkjgfVvjafzqqMj0edaieh-IKVmgnne04tjgcv_GyO2o_HPOqQtmdvKCn k6A8Mut2jUSfZgBuIpelNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailma n%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzy... https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzyrvMmBCQCY35Pg28byQDOvYEpcmgqtgfk9PV8BwpYzE0uNrf2UKDiB0zDuCkhnoMcTxLeh7Nrz6mlvpFvXI0jlaupScnsdaDk-Ht_vMfBjOtF3bXeXKwIeSvzOPCnhmPhcrmqyUqwYE2lm8kNZTKvZI-Fwv6mi7nMWLVamAHFGJAi75EJ-J8nkhu2l3NEZdXBHIGPsDVTuAcnCceQ5Pmrm5rCKVwy92Z4QZZ7-M2-RYfZyV8g1MAhlRbsjsHP2VWrLfmIOfWXYsJdexePxZTO3KoL_IrCJ-9dRdUzKzPw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vay_rnyLwStpfM1_RoiTPX1-i-phNLbKUVsE83QCr5VLsW... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1hzcLY9mMiX59Sv45qTwg-uA7sv59kBnv3_acfLA_B4Srbo... https://secure-web.cisco.com/1hzcLY9mMiX59Sv45qTwg-uA7sv59kBnv3_acfLA_B4Srbo1rSIcFt24su8TXgMdw9iAduljVGQ_RW8QHedyFXxJmxlIMkv83TSyANsqto-UkriJ5VWQzBkm62fxQHGXPKI5BHcAjaOFw25wx2X8ST0CJfb1NlYxsTlZhIKzytJKpzDaIc3vWUfsz0BUTbRdK9xOiPe-evbUfuuZi665SOfvlO40xRhbIaEDjyhYCoGL77fAKYrVUQAAz2yljRLF7QFwbtJVlRnf7MAVdXes_PtPYNxgRdP1diHlkIG_mw5gdg6_XJJ5Trv2CmnzGKzZKMEeXcSfUSn2Qvke-OfDS3w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Hi again, Edward. I would totally run mri_synthsr on the images to “wipe” the tumors, register those images, and apply the fields to the original scans :-) Cheers, /Eugenio

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Edward Su r04458005@ntu.edu.tw Date: Thursday, April 4, 2024 at 11:51 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 Malte

Thank you for your response. I am writing to express my interest in utilizing the easy_reg tool for the purpose of normalizing patient data, specifically those diagnosed with Gliomas, to MNI space.

A particular concern of mine is the potential impact of the tumor region on the loss function during the registration process.

It is my hope that the loss function attributed to the tumor region could be excluded or minimized to ensure the accuracy of the normalization.

Furthermore, I am keen to know whether easy_reg supports the application of cost function masking, or if there exists an alternative approach within FreeSurfer that you might recommend for achieving this objective.

Thanks in advance!

Best regards, Edward

Sent from my iPad

On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:

What are you trying to achieve?

---

From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, April 4, 2024 09:02 To: Freesurfer support list Cc: Hoffmann, Malte,PhD Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...http://secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com%3chttp:/secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.com%3e

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Monday, April 1, 2024 at 10:24 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...http://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com%3chttp:/secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com%3e

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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?

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1yHEkeBnbAAzb8GXeE9RJC5tvBqLBv6ecNOIKAr7wnWNuqV... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzy... https://secure-web.cisco.com/1cxev3tGRl_8H4xhcSP0NnuH2I_siEF3gsYZU67UQRSvyzyrvMmBCQCY35Pg28byQDOvYEpcmgqtgfk9PV8BwpYzE0uNrf2UKDiB0zDuCkhnoMcTxLeh7Nrz6mlvpFvXI0jlaupScnsdaDk-Ht_vMfBjOtF3bXeXKwIeSvzOPCnhmPhcrmqyUqwYE2lm8kNZTKvZI-Fwv6mi7nMWLVamAHFGJAi75EJ-J8nkhu2l3NEZdXBHIGPsDVTuAcnCceQ5Pmrm5rCKVwy92Z4QZZ7-M2-RYfZyV8g1MAhlRbsjsHP2VWrLfmIOfWXYsJdexePxZTO3KoL_IrCJ-9dRdUzKzPw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Glad to hear, Edward! I am not surprised that the effect of masking and inpaiting with “boring” healthy tissue (the inpainted area is normally flat in terms of texture) is similar. Cheers, /Eugenio

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of r04458005@ntu.edu.tw r04458005@ntu.edu.tw Date: Saturday, April 6, 2024 at 4:11 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 Dear Eugenio,

Thank you for your valuable suggestion.

