HI
When I wanna process my own dmri data
forest@DESKTOP-DM8SQ21:~/linmin$ sct_maths -i linmin.nii.gz -mean t -o dmri_mean.nii.gz
--
Spinal Cord Toolbox (git-HEAD-95e66208c9d6937fbe00e86db6176e4001196e56)
sct_maths -i linmin.nii.gz -mean t -o dmri_mean.nii.gz
--
Segmentation fault (core dumped)
Something went wrong.
Hi,
Could you please run:
sct_check_dependencies
and show us the output.
thanks
forest@DESKTOP-DM8SQ21:~/sct_course_london20/single_subject/data$ sct_check_dependencies
--
Spinal Cord Toolbox (git-HEAD-95e66208c9d6937fbe00e86db6176e4001196e56)
sct_check_dependencies
--
SCT info:
- version: git-HEAD-95e66208c9d6937fbe00e86db6176e4001196e56
- path: /home/forest/sct
OS: linux (Linux-4.4.0-19041-Microsoft-x86_64-with-debian-buster-sid)
CPU cores: Available: 6, Used by ITK functions: 6
RAM: Total: 16221MB, Used: 6968MB, Available: 9212MB
Check Python executable.............................[OK]
Using bundled python 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01)
[GCC 9.3.0] at /home/forest/sct/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if colored is installed.......................[OK] (1.4.2)
Check if dipy is installed..........................[OK] (1.3.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.1.5) is installed.................[OK] (2.1.5)
Check if ivadomed (2.7.2) is installed..............[OK] (2.7.2)
Check if matplotlib is installed....................[OK] (3.3.4)
Check if nibabel is installed.......................[OK] (3.2.1)
Check if numpy is installed.........................[OK] (1.19.5)
Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0)
Check if pandas is installed........................[OK] (1.1.5)
Check if psutil is installed........................[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.2.2)
Check if pytest-cov is installed....................[OK] (__version__ = '2.11.1')
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.25.1)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.5.3)
Check if scikit-image is installed..................[OK] (0.17.2)
Check if scikit-learn is installed..................[OK] (0.24.1)
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.57.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.3)
Check if pytest_console_scripts is installed........[OK]
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............failed to get the current screen resources
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-forest'
[OK]
OK, can you please now run:
sct_testing
forest@DESKTOP-DM8SQ21:~$ sct_testing
--
Spinal Cord Toolbox (git-HEAD-95e66208c9d6937fbe00e86db6176e4001196e56)
sct_testing
--
Creating temporary folder (/tmp/sct-20210318232327.723511-dllwwgiz)
Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 6 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking sct_deepseg_gm.............................[OK]
Checking sct_deepseg_lesion.........................[OK]
Checking sct_deepseg_sc.............................[OK]
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_convert................................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_b0_and_dwi.................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[OK]
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
Checking sct_qc.....................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_resample...............................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_warp_template..........................[OK]
status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Finished! Elapsed time: 155s
Excellent news, it means that SCT is working well on your end, and the problem likely comes from the data. Can you please share linmin.nii.gz
Hi jcohenadad
It is too big (about 13 MB) to upload ,so I emailed it to you.
hi,
this is too big for my email, can you just put it on the cloud (could be a private link), e.g. dropbox, google drive, OSF, etc.
Hum, I can successfully run the following command:
sct_maths -i linmin.nii.gz -mean t -o dmri_mean.nii.gz
Here is the output image: dmri_mean.nii.gz (1.6 MB)
You seem to have enough RAM available (~10GB), so I am wondering what is the problem on your end. Could you please download this smaller dataset linmin_small.nii.gz (4.0 MB) and try the following command:
sct_maths -i linmin_small.nii.gz -mean t -o dmri_mean.nii.gz
Hi jcohenadad
Thank you very much for your concern！
I finally found the problem was the file permissions, I changed the permissions to solve the problem.
Hello @chang, this bug mystifies us, so I am hoping you can help us track this down in more detail. How exactly did you change the permissions? What were they before?
Would you be willing to share what
history
says, at least for the section from the first time you ran sct_maths -i linmin.nii.gz to the time it finally worked.
That would help us avoid this problem for other people in the future.
Thanks! Have a good day.
