Comments (4)
Hi Iurii,
Thanks for this bug report. I think I encountered this recently and thought I had fixed it, but I neglected to check the example data. Could you try updating to the most recent version (1.1.4) and try again? I was uploaded to the conda channel yesterday. I'll also look into this shortly.
Will
from fsl_mrs.
Hi Will,
Thank you very much for your respond! I have update it to most recent version (1.1.4) but the problem still exist. Also I try it with wsl on Windows 10 but there I have even not able to use segmentation:
['',
'Part of FSL (build 508)',
'applywarp ',
'Copyright(c) 2001, University of Oxford (Jesper Andersson)',
'',
'Usage: ',
'applywarp -i invol -o outvol -r refvol -w warpvol',
'applywarp -i invol -o outvol -r refvol -w coefvol',
'',
'',
'Compulsory arguments (You MUST set one or more of):',
'\t-i,--in\tfilename of input image (to be warped)',
'\t-r,--ref\tfilename for reference image',
'\t-o,--out\tfilename for output (warped) image',
'',
'Optional arguments (You may optionally specify one or more of):',
'\t-w,--warp\tfilename for warp/coefficient (volume)',
"\t--abs\t\ttreat warp field as absolute: x' = w(x)",
"\t--rel\t\ttreat warp field as relative: x' = x + w(x)",
'\t-d,--datatype\tForce output data type [char short int float double].',
'\t-s,--super\tintermediary supersampling of output, default is off',
"\t--superlevel\tlevel of intermediary supersampling, a for 'automatic' or integer level. Default = 2",
'\t--premat\tfilename for pre-transform (affine matrix)',
'\t--postmat\tfilename for post-transform (affine matrix)',
'\t-m,--mask\tfilename for mask image (in reference space)',
'\t--interp\tinterpolation method {nn,trilinear,sinc,spline}',
'\t--paddingsize\tExtrapolates outside original volume by n voxels',
'\t-v,--verbose\tswitch on diagnostic messages',
'\t-h,--help\tdisplay this message',
'',
'',
'',
'Exception in thread Thread-2:',
'Traceback (most recent call last):',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/threading.py", line 932, in _bootstrap_inner',
' self.run()',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/threading.py", line 870, in run',
' self._target(*self._args, **self._kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 116, in realForward',
" else: o.write(line.decode('utf-8'))",
"UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf0 in position 1: invalid continuation byte",
'Traceback (most recent call last):',
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 76, in ',
' main()',
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 65, in main',
" applywarp_func(op.join(anat, 'T1_fast_pve_0.nii.gz'),",
' File "/home/iurii/anaconda3/envs/fsl_mrs/bin/mrsi_segment", line 56, in applywarp_func',
' applywarp(i,',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 1094, in wrapper',
' result = fot(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 756, in call',
' result = func(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 1136, in wrapper',
' return fot(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 756, in call',
' result = func(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 197, in wrapper',
' return runner(cmd,',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 390, in runfsl',
' return run(*args, **kwargs)',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 225, in run',
' stdout, stderr, exitcode = _realrun(',
' File "/home/iurii/anaconda3/envs/fsl_mrs/lib/python3.8/site-packages/fsl/utils/run.py", line 343, in _realrun',
" stderr = stderr.decode('utf-8')",
"UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf0 in position 1204: invalid continuation byte"]
Regards,
Iurii
from fsl_mrs.
Hi @inokentiyTTT Thanks for confirming this. I've reopened the issue so it says on my radar. I'll take a look at this soon.
Will
from fsl_mrs.
Hi @inokentiyTTT I believe everything should be fixed in version 1.1.5 which has now been released. Thanks again for the bug report.
from fsl_mrs.
Related Issues (18)
- version `GLIBC_2.27' not found HOT 4
- nifti_mrs_proc slow ? HOT 4
- Using LCModel Basis Set: ValueError: could not convert string to float: 'badelt=-3.99999990e-04' HOT 11
- XA31: Differences between .rda and .dat HOT 4
- 3T GE 35TE PRESS - TE "unusal value. Expecting a value < 0.5s" HOT 4
- 3T GE with unsupressed water: null for mMol/kg HOT 4
- $FSLDIR not found during segmentation task HOT 12
- problem with fsl_mrs_proc coilcombine HOT 1
- Processing GE p-files HOT 1
- dimension error in philips 3T MRS data reprocessing HOT 1
- spec2nii ge Pfile: spec2nii.GE.ge_read_pfile.UnknownPfile: No Pfile mapper for pulse sequence = slaser
- Problem converting and visualizing GE P-file data HOT 10
- Windows installation aux directory name HOT 1
- Problem converting GE P-file HOT 8
- Create basis data with Vespa HOT 2
- Show SVS voxel locations - notebook HOT 2
- FSL MRS standard fitting model HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from fsl_mrs.