Following the implementation of the method you recommended, I observed a notable improvement in the results when compared to those obtained solely using EasyReg. Moreover, I have undertaken a comparative analysis between your suggested method and the cost function masking technique as implemented in ANTs. The preliminary outcomes indicate that both approaches yield remarkably similar results with my dataset.

I intend to continue exploring both methodologies to ascertain the most effective technique for normalizing my data to MNI Space. Your insight has been instrumental in advancing my research, and I wish to express my sincere appreciation for your assistance.

Warm regards, Edward From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Saturday, April 6, 2024 3:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

Hi again, Edward. I would totally run mri_synthsr on the images to “wipe” the tumors, register those images, and apply the fields to the original scans :-) Cheers, /Eugenio

-- Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1M3SoafGSVXaU77A6ezZXvK1VbCrpi0uDSbaQ3S5sFjrIWWsrqu48Nphi59DtTAgDzxQWKHBmXHWYwq_8Bm1RCDLYFLgzMPB_nj8uPo4agTasGzvj8yJ4rGXxmcgD1QiucykJ947v_qd25X3ZaPMtbgNzA9mI3YjF5VcA_jHU1np3l4Kmtm4n-dl2ZqJHuqlaollbdx6Ba--KeqVbtAMmr8UpIIUoB1674qDT8_g3vI0O_gHxKr3MaXqtfe3V_0xH8w6rlHKz3FdU2GYWeL8IijsoMBsWuipV07Q6KtSOoRiYSsouQun9dja17Z8pojO3/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Edward Su <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Thursday, April 4, 2024 at 11:51 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ? External Email - Use Caution

Hello Malte

Thank you for your response. I am writing to express my interest in utilizing the easy_reg tool for the purpose of normalizing patient data, specifically those diagnosed with Gliomas, to MNI space.

A particular concern of mine is the potential impact of the tumor region on the loss function during the registration process.

It is my hope that the loss function attributed to the tumor region could be excluded or minimized to ensure the accuracy of the normalization.

Furthermore, I am keen to know whether easy_reg supports the application of cost function masking, or if there exists an alternative approach within FreeSurfer that you might recommend for achieving this objective.

Thanks in advance!

Best regards, Edward

Sent from my iPad

On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD <MHOFFMANN@mgh.harvard.edumailto:MHOFFMANN@mgh.harvard.edu> wrote:

What are you trying to achieve?

---

From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Sent: Thursday, April 4, 2024 09:02 To: Freesurfer support list Cc: Hoffmann, Malte,PhD Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw <r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw> Date: Wednesday, April 3, 2024 at 7:43 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...http://secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com%3chttp:/secure-web.cisco.com/1cT1MaLk1hUpIx5e993JvHDib3de8-4C_3q8iR19MMJyY_iyDOtcZHVEmcDwwRYd-jgjil8XL4mkI9SMIOT_GLVKDgVT39pEAOBvmVthK_Xgn3NG7fmuuH3s7TnNBrdBo5-GXN83iwCCFSP76ytMb2783KOC6SoR3RZ5stbB9h5RCT-PPQn3I3L8ExS1qdiwuv6ZYdGa3vAPxn78CHcd2BQK7nBDKEj4wPahZdiL0x_ctHCGRqG4sQL-VBmIKReZZVLMhLUCewgN1Qwj15012Ib_ucdC9X1eHuomZDBGMveOzekfh4SCRzO_6At_hfgmK/http%3A%2F%2Fwww.jeiglesias.com%3e

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of r04458005@ntu.edu.tw<mailto:r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw%3cmailto:r04458005@ntu.edu.tw> <r04458005@ntu.edu.tw<mailto:r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw%3cmailto:r04458005@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.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto: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-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto: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 http://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rh...http://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.comhttp://secure-web.cisco.com/1ouhZwEqdGpAUrt0N7u1qdOMaij5zz0Vs6QXgRKV6i_ZM-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com%3chttp:/secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com%3e

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of r04458005@ntu.edu.tw<mailto:r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw%3cmailto:r04458005@ntu.edu.tw> <r04458005@ntu.edu.tw<mailto:r04458005@ntu.edu.twmailto:r04458005@ntu.edu.tw%3cmailto:r04458005@ntu.edu.tw>> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto: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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