Hi
(venv_sct) forest@DESKTOP-DM8SQ21:~$ history
1 cd/
2 ls
3 cd /
4 cd mnt
5 quit
6 exit
7 sct.exe clean
8 sct
9 cd sct
10 sudo passwd root
11 sudo cp /etc/apt/sources.list ~/.sources.listbf
12 sudo vim /etc/apt/sources.list
13 cd /etc/apt
14 sudo cp /etc/apt/sources.list /etc/apt/sources.list.20210305
15 sudo vim
16 sudo cp /etc/apt/sources.list /etc/apt/sources.list.20210305
17 sudo vim
18 sudo vim sources.list
19 sudo cp /etc/apt/sources.list /etc/apt/sources.list.20210305
20 sudo vim sources.list
21 cd /etc/apt
22 sudo vim sources.list
23 sudo apt update
24 exit
25 sudo apt-get update
26 sudo apt-get install language-pack-zh-han*
27 sudo vim /etc/profile
28 sudo vim /etc/ssh/sshd_config
29 sudo service ssh --full-restart
30 sudo apt-get -y update
31 sudo apt-get -y install gcc
32 sudo apt-get -y install unzip
33 sudo apt-get install -y python-pip python
34 sudo apt-get install -y psmisc net-tools
35 sudo apt-get install -y git
36 sudo apt-get install -y gfortran
37 sudo apt-get install -y libjpeg-dev
38 echo 'export DISPLAY=127.0.0.1:0.0' >> .profile
39 git clone https://github.com/neuropoly/spinalcordtoolbox.git sct
40 echo 'export DISPLAY=127.0.0.1:0.0' >> .profile
41 git clone https://github.com/neuropoly/spinalcordtoolbox.git sct
42 cd sct
43 git checkout 5.2.0
44 yes | ./install_sct
45 cd ~
46 source .profile
47 source .bashrc
48 cd /mnt/c
49 $SCT_DIR/batch_processing.sh
50 exit
51 cd sct
52 yes | ./install_sct
53 xclock
54 echo 'export DISPLAY=:0.0' >> .profile
55 yes | ./install_sct
56 cd sct
57 echo 'export DISPLAY=:0.0' >> .profile
58 yes | ./install_sct
59 pwd
60 cd sct
61 ls
62 ll
63 cd /tmp
64 ls
65 ll
66 rm -rf sct-20210306110821.709913-4ylurit9/
67 ll
68 cd
69 pwd
70 cd sct
71 ll
72 yes | ./instal_sct
73 yes | ./install_sct
74 cd ~
75 source .profile
76 source .bashrc
77 source/home/forest/.bashrc
78 cd sct
79 source/home/forest/.bashrc
80 cd /mnt/c
81 $SCT_DIR/batch_processing.sh
82 cd~
83 cd ~
84 xhost+
85 sct_check_dependencies
86 exit
87 sudo apt-get install x11-xserver-utils dconf-editor dbus-x11 -y
88 xhost +
89 sudo apt-get install xfce4-terminal
90 echo "export DISPLAY=:1.0">> ~/.bashrc
91 sudo xfce4-terminal
92 apt-get update
93 sudo apt install lubuntu-core lxde fcitx fcitx-googlepinyin
94 sudo apt install language-pack-gnome-zh-hans
95 sudo apt install fonts-wqy-zenhei
96 sudo startlxde
97 sudo apt-get install synaptic
98 sudo synaptic
99 sudo apt install lubuntu-core lxde fcitx fcitx-googlepinyin
100 apt-get update
101 sudo -s
102 sudo startlxde
103 sudo xfce4-terminal
104 source/home/forest/.bashrc
105 cd sct
106 source/home/forest/.bashrc
107 cd~
108 pwd
109 cd -
110 conda activate venv_sct
111 cd~sct
112 cd sct
113 conda activate venv_sct
114 cd -
115 sudo apt-get install build-essential
116 sudo apt-get install libgtk2.0-dev libgtk-3-dev libwebkitgtk-dev libwebkitgtk-3.0-dev
117 sudo apt-get install libjpeg-turbo8-dev libtiff5-dev libsdl1.2-dev libgstreamer1.0-dev libgstreamer-plugins-base1.0-dev libnotify-dev freeglut3-dev
118 source ${SCT_DIR}/python/etc/profile.d/conda.sh
119 conda activate venv_sct
120 conda config --set channel_priority strict
121 conda install -y -c conda-forge fsleyes
122 cd /mnt/c
123 cd -
124 sudo xfce4-terminal
125 sct_testing
126 #!/bin/bash
127 $SCT_DIR/batch_processing.sh
128 echo $0
129 if uname -a | grep -i darwin > /dev/null 2>&1; then open_cmd="open"; else open_cmd="xdg-open"; f; exit; d;
130 echo $0
131 if uname -a | grep -i darwin > /dev/null 2>&1; then open_cmd="open"; else open_cmd="xdg-open"; fi
132 cd ~
133 sct_download_data -d course_beijing19
134 cd sct_course-beijing19/single_subject
135 cd sct
136 cd sct_course-beijing19/single_subject
137 pwd
138 cd -
139 cd sct_course-beijing19
140 echo $0
