Open rsipahi opened 6 years ago
Hi,
what's the error message? Did you tell your script where TRENTOOL and it's TSTOOL mex-files are located?
Best,
Michael
On 08.01.2018 18:25, rsipahi wrote:
I have all the lines in range_search.m commented out. When attempting to call this m file, Matlab returns an error. Should this file be configured as a function? How is the output of this function calculated? Any updates on range_search.m will be appreciated?
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Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10 60528 Frankfurt am Main
Thank you for your email. Yes, TRENTOOL is on the path, so is fieldtrip folder.
For example, I run "example_script_CPUmethod.m" and the code starts running as I can follow from the command window.
At some point, I get this:
################### OPTIMIZING INFORMATION TRANSFER DELAY
TEfindDelay.m - line 45: Estimating TE for u = 40 ms
and immediately after, I get this error in red text:
Attempt to execute SCRIPT range_search as a function: C:\Users\Nir\Desktop\TRENTOOL3\tstool_functions\range_search.m
Error in TEC_dsvalues (line 206) ncount_p21_p2 = range_search(pointset_p2,atria_p2,1:L,distance_p21(1:L,k_th)-eps,TheilerT);
Error in transferentropy (line 388) [te, mi] = TEC_dsvalues( ...
Error in TEsurrogatestats (line 517) [TEresult] = transferentropy(cfg,data);
Error in TEfindDelay (line 59) TGA_results{uu}=TEsurrogatestats(cfgTESS,data);
Error in InteractionDelayReconstruction_calculate (line 115) [dataprep, TEmat] = TEfindDelay(predicttimevec_u,cfgTESS,dataprep);
Error in example_script_CPUmethod (line 67) TGA_results = InteractionDelayReconstruction_calculate(cfgTEP,cfgTESS,data);
Any help would be great!
Thank you,
Rifat
On Mon, Jan 8, 2018 at 12:38 PM, mwibral notifications@github.com wrote:
Hi,
what's the error message? Did you tell your script where TRENTOOL and it's TSTOOL mex-files are located?
Best,
Michael
On 08.01.2018 18:25, rsipahi wrote:
I have all the lines in range_search.m commented out. When attempting to call this m file, Matlab returns an error. Should this file be configured as a function? How is the output of this function calculated? Any updates on range_search.m will be appreciated?
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{"api_version":"1.0","publisher":{"api_key":" 05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity": {"external_key":"github/trentool/TRENTOOL3","title":" trentool/TRENTOOL3","subtitle":"GitHub repository","main_image_url":"https://cloud. githubusercontent.com/assets/143418/17495839/a5054eac-5d88- 11e6-95fc-7290892c7bb5.png","avatar_image_url":"https:// cloud.githubusercontent.com/assets/143418/15842166/ 7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/trentool/TRENTOOL3"}}," updates":{"snippets":[{"icon":"DESCRIPTION","message":"range_search.m issue (#25)"}],"action":{"name":"View Issue","url":"https://github.com/trentool/TRENTOOL3/issues/25"}}}
--
Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10 https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+%0D+60528+Frankfurt+am+Main&entry=gmail&source=g 60528 Frankfurt am Main
Phone: +49 69 6301 83193 <+49%2069%20630183193> Fax: +49 69 6301 83231 <+49%2069%20630183231>
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Hi,
this still looks like an error caused by not finding the the correct mex files. You could try to 'recompile/remex' them, and check that the TSTTOOL location is sset correctly as per the manual.
What's your MATLAB version and OS?
Michael
On 09.01.2018 03:36, rsipahi wrote:
Thank you for your email. Yes, TRENTOOL is on the path, so is fieldtrip folder.
For example, I run "example_script_CPUmethod.m" and the code starts running as I can follow from the command window.
At some point, I get this:
################### OPTIMIZING INFORMATION TRANSFER DELAY
TEfindDelay.m - line 45: Estimating TE for u = 40 ms
and immediately after, I get this error in red text:
Attempt to execute SCRIPT range_search as a function: C:\Users\Nir\Desktop\TRENTOOL3\tstool_functions\range_search.m
Error in TEC_dsvalues (line 206) ncount_p21_p2 = range_search(pointset_p2,atria_p2,1:L,distance_p21(1:L,k_th)-eps,TheilerT);
Error in transferentropy (line 388) [te, mi] = TEC_dsvalues( ...
