Re: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")

2024-04-03 Thread fsbuild 
External Email - Use Caution

The permissions on /scratch may not be set to allow you to write files 
there. If it does not work from the terminal window to create a plain 
file there via the command,
$ touch /scratch/foo
- then you will get the same permission denied error.
If the above fails, then you should contact whoever setup the machine, your IT 
department, etc. and ask them to provide write permission there.
- R,

Begin forwarded message:From:XinRan Wu wxr1173199...@gmail.com
Subject:[Freesurfer] Question about mris_compute_lgi error: 
/scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission 
denied")
Date:April 3, 2024 at 12:14:38 EDT
To:freesurfer@nmr.mgh.harvard.edu
Reply-To:Freesurfer support list freesurfer@nmr.mgh.harvard.edu

ERROR: could not open /scratch/

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Re: [Freesurfer] Support for GPU on Freesurfer

2024-04-03 Thread fsbuild 
External Email - Use Caution

Use of parallelization depends upon the order of how the data needs to be 
processed. The recon-all command is not single command, but a 
wrapper command that runs a sequence or pipeline of many lower level freesurfer 
commands in a certain order.  It’s not unexpected for recon-all of the 
subject bert data to take ~8 hours on a consumer (non-server, non-cluster), 
stand-alone machine, e.g. recent Intel I9 chip with 8 physical (performance) ~3 
GHz cores, 8 virtual cores, 32G of DDR4 RAM and an SSD drive. If you have 
access to a computing cluster, you could try running recon-all there - which 
should reduce the processing time.
- R.

On Apr 3, 2024, at 14:58, Camargo, Aldo acama...@som.umaryland.edu 
wrote:External Email - Use 
CautionHi there,I was 
wonderingif there is support for GPU on FreeSurfer. I really would like 
to use it on GPU because is taking 9 hours per subject to recon-all.Thanks a 
lot and have a nice day,Aldo CamargoSenior Postdoctoral Fellow at the 
University of Maryland, 
Baltimore___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Question on using thalseg_1.1.h5

2024-04-03 Thread Georgios Argyropoulos 
External Email - Use Caution

Dear Colleagues,

Hope you're well.

I have been trying to use the thalseg_1.1.h5 patch (MRI Segment Thalamic
Nuclei CNN model v1.1 update). I use the following command:

mri_segment_thalamic_nuclei_dti_cnn --t1 mri/norm.dwispace.mgz --aseg
mri/aseg.dwispace.mgz --fa dmri/dtifit_FA.nii.gz --v1 dmri/dtifit_V1.nii.gz
--o outputSegmentation.nii.gz --vol measuredVolumes.csv --model
/usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 --threads 3

However, I have been encountering the following error message. I was
wondering whether you may be able to help.

many thanks

georgios



Using user-specified model:
/usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5
DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is
deprecated, and will error in future. Ensure you extract a single element
from your array before performing this operation. (Deprecated NumPy 1.25.)
DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is
deprecated, and will error in future. Ensure you extract a single element
from your array before performing this operation. (Deprecated NumPy 1.25.)
DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is
deprecated, and will error in future. Ensure you extract a single element
from your array before performing this operation. (Deprecated NumPy 1.25.)
Traceback (most recent call last):
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
2551, in 
main()
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
164, in main
predict(
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
258, in predict
net = build_model(model_file_segmentation=path_model_segmentation,
  
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
661, in build_model
net = unet(nb_features=24,
  
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
942, in unet
dec_model = conv_dec(nb_features,
^
  File
"/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line
1125, in conv_dec
input_shape = last_tensor.shape.as_list()[1:]
  ^
AttributeError: 'list' object has no attribute 'shape'

-- 
Georgios P. D. Argyropoulos
PhD, CPsychol, FHEA
Division of Psychology, Faculty of Natural Sciences; University of
Stirling; FK9 4LA Scotland UK
*Personal Website 
*
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Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

2024-04-03 Thread r04458005 
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
 On Behalf Of Iglesias Gonzalez,
Juan E.
Sent: Wednesday, April 3, 2024 4:16 AM
To: Freesurfer support list 
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_1.0
mm_T1_scalp_trip_synthseg.nii

And

/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042
/pre_042__synthseg.nii.gz

?

Cheers,

/E

--

Juan Eugenio Iglesias

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-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of
r04458...@ntu.edu.tw   mailto:r04458...@ntu.edu.tw> >
Date: Monday, April 1, 2024 at 10:24 AM
To: 'Freesurfer support list' 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_tirq_1.0
mm_T1_scalp_trip.nii --flo
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_
.nii.gz --ref_seg
/home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0
mm_T1_scalp_trip_synthseg.nii --flo_seg
/home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042
/pre_042__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

[Freesurfer] Support for GPU on Freesurfer

2024-04-03 Thread Camargo, Aldo 
External Email - Use Caution

Hi there,

I was wondering if there is support for GPU on FreeSurfer. I really would like 
to use it on GPU because is taking 9 hours per subject to recon-all.

Thanks a lot and have a nice day,

Aldo Camargo
Senior Postdoctoral Fellow at the University of Maryland, Baltimore


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[Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")

2024-04-03 Thread XinRan Wu 
External Email - Use Caution

I am a researcher currently working with the Freesurfer 7.1.1 version for a
research project. I have encountered an issue while trying to compute the
local gyrification index (LGI).

We have pre-existing Freesurfer analysis results, and we want to use the
mris_compute_lgi script to calculate the LGI values. However, we are facing
difficulties in the first step of running the mris_fill command to generate
the ?h.pial.filled.mgz file. After the command completes, we are unable to
read the generated ?h.pial.filled.mgz file, and we receive the following
error:

reading filled volume...
/bin/bash: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh:
Permission denied
ERROR: could not open
/scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh for reading
ERROR: loading lh.pial.filled.mgz as MGH
Dot indexing is not supported for variables of this type.
Error in make_outer_surface (line 25)
volume=vol.vol;

We have also tried to read the lh.pial.filled.mgz file generated by
mris_fill using the load_mgh function individually, but we are still unable
to read it successfully.

Could you please provide us with some guidance on how to resolve this
issue?
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