141 if uname -a | grep -i darwin > /dev/null 2>&1; then open_cmd="open"; else open_cmd="xdg-open"; fi
142 cd sct_course-beijing19/single_subject
143 sct_download_data -d course_beijing19
144 cd sct_course_beijing19/single_subject
145 cd sct_course_beijing19
146 cd sct_data -d course_beijing19
147 cd sct_course-beijing19/single_subject
148 cd sct_course_beijing19/single_subject
149 chmod 775 *.sh
150 ./batch_single_subject.sh
151 batch_single_subject.sh
152 curl -L https://osf.io/bze7v/?action=download -o sct_course_london20.zip
153 sct
154 cd sct
155 sct
156 cd -
157 source /home/forest/.bashrc
158 pwd
159 cd sct
160 pwd
161 ll
162 sct_version
163 sct_testing
164 cd -
165 ll
166 unzip -o sct_course_london20.zip
167 cd sct_course_london20/single_subject
168 ll
169 cd batch_single_subject.sh*
170 chmod 775 *.sh
171 ./batch_single_subject.sh
172 cd data/t2
173 ls
174 t2.nii.gz
175 sct_pro
176 sct_propseg
177 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
178 exit
179 cd sct_course_london20/single_subject
180 chmod 775 *.sh
181 ./batch_single_subject.sh
182 echo $0
183 if uname -a | grep -i darwin > /dev/null 2>&1; then open_cmd="open"; else open_cmd="xdg-open"; fi
184 cd sct_course_london20/single_subject
185 chmod 775 *.sh
186 ./batch_single_subject.sh
187 ls
188 ll
189 sct_testing
190 cd fsleyes
191 ll
192 cd sct
193 ll
194 cd install/
195 ll
196 cd -
197 cd ~
198 cd fsleyes
199 ll
200 cd conda
201 cd .conda/
202 ll
203 cd -
204 source ${SCT_DIR}/python/etc/profile.d/conda.sh
205 conda activate venv_sct
206 fsleyes
207 sct_check_dependencies
208 cd /tmp/runtime-forest
209 ll
210 cd sct_course_london20/single_subject
211 chmod 775 *.sh
212 ./batch_single_subject.sh
213 cd data/t2
214 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
215 cd ~
216 fsleyes
217 cd fsleyes
218 source ${SCT_DIR}/python/etc/profile.d/conda.sh
219 conda activate venv_sct
220 fsleyes
221 #rpm -q -a
222 #rpm-q-a
223 exit
224 cd sct
225 git checkout 4.2.1
226 yes | ./install_sct
227 git checkout 4.2.1
228 yes | ./install_sct
229 git checkout 4.2.1
230 yes | ./install_sct
231 cd ~
232 rm -rf sct
233 cd sct
234 git clone https://github.com/neuropoly/spinalcordtoolbox.git sct
235 cd sct
236 git checkout 4.2.1
237 yes | ./install_sct
238 cd sct
239 git checkout 4.2.1
240 yes | ./install_sct
241 git checkout 5.2.0
242 yes | ./install_sct
243 cd <PATH_TO_SCT_INSTALLATION>
244 cd sct
245 cd <PATH_TO_SCT_INSTALLATION>
246 <PATH_TO_SCT_INSTALLATION>
247 git checkout 5.2.0
248 ./install_sct
249 source .profile
250 source .bashrc
251 cd /mnt/c
252 cd ~
253 sct_testing
254 ll
255 source ${SCT_DIR}/python/etc/profile.d/conda.sh
256 conda activate venv_sct
257 cd sct_course_london20/single_subject
258 chmod 775 *.sh
259 ./batch_single_subject.sh
260 cd data/t2
261 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
262 cd data/t2
263 cd ../t1
264 sct_propseg -i t1.nii.gz -c t1 -qc ~/qc_singleSubj
265 cd ~
266 fsleyes
267 ll
268 cd sct
269 ll
270 cd ~
271 ll
272 FSLeyes
273 cd fsleyes
274 exit
275 sudo apt-get install build-essential
276 source ${SCT_DIR}/python/etc/profile.d/conda.sh
277 conda activate venv_sct
278 conda config --set channel_priority strict
279 conda install -y -c conda-forge fsleyes
280 ll
281 cd ~
282 fsleyes
283 cd sct_course_london20/single_subject
284 chmod 775 *.sh
285 ./batch_single_subject.sh
286 cd data/t2
287 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
288 fsleyes /home/forest/sct_course_london20/single_subject/data/t2/t2.nii.gz -cm greyscale /home/forest/sct_course_london20/single_subject/data/t2/t2_seg.nii.gz -cm red -a 100.0 &
289 exit
290 source ${SCT_DIR}/python/etc/profile.d/conda.sh
291 conda activate venv_sct
292 cd sct_course_london20/single_subject
293 cd data/t2