Error in TEsurrogatestats (line 517) [TEresult] = transferentropy(cfg,data);
Error in TEfindDelay (line 59) TGA_results{uu}=TEsurrogatestats(cfgTESS,data);
Error in InteractionDelayReconstruction_calculate (line 115) [dataprep, TEmat] = TEfindDelay(predicttimevec_u,cfgTESS,dataprep);
Error in example_script_CPUmethod (line 67) TGA_results = InteractionDelayReconstruction_calculate(cfgTEP,cfgTESS,data);
Any help would be great!
Thank you,
Rifat
On Mon, Jan 8, 2018 at 12:38 PM, mwibral notifications@github.com wrote:
Hi,
what's the error message? Did you tell your script where TRENTOOL and it's TSTOOL mex-files are located?
Best,
Michael
On 08.01.2018 18:25, rsipahi wrote:
I have all the lines in range_search.m commented out. When attempting to call this m file, Matlab returns an error. Should this file be configured as a function? How is the output of this function calculated? Any updates on range_search.m will be appreciated?
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{"api_version":"1.0","publisher":{"api_key":" 05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity": {"external_key":"github/trentool/TRENTOOL3","title":" trentool/TRENTOOL3","subtitle":"GitHub repository","main_image_url":"https://cloud. githubusercontent.com/assets/143418/17495839/a5054eac-5d88- 11e6-95fc-7290892c7bb5.png","avatar_image_url":"https:// cloud.githubusercontent.com/assets/143418/15842166/ 7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/trentool/TRENTOOL3"}}," updates":{"snippets":[{"icon":"DESCRIPTION","message":"range_search.m issue (#25)"}],"action":{"name":"View Issue","url":"https://github.com/trentool/TRENTOOL3/issues/25"}}}
--
Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10
https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+%0D+60528+Frankfurt+am+Main&entry=gmail&source=g 60528 Frankfurt am Main
Phone: +49 69 6301 83193 <+49%2069%20630183193> Fax: +49 69 6301 83231 <+49%2069%20630183231>
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub
https://github.com/trentool/TRENTOOL3/issues/25#issuecomment-356037840, or mute the thread
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{"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/trentool/TRENTOOL3","title":"trentool/TRENTOOL3","subtitle":"GitHub repository","main_image_url":"https://cloud.githubusercontent.com/assets/143418/17495839/a5054eac-5d88-11e6-95fc-7290892c7bb5.png","avatar_image_url":"https://cloud.githubusercontent.com/assets/143418/15842166/7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/trentool/TRENTOOL3"}},"updates":{"snippets":[{"icon":"PERSON","message":"@rsipahi in #25: Thank you for your email.\nYes, TRENTOOL is on the path, so is fieldtrip folder.\n\nFor example, I run \"example_script_CPUmethod.m\" and the code starts running\nas I can follow from the command window.\n\nAt some point, I get this:\n\n################### OPTIMIZING INFORMATION TRANSFER DELAY\n\n TEfindDelay.m - line 45: Estimating TE for u = 40 ms\n\nand immediately after, I get this error in red text:\n\nAttempt to execute SCRIPT range_search as a function:\nC:\Users\Nir\Desktop\TRENTOOL3\tstool_functions\range_search.m\n\nError in TEC_dsvalues (line 206)\nncount_p21_p2 =\nrange_search(pointset_p2,atria_p2,1:L,distance_p21(1:L,k_th)-eps,TheilerT);\n\nError in transferentropy (line 388)\n [te, mi] = TEC_dsvalues( ...\n\nError in TEsurrogatestats (line 517)\n[TEresult] = transferentropy(cfg,data);\n\nError in TEfindDelay (line 59)\n TGA_results{uu}=TEsurrogatestats(cfgTESS,data);\n\nError in InteractionDelayReconstruction_calculate (line 115)\n[dataprep, TEmat] = TEfindDelay(predicttimevec_u,cfgTESS,dataprep);\n\nError in example_script_CPUmethod (line 67)\nTGA_results = InteractionDelayReconstruction_calculate(cfgTEP,cfgTESS,data);\n\n----------\n\n\nAny help would be great!