Hi Edward,
What did you run exactly, and could you share the image before and after?
Thanks,
Malte
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of r04458...@ntu.edu.tw
<r04458...@ntu.edu.tw>
Sent: Sunday, April 7, 2024 05:36
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after
SynthSeg with --parc option ?
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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_fONoii_c8lBO6aBLKRVPgXehgkYx-8D09m63SQ83bydPp2nr6yCIeSp8HuU3PjDt6RA9zIiq5-QXujF5T-RkVZK7f9J7pajAVutBpaP9GjrozIbIcqpGFkIePMb8D6NrjLJnfLYu3V5TRqaDKHZ53l5MKgjN6wt31oqLGFK-WGyct6pjHscj2fOwZ2mP_yJIzJ9H5af6EmIcGx96YIQqud11Ou-im2l95OHrv98E_xLpwpTiJXjDxG-r451HUyW6-x3EZ5em3maPIt04N3lUhW_r3MSZ0a5GfMkJjmw/https%3A%2F%2Farxiv.org%2Fabs%2F2301.11329
(see top right of Figures 1 and 13, for example).
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Edward Su
<r04458...@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 <mhoffm...@mgh.harvard.edu>
> wrote:
>
> What are you trying to achieve?
>
> ________________________________________
> From: Iglesias Gonzalez, Juan E. <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-rhSzzKp9j0xMOL8h0yOO07WMmSYRrpdyMJF4586c3tir4vL3M3rq0ChdHVO5moZBV9
> oev4gcSu5npfWMRAikoveO6sfzUSf9F2Mgc6ki0GVT_C7oQoKZTN0zxyz_ob_aLHIyfeMw
> 5rVBM1EWuzv6Xmcca_e0aa8I7IrLRYSCsBSiTX2Yy86COMdgb9tQPIZCWuU-rAMq_ZYE3K
> XDERV8FeDQCqCgxz_LnH59M9oi-tSND3q9ofUg_ljVaYKkHk-TlACgda6hstyPztwQf74/
> http%3A%2F%2Fwww.jeiglesias.com
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
> r04458...@ntu.edu.tw <r04458...@ntu.edu.tw>
> Date: Wednesday, April 3, 2024 at 7:43 PM
> To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
> with --parc option ?
>
> External Email - Use Caution
> Hello Eugenio
>
> I just wanted you to know that the issue with the command has been resolved
> successfully after employing an alternative MNI template.
> The modification appears to have rectified the problem, and the command is
> now functioning as expected.
> However, I would like to inquire about the capabilities of Easyreg pertaining
> to registration processes. Specifically, does Easyreg facilitate the
> implementation of cost function masking during registration?
>
>
> Thanks in advance for your help.
>
>
>
> Best,
>
>
>
> Edward
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Iglesias Gonzalez, Juan
> E.
> Sent: Wednesday, April 3, 2024 4:16 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
> with --parc option ?
>
> Ha! I understand that sharing the images may be tricky, but do you
> think you could send me the segmentations
> /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_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.com<http://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.m
> gh.harvard.edu>
> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.
> mgh.harvard.edu>> on behalf of
> r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>
> <r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>>
> Date: Monday, April 1, 2024 at 10:24 AM
> To: 'Freesurfer support list'
> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> >
> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
> with --parc option ?
>
> External Email - Use Caution
> Hello Eugenio
>
> Thanks for the reply!
>
> After I follow your instruction, the command works for a while for the
> segmentation part and some errors come up as following.
>
>
> Any hints?
>
>
>
> Thanks in advance for your help.
>
>
>
> Best,
>
>
>
> Edward
>
>
> mri_easyreg --ref
> /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>
> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> On Behalf Of Iglesias Gonzalez, Juan E.
> Sent: Monday, April 1, 2024 8:41 PM
> To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> >
> Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg
> with --parc option ?
>
> Dear Edward,
> Try deleting:
> /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_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.com<http://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.m
> gh.harvard.edu>
> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.
> mgh.harvard.edu>> on behalf of
> r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>
> <r04458...@ntu.edu.tw<mailto:r04458...@ntu.edu.tw>>
> Date: Sunday, March 31, 2024 at 3:55 AM
> To:
> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> >
> Subject: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with
> --parc option ?
>
> External Email - Use Caution
> Hello Freesurfer Developpers,
>
>
> I attempted to run mri_easyreg (Freesurfer 7.4) between two images.
>
> After I ran mri-easyreg adding these images (--ref_seg
>
> --flo_reg), I get again the > no cortical parcels.
>
> The following is the command I used and the error code.
>
>
>
> What did I do wong?
>
>
>
> Any hints?
>
>
>
> Thanks in advance for your help.
>
>
>
> Best,
>
>
>
> Edward
>
> mri_easyreg --ref
> /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_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
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> 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
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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
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<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
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