294 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
295 fsleyes /home/forest/sct_course_london20/single_subject/data/t2/t2.nii.gz -cm greyscale /home/forest/sct_course_london20/single_subject/data/t2/t2_seg.nii.gz -cm red -a 100.0 &
296 cd -
297 cd data/t2
298 $open_cmd "/Users/julien/qc_singleSubj/index.html"
299 $open_cmd "/Users/julien/qc_singleSubj/index.html
300 cd-
301 cd -
302 exit
303 cd sct_course_london20/single_subject
304 ls
305 exit
306 source ${SCT_DIR}/python/etc/profile.d/conda.sh
307 conda activate venv_sct
308 cd sct_course_london20/single_subject
309 cd ../t1
310 ll
311 cd data
312 ll
313 cd t1
314 sct_propseg -i t1.nii.gz -c t1 -qc ~/qc_singleSubj
315 fsleyes /home/forest/sct_course_london20/single_subject/data/t1/t1.nii.gz -cm greyscale /home/forest/sct_course_london20/single_subject/data/t1/t1_seg.nii.gz -cm red -a 100.0 &
316 cd -
317 cd t2
318 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
319 cd ~
320 sudo synaptic
321 $open_cmd "/Users/chang/qc_singleSubj/index.html"
322 $open_cmd "/Users/chang/AppData/Local/Packages/CanonicalGroupLimited.Ubuntu18.04onWindows_79rhkp1fndgsc/LocalState/rootfs/home/forest/qc_singleSubj
323 exit
324 ssssssssss
325 ll
326 cd sct_course_london20
327 ll
328 cd single_subject
329 ll
330 cd t1
331 ll
332 cd data
333 cd t1
334 sct-warp-template
335 sct_warp_template
336 source ${SCT_DIR}/python/etc/profile.d/conda.sh
337 conda activate venv_sct
338 cd sct_course_london20/single_subject
339 cd t1
340 ll
341 cd data
342 cd t1
343 sct_deepseg_sc -i t1.nii.gz -c t1 -ofolder deepseg -qc ~/qc_singleSubj
344 cd ../t2
345 ls
346 sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc ~/qc_singleSubj
347 sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 3,9 -o t2_labels_vert.nii.gz
348 fsleyes t2_seg_labeled.nii.gz t2_labels_vert.nii.gz &
349 D
350 fsleyes /home/forest/sct_course_london20/single_subject/data/t2/t2.nii.gz -a 100.0 t2_seg_labeled.nii.gz -cm subcortical -a 50.0 &
351 DD\
352 sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -c t2 -qc ~/qc_singleSubj
353 fsleyes t2.nii.gz template2anat.nii.gz &
354 fsleyes /home/forest/sct/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz &
355 ls -la
356 sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0 -qc ~/qc_singleSubj
357 fsleyes t2.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &
358 sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -o csa_c3c4.csv
359 xdg-open /home/forest/sct_course_london20/single_subject/data/t2/csa_c3c4.csv
360 exit
361 C:\Users\chang\AppData\Local\Packages\CanonicalGroupLimited.Ubuntu18.04onWindows_79rhkp1fndgsc\LocalState\rootfs\home\forest\sct_course_london20\single_subject\batch_single_subject.sh
362 cat batch_single_subject
363 cd sct
364 ll
365 cd ~
366 C:\Users\chang\Desktop\batch_single_subject.sh
367 source ${SCT_DIR}/python/etc/profile.d/conda.sh
368 conda activate venv_sct
369 ll
370 cd sct_course_london20
371 ll
372 cd single_subject
373 cd data
374 cd t2
375 sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -o csa_c3c4.csv
376 cd ../mt
377 ll
378 sct_deepseg_sc -i mt1.nii.gz -c t2 -qc ~/qc_singleSubj
379 source ${SCT_DIR}/python/etc/profile.d/conda.sh
380 conda activate venv_sct
381 ll
382 cd sct_course_london20
383 ll
384 cd single_subject
385 ll
386 cd data
387 ll
388 cd mt
389 sct_deepseg_sc -i mt1.nii.gz -c t2 -qc ~/qc_singleSubj
390 cd ~
391 fsleyes
392 ll
393 cd sct_course_london20
394 ll
395 cd single_subject
396 cd data
397 cd mt
398 sct_deepseg_sc -i mt1.nii.gz -c t2 -qc ~/qc_singleSubj
399 cd ../t2s
400 sct_deepseg_sc -i t2s.nii.gz -c t2s -qc ~/qc_singleSubj
401 cd -
402 pwd
403 cd ~
404 cd sct_course_london20
405 cd single_subject
406 cd data
407 cd t2
408 sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