\n\nThank you,\n\nRifat\n\n\n\n\nOn Mon, Jan 8, 2018 at 12:38 PM, mwibral \u003cnotifications@github.com\u003e wrote:\n\n\u003e Hi,\n\u003e\n\u003e what's the error message? Did you tell your script where TRENTOOL and\n\u003e it's TSTOOL mex-files are located?\n\u003e\n\u003e Best,\n\u003e\n\u003e Michael\n\u003e\n\u003e\n\u003e On 08.01.2018 18:25, rsipahi wrote:\n\u003e \u003e\n\u003e \u003e I have all the lines in range_search.m commented out. When attempting\n\u003e \u003e to call this m file, Matlab returns an error. Should this file be\n\u003e \u003e configured as a function? How is the output of this function\n\u003e \u003e calculated? Any updates on range_search.m will be appreciated?\n\u003e \u003e\n\u003e \u003e —\n\u003e \u003e You are receiving this because you are subscribed to this thread.\n\u003e \u003e Reply to this email directly, view it on GitHub\n\u003e \u003e \u003chttps://github.com/trentool/TRENTOOL3/issues/25\u003e, or mute the thread\n\u003e \u003e \u003chttps://github.com/notifications/unsubscribe-auth/AIqYGrGx-\n\u003e i1rBkro5WtsJaeB3SDdSep_ks5tIk-agaJpZM4RWsW1\u003e.\n\u003e \u003e\n\u003e \u003e {\"api_version\":\"1.0\",\"publisher\":{\"api_key\":\"\n\u003e 05dde50f1d1a384dd78767c55493e4bb\",\"name\":\"GitHub\"},\"entity\":\n\u003e {\"external_key\":\"github/trentool/TRENTOOL3\",\"title\":\"\n\u003e trentool/TRENTOOL3\",\"subtitle\":\"GitHub\n\u003e \u003e repository\",\"main_image_url\":\"https://cloud.\n\u003e githubusercontent.com/assets/143418/17495839/a5054eac-5d88-\n\u003e 11e6-95fc-7290892c7bb5.png\",\"avatar_image_url\":\"https://\n\u003e cloud.githubusercontent.com/assets/143418/15842166/\n\u003e 7c72db34-2c0b-11e6-9aed-b52498112777.png\",\"action\":{\"name\":\"Open\n\u003e \u003e in\n\u003e \u003e GitHub\",\"url\":\"https://github.com/trentool/TRENTOOL3\"}},\"\n\u003e updates\":{\"snippets\":[{\"icon\":\"DESCRIPTION\",\"message\":\"range_search.m\n\u003e \u003e issue (#25)\"}],\"action\":{\"name\":\"View\n\u003e \u003e Issue\",\"url\":\"https://github.com/trentool/TRENTOOL3/issues/25\"}}}\n\u003e\n\u003e --\n\u003e ----------------------------------\n\u003e Prof. Dr. rer. nat. Michael Wibral\n\u003e MEG Labor, Brain Imaging Center\n\u003e Goethe Universität\n\u003e\n\u003e Heinrich Hoffmann Strasse 10\n\u003e \u003chttps://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+%0D+60528+Frankfurt+am+Main\u0026entry=gmail\u0026source=g\u003e\n\u003e 60528 Frankfurt am Main\n\u003e\n\u003e Phone: +49 69 6301 83193 \u003c+49%2069%20630183193\u003e\n\u003e Fax: +49 69 6301 83231 \u003c+49%2069%20630183231\u003e\n\u003e -----------------------------------\n\u003e\n\u003e —\n\u003e You are receiving this because you authored the thread.\n\u003e Reply to this email directly, view it on GitHub\n\u003e \u003chttps://github.com/trentool/TRENTOOL3/issues/25#issuecomment-356037840\u003e,\n\u003e or mute the thread\n\u003e \u003chttps://github.com/notifications/unsubscribe-auth/AhmcpORa4m0WMOL3oL4vN_axolsv0Q00ks5tIlKLgaJpZM4RWsW1\u003e\n\u003e .\n\u003e\n"}],"action":{"name":"View Issue","url":"https://github.com/trentool/TRENTOOL3/issues/25#issuecomment-356161836"}}}
Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10 60528 Frankfurt am Main
Dear Professor Wibral,
Thank you so much for your time.
I am using Matlab ver 2015b with OS Win 8, 64 bit. I do not have a CUDA GPU, so this might be one of the issues (I think for some reconstructing operations, CUDA is a requirement). I wonder if I can still run some analysis without a CUDA GPU?
Thank you for your time and patience.
Best regards, Rifat Sipahi
On Tue, Jan 9, 2018 at 10:27 AM, mwibral notifications@github.com wrote:
Hi,
this still looks like an error caused by not finding the the correct mex files. You could try to 'recompile/remex' them, and check that the TSTTOOL location is sset correctly as per the manual.
What's your MATLAB version and OS?
Michael
On 09.01.2018 03:36, rsipahi wrote:
Thank you for your email. Yes, TRENTOOL is on the path, so is fieldtrip folder.
