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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of r04458...@ntu.edu.tw <r04458...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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.com<http://secure-web.cisco.com/1M3SoafGSVXaU77A6ezZXvK1VbCrpi0uDSbaQ3S5sFjrIWWsrqu48Nphi59DtTAgDzxQWKHBmXHWYwq_8Bm1RCDLYFLgzMPB_nj8uPo4agTasGzvj8yJ4rGXxmcgD1QiucykJ947v_qd25X3ZaPMtbgNzA9mI3YjF5VcA_jHU1np3l4Kmtm4n-dl2ZqJHuqlaollbdx6Ba--KeqVbtAMmr8UpIIUoB1674qDT8_g3vI0O_gHxKr3MaXqtfe3V_0xH8w6rlHKz3FdU2GYWeL8IijsoMBsWuipV07Q6KtSOoRiYSsouQun9dja17Z8pojO3/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 Edward Su <r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>> Date: Thursday, April 4, 2024 at 11:51 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 ? 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 > <mhoffm...@mgh.harvard.edu<mailto:mhoffm...@mgh.harvard.edu>> wrote: > > What are you trying to achieve? > > ________________________________________ > From: Iglesias Gonzalez, Juan E. > <jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@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-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/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: Wednesday, April 3, 2024 at 7:43 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 ? > > 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<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: Wednesday, April 3, 2024 4:16 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 ? > > 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-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com<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><http://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> > on behalf of > r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw%3cmailto:r04458...@ntu.edu.tw>> > > <r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw%3cmailto: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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto: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<mailto: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-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3KXDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/http%3A%2F%2Fwww.jeiglesias.com<http://secure-web.cisco.com/1-q3mT9vTdAapiqbsXI3OPjVT3m8xjQKkHHLvyVZZFFM9DJ_5k0PAnQnJX6I4Cl4Q0ET_kF2QuivsdvaRRLnKGUY3-p9v8vRR-YtaT47YWeAJwR7cvWfk9HLDY3ninRU7SRlACRb9gf2xr4m3_cvdcb01Mkixcxdqur8fPlcUevmMl_UedfbZ7AfamE7MOmv4LOSo3F80ZVCWW6Ag9IjPMWiHAmC-pr3DJ4lyDxk8adwWkRbcbABEj0E6MBEoWChyxIszaQWb9zgG_gaDaSlF0WrtDGGGutc_Qa1Q9JlvByRARNCt6T_00GOWSxfalQgU/http%3A%2F%2Fwww.jeiglesias.com><http://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu%3cmailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> > on behalf of > r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw%3cmailto:r04458...@ntu.edu.tw>> > > <r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw%3cmailto: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<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>> > > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu<mailto: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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