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,

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,

Juan Eugenio Iglesias

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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.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: Sunday, March 31, 2024 at 3:55 AM
To: freesurfer@nmr.mgh.harvard.edu <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

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?