For example, I run "example_script_CPUmethod.m" and the code starts running as I can follow from the command window.
At some point, I get this:
################### OPTIMIZING INFORMATION TRANSFER DELAY
TEfindDelay.m - line 45: Estimating TE for u = 40 ms
and immediately after, I get this error in red text:
Attempt to execute SCRIPT range_search as a function: C:\Users\Nir\Desktop\TRENTOOL3\tstool_functions\range_search.m
Error in TEC_dsvalues (line 206) ncount_p21_p2 = range_search(pointset_p2,atria_p2,1:L,distance_p21(1:L, k_th)-eps,TheilerT);
Error in transferentropy (line 388) [te, mi] = TEC_dsvalues( ...
Error in TEsurrogatestats (line 517) [TEresult] = transferentropy(cfg,data);
Error in TEfindDelay (line 59) TGA_results{uu}=TEsurrogatestats(cfgTESS,data);
Error in InteractionDelayReconstruction_calculate (line 115) [dataprep, TEmat] = TEfindDelay(predicttimevec_u,cfgTESS,dataprep);
Error in example_script_CPUmethod (line 67) TGA_results = InteractionDelayReconstruction_calculate(cfgTEP,cfgTESS,data);
Any help would be great!
Thank you,
Rifat
On Mon, Jan 8, 2018 at 12:38 PM, mwibral notifications@github.com wrote:
Hi,
what's the error message? Did you tell your script where TRENTOOL and it's TSTOOL mex-files are located?
Best,
Michael
On 08.01.2018 18:25, rsipahi wrote:
I have all the lines in range_search.m commented out. When attempting to call this m file, Matlab returns an error. Should this file be configured as a function? How is the output of this function calculated? Any updates on range_search.m will be appreciated?
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/trentool/TRENTOOL3/issues/25, or mute the thread https://github.com/notifications/unsubscribe-auth/AIqYGrGx- i1rBkro5WtsJaeB3SDdSep_ks5tIk-agaJpZM4RWsW1.
{"api_version":"1.0","publisher":{"api_key":" 05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity": {"external_key":"github/trentool/TRENTOOL3","title":" trentool/TRENTOOL3","subtitle":"GitHub repository","main_image_url":"https://cloud. githubusercontent.com/assets/143418/17495839/a5054eac-5d88- 11e6-95fc-7290892c7bb5.png","avatar_image_url":"https:// cloud.githubusercontent.com/assets/143418/15842166/ 7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/trentool/TRENTOOL3"}}," updates":{"snippets":[{"icon":"DESCRIPTION","message":"range_search.m issue (#25)"}],"action":{"name":"View Issue","url":"https://github.com/trentool/TRENTOOL3/issues/25"}}}
--
Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10 https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10&entry=gmail&source=g
https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+% 0D+60528+Frankfurt+am+Main&entry=gmail&source=g 60528 Frankfurt am Main
Phone: +49 69 6301 83193 <+49%2069%20630183193> <+49%2069%20630183193> Fax: +49 69 6301 83231 <+49%2069%20630183231> <+49%2069%20630183231>
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in transferentropy (line 388)\n [te, mi] = TEC_dsvalues( ...\n\nError in TEsurrogatestats (line 517)\n[TEresult] = transferentropy(cfg,data);\n\nError in TEfindDelay (line 59)\n TGA_results{uu}=TEsurrogatestats(cfgTESS,data);\n\nError in InteractionDelayReconstruction_calculate (line 115)\n[dataprep, TEmat] = TEfindDelay(predicttimevec_u,cfgTESS,dataprep);\n\nError in example_script_CPUmethod (line 67)\nTGA_results = InteractionDelayReconstruction_calculate(cfgTEP,cfgTESS,data);\n\n----------\n\n\nAny
