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

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?