409 cd ~
410 pip3 install h5py==2.10.0
411 cd sct_course_london20
412 cd single_subject
413 cd data
414 cd mt
415 sct_deepseg_sc -i mt1.nii.gz -c t2 -qc ~/qc_singleSubj
416 sct_create_mask -i mt1.nii.gz -p centerline,mt1_seg.nii.gz -size 35mm -f cylinder -o mask_mt1.nii.gz
417 fsleyes /home/forest/sct_course_london20/single_subject/data/mt/mt1.nii.gz -cm greyscale /home/forest/sct_course_london20/single_subject/data/mt/mask_mt1.nii.gz -cm red -a 50.0 &
418 d
419 sct_register_multimodal -i mt0.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -m mask_mt1.nii.gz -x spline -qc ~/qc_singleSubj
420 fsleyes mt1.nii.gz mt0_reg.nii.gz &
421 sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1.nii.gz
422 fsleyes mt0_reg.nii.gz mt1.nii.gz ./mtr.nii.gz &
423 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -qc ~/qc_singleSubj
424 fsleyes dest_seg_RPI.nii src_seg_reg.nii &
425 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -qc ~/qc_singleSubj
426 cd ../t2s
427 sct_deepseg_sc -i t2s.nii.gz -c t2s -qc ~/qc_singleSubj
428 sct_deepseg_gm -i t2s.nii.gz -qc ~/qc_singleSubj
429 sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -o t2s_wmseg.nii.gz
430 fsleyes t2s_wmseg.nii.gz &
431 sct_register_multimodal -i ${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz -iseg ${SCT_DIR}/
432 data/PAM50/template/PAM50_wm.nii.gz -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -param
433 step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/
434 warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc ~/qc_singleSubj
435 sct_register_multimodal -i ${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz -iseg ${SCT_DIR}/data/PAM50/template/PAM50_wm.nii.gz -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc ~/qc_singleSubj
436 mv warp_PAM50_t2s2t2s.nii.gz warp_template2t2s.nii.gz
437 mv warp_t2s2PAM50_t2s.nii.gz warp_t2s2template.nii.gz
438 sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz -qc ~/qc_singleSubj
439 fsleyes t2s.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &
440 sct_process_segmentation -i t2s_gmseg.nii.gz -o csa_gm.csv -angle-corr 0
441 sct_process_segmentation -i t2s_wmseg.nii.gz -o csa_wm.csv -angle-corr 0
442 cd ../mt
443 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/
444 PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param
445 step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m
446 mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gzsct_warp_template -d t2s.nii.gz -w
447 warp_template2t2s.nii.gz -qc ~/qc_singleSubj
448 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz
449 cd ../dmri
450 sct_maths -i dmri.nii.gz -mean t -o dmri_mean.nii.gz
451 sct_propseg -i dmri_mean.nii.gz -c dwi -qc ~/qc_singleSubj
452 sct_create_mask -i dmri_mean.nii.gz -p centerline,dmri_mean_seg.nii.gz -size 35mm
453 sct_crop_image -i dmri.nii.gz -m mask_dmri_mean.nii.gz -o dmri_crop.nii.gz
454 fsleyes dmri.nii.gz dmri_crop.nii.gz &
455 sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt
456 fsleyes dmri_crop_moco.nii.gz dmri_crop.nii.gz &
457 sct_propseg -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc ~/qc_singleSubj
458 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t1.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz -qc ~/qc_singleSubj
459 mv warp_PAM50_t12dmri_crop_moco_dwi_mean.nii.gz warp_template2dmri.nii.gz
460 mv warp_dmri_crop_moco_dwi_mean2PAM50_t1.nii.gz warp_dmri2template.nii.gz
461 sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz
462 sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_singleSubj
463 sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt
464 sct_dmri_compute_dti
465 sct_extract_metric -i dti_FA.nii.gz -vert 2:5 -perlevel 1 -method map -l 51 -o fa_in_wm.csv
466 cd ..