help would be great!\n\nThank you,\n\nRifat\n\n\n\n\nOn Mon, Jan 8, 2018 at 12:38 PM, mwibral \u003cnotifications@github.com\u003e wrote:\n\n\u003e Hi,\n\u003e\n\u003e what's the error message? Did you tell your script where TRENTOOL and\n\u003e it's TSTOOL mex-files are located?\n\u003e\n\u003e Best,\n\u003e\n\u003e Michael\n\u003e\n\u003e\n\u003e On 08.01.2018 18:25, rsipahi wrote:\n\u003e \u003e\n\u003e \u003e I have all the lines in range_search.m commented out. When attempting\n\u003e \u003e to call this m file, Matlab returns an error. Should this file be\n\u003e \u003e configured as a function? How is the output of this function\n\u003e \u003e calculated? Any updates on range_search.m will be appreciated?\n\u003e \u003e\n\u003e \u003e —\n\u003e \u003e You are receiving this because you are subscribed to this thread.\n\u003e \u003e Reply to this email directly, view it on GitHub\n\u003e \u003e \u003chttps://github.com/trentool/TRENTOOL3/issues/25\u003e http://github.com/trentool/TRENTOOL3/issues/25%5Cu003e, or mute the thread\n\u003e \u003e \u003chttps://github.com/notifications/unsubscribe- auth/AIqYGrGx-\n\u003e http://github.com/notifications/unsubscribe-auth/AIqYGrGx-%5Cn%5Cu003e i1rBkro5WtsJaeB3SDdSep_ks5tIk-agaJpZM4RWsW1\u003e.\n\u003e \u003e\n\u003e \u003e {\"api_version\":\"1.0\",\"publisher\":{\"api_key\":\"\n\u003e 05dde50f1d1a384dd78767c55493e4bb\",\"name\":\"GitHub\"},\"entity\":\n\u003e
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\u003e in\n\u003e \u003e GitHub\",\"url\":\"https://github.com/trentool/TRENTOOL3\"}},\"\n\u003e updates\":{\"snippets\":[{\"icon\":\"DESCRIPTION\",\" message\":\"range_search.m\n\u003e \u003e issue (#25)\"}],\"action\":{\"name\":\"View\n\u003e \u003e Issue\",\"url\":\"https://github.com/trentool/TRENTOOL3/issues/25\"}}}\n\u003e\n\u003e
--\n\u003e ----------------------------------\n\u003e Prof. Dr. rer. nat. Michael Wibral\n\u003e MEG Labor, Brain Imaging Center\n\u003e Goethe Universität\n\u003e\n\u003e Heinrich Hoffmann Strasse https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+%0D+%3E+10&entry=gmail&source=g 10\n\u003e \u003chttps://maps.google.com/?q=Heinrich+Hoffmann+Strasse+ 10+%0D+60528+Frankfurt+am+Main\u0026entry=gmail\ u0026source=g\u003e\n\u003e http://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+%0D+60528+Frankfurt+am+Main%5Cu0026entry=gmail%5Cu0026source=g%5Cu003e%5Cn%5Cu003e 60528 Frankfurt am Main\n\u003e\n\u003e Phone: +49 69 6301 83193 <+49%2069%20630183193> \u003c+49%2069%20630183193\u003e\n\u003e Fax: +49 69 6301 83231 <+49%2069%20630183231> \u003c+49%2069%20630183231\u003e\n\u003e -----------------------------------\n\u003e\n\u003e —\n\u003e You are receiving this because you authored the thread.\n\u003e Reply to this email directly, view it on GitHub\n\u003e \u003chttps://github.com/trentool/TRENTOOL3/issues/25# issuecomment-356037840\u003e,\n\u003e http://github.com/trentool/TRENTOOL3/issues/25#issuecomment-356037840%5Cu003e,%5Cn%5Cu003e or mute the thread\n\u003e \u003chttps://github.com/notifications/unsubscribe- auth/AhmcpORa4m0WMOL3oL4vN_axolsv0Q00ks5tIlKLgaJpZM4RWsW1\u003e\n\u003e http://github.com/notifications/unsubscribe-auth/AhmcpORa4m0WMOL3oL4vN_axolsv0Q00ks5tIlKLgaJpZM4RWsW1%5Cu003e%5Cn%5Cu003e .\n\u003e\n"}],"action":{"name":"View Issue","url":"https://github.com/trentool/TRENTOOL3/issues/ 25#issuecomment-356161836"}}}
--
Prof. Dr. rer. nat. Michael Wibral MEG Labor, Brain Imaging Center Goethe Universität
Heinrich Hoffmann Strasse 10 https://maps.google.com/?q=Heinrich+Hoffmann+Strasse+10+%0D+60528+Frankfurt+am+Main&entry=gmail&source=g 60528 Frankfurt am Main
Phone: +49 69 6301 83193 <+49%2069%20630183193> Fax: +49 69 6301 83231 <+49%2069%20630183231>
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I have all the lines in range_search.m commented out. When attempting to call this m file, Matlab returns an error. Should this file be configured as a function? How is the output of this function calculated? Any updates on range_search.m will be appreciated?