467 cd ~
468 fsleyes
469 source ${SCT_DIR}/python/etc/profile.d/conda.sh
470 conda activate venv_sct
471 fsleyes
472 ll
473 cd sct_course_london20
474 ll
475 cd single_subject
476 cd data
477 cd dmri
478 ll
479 sct_extract_metric -i dti_FA.nii.gz -method map -l 51 -o mtr_in_wm.csv
480 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 5:15 -o fa_in_cst.csv
481 sct_extract_metric -i dti_fa.nii.gz -method map -l 4,5 -z 5:15 -o fa_in_cst.csv
482 sct_extract_metric -i dti_FA.nii.gz -method map -l 51 -o dti_in_wm.csv
483 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 5:15 -o dti_in_cst.csv
484 sct_extract_metric -i dti_FA.nii.gz -method map -l 51 -o fa_in_wm.csv
485 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 5:15 -o fa_in_cst.csv
486 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 0:9 -o fa_in_cst.csv
487 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -o fa_in_cst.csv
488 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 0:8 -o fa_in_cst.csv
489 sct_extract_metric -i dti_FA.nii.gz -method map -l 4,5 -z 0:9 -o fa_in_cst.csv
490 ll
491 cd sct_course_london20
492 ll
493 cd single_subject
494 cd data
495 cd mt
496 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/
497 PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param
498 step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/
499 warp_template2anat.nii.gz -qc ~/qc_singleSubj
500 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -qc ~/qc_singleSubj
501 source ${SCT_DIR}/python/etc/profile.d/conda.sh
502 conda activate venv_sct
503 ll
504 cd sct_course_london20
505 ll
506 cd single_subject
507 cd data
508 cd mt
509 sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz
510 sct_extract_metric -i mtr.nii.gz -method map -l 51 -o mtr_in_wm.csv
511 cd ../dmri
512 sct_maths -i dmri.nii.gz -mean t -o dmri_mean.nii.gz
513 sct_propseg -i dmri_mean.nii.gz -c dwi -qc ~/qc_singleSubj
514 cd ../mt
515 sct_extract_metric -i mtr.nii.gz -method map -l 51 -o mtr_in_wm.csv
516 cd ../dmri
517 sct_extract_metric -i dti_FA.nii.gz -vert 2:5 -perlevel 1 -method map -l 4,5 -o fa_in_wm.csv
518 sct_extract_metric -i dti_FA.nii.gz -vert 2:5 -perlevel 1 -method map -l 4,5 -o fa_in_cst.csv
519 cd ~
520 fsleyes
521 ll
522 cd sct_course_london20
523 ll
This includes all the actions before the error
Thanks so much! I’m going to look into it and get back to everyone.
Hi again @chang, I’ve been working but haven’t yet figured out what caused the the crash. Here’s my attempt: https://showterm.io/c82a348d19d20ecd23e88
Your environment is different than mine. Our WSL support is still new and shaky and we don’t test very widely. We’ve never tested on Debian-on-WSL and especially not on Debian-sid-on-WSL, which you seem to be running.
If you are able to provide some more details it would help us improve. Would you please be able to show me:
cmd.exe /c verwsl.exe -l -vcat /proc/versionuname -acat /etc/os-releasecat /etc/apt/sources.listcat /etc/apt/sources.list.20210305apt list --installedI am also curious what you meant by changed the permissions. Do you still have those commands in your history? Were they unix permissions or Windows permissions? Can you describe how you changed them? Do you remember what the permissions were before the change?
I don’t see any chmods or linmin.nii.gz lines in your history so I am just guessing a bit. If you could fill in the details it would help me track this down.
Thanks. Have a good week.
Hi nguenthe
Thank you for your concern!
forest@DESKTOP-DM8SQ21:~$ cmd.exe /c ver
'\\wsl$\Ubuntu-18.04\home\forest'
Microsoft Windows [ 10.0.19041.867]
forest@DESKTOP-DM8SQ21:~$ wsl.exe -l -v
NAME STATE VERSION
* Ubuntu-18.04 Running 1
forest@DESKTOP-DM8SQ21:~$ cat /proc/version
Linux version 4.4.0-19041-Microsoft (Microsoft@Microsoft.com) (gcc version 5.4.0 (GCC) ) #488-Microsoft Mon Sep 01 13:43:00 PST 2020
forest@DESKTOP-DM8SQ21:~$ uname -a
Linux DESKTOP-DM8SQ21 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux
forest@DESKTOP-DM8SQ21:~$ cat /etc/os-release
NAME="Ubuntu"
VERSION="18.04.5 LTS (Bionic Beaver)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 18.04.5 LTS"
VERSION_ID="18.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=bionic
UBUNTU_CODENAME=bionic
forest@DESKTOP-DM8SQ21:~$ cat /etc/apt/sources.list
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://mirrors.aliyun.com/ubuntu/ bionic main restricted
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic main restricted
## Major bug fix updates produced after the final release of the
## distribution.
deb http://mirrors.aliyun.com/ubuntu/ bionic-updates main restricted
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-updates main restricted
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://mirrors.aliyun.com/ubuntu/ bionic universe
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic universe
deb http://mirrors.aliyun.com/ubuntu/ bionic-updates universe
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-updates universe
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://mirrors.aliyun.com/ubuntu/ bionic multiverse
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic multiverse
deb http://mirrors.aliyun.com/ubuntu/ bionic-updates multiverse
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-updates multiverse
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://mirrors.aliyun.com/ubuntu/ bionic-backports main restricted universe multiverse
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-backports main restricted universe multiverse
## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu bionic partner
# deb-src http://archive.canonical.com/ubuntu bionic partner
deb http://mirrors.aliyun.com/ubuntu/ bionic-security main restricted
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-security main restricted
deb http://mirrors.aliyun.com/ubuntu/ bionic-security universe
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-security universe
deb http://mirrors.aliyun.com/ubuntu/ bionic-security multiverse
# deb-src http://mirrors.aliyun.com/ubuntu/ bionic-security multiverse
forest@DESKTOP-DM8SQ21:~$ cat /etc/apt/sources.list.20210305
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://archive.ubuntu.com/ubuntu/ bionic main restricted
# deb-src http://archive.ubuntu.com/ubuntu/ bionic main restricted
## Major bug fix updates produced after the final release of the
## distribution.
deb http://archive.ubuntu.com/ubuntu/ bionic-updates main restricted
# deb-src http://archive.ubuntu.com/ubuntu/ bionic-updates main restricted
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://archive.ubuntu.com/ubuntu/ bionic universe
# deb-src http://archive.ubuntu.com/ubuntu/ bionic universe
deb http://archive.ubuntu.com/ubuntu/ bionic-updates universe
# deb-src http://archive.ubuntu.com/ubuntu/ bionic-updates universe
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://archive.ubuntu.com/ubuntu/ bionic multiverse
# deb-src http://archive.ubuntu.com/ubuntu/ bionic multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-updates multiverse
# deb-src http://archive.ubuntu.com/ubuntu/ bionic-updates multiverse
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
# deb-src http://archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu bionic partner
# deb-src http://archive.canonical.com/ubuntu bionic partner
deb http://security.ubuntu.com/ubuntu/ bionic-security main restricted
# deb-src http://security.ubuntu.com/ubuntu/ bionic-security main restricted
deb http://security.ubuntu.com/ubuntu/ bionic-security universe
# deb-src http://security.ubuntu.com/ubuntu/ bionic-security universe
deb http://security.ubuntu.com/ubuntu/ bionic-security multiverse
# deb-src http://security.ubuntu.com/ubuntu/ bionic-security multiverse
I’m running Linux on a Windows system.
I found the Linux system folder where the files were stored, and then copied the image files I wanted to work with from the Windows folder into it. Then I use SCT to process these files. But the above error will occur. Finally, I run the code in the terminal.
chmod 754 [filename]
and changed the permissions.
Thanks. Have a good week.