Error installing tutorial data
Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz
Dear Diana, Thank you for your feedback. Your problem will be fixed on Monday with the future new DIPY release (1.7). For now, you can use the following command line, it will fetch 97% of the tutorial data. You will be able to finalize the 3% this Monday. Command dipy_fetch DiB_217_lte_pte_ste DiB_70_lte_pte_ste bundle_atlas_hcp842 bundle_fa_hcp bundles_2_subjects cenir_multib cfin_multib evac_test evac_weights file_formats fury_surface gold_standard_io isbi2013_2shell ivim mni_template ptt_minimal_dataset qtdMRI_test_retest_2subjects qte_lte_pte resdnn_weights scil_b0 sherbrooke_3shell stanford_hardi stanford_labels stanford_pve_maps stanford_t1 syn_data synb0_test synb0_weights taiwan_ntu_dsi target_tractogram_hcp tissue_datalist Have a great week end Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro@iu.edu<mailto:skoudoro@indiana.edu> ________________________________ From: Patterson, Dianne K - (dkp) <dkp@arizona.edu> Sent: Saturday, April 22, 2023 7:34 PM To: dipy@python.org <dipy@python.org> Subject: [External] [DIPY] Error installing tutorial data You don't often get email from dkp@arizona.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai/> Mastodon: @dpat@scicomm.xyz
Thank you Serge and Eleftherios, You were do fast to reply! wow! I'm installing the 97% INFO:Fetched 22 / 31 Files WARNING:Skipped data name(s): dib_217_lte_pte_ste dib_70_lte_pte_ste evac_test evac_weights ptt_minimal_dataset qtdmri_test_retest_2subjects synb0_test synb0_weights tissue_datalist WARNING:Please, select between the following data names: DiB_217_lte_pte_ste, DiB_70_lte_pte_ste, bundle_atlas_hcp842, bundle_fa_hcp, bundles_2_subjects, cenir_multib, cfin_multib, file_formats, fury_surface, gold_standard_io, hbn, hcp, isbi2013_2shell, ivim, mni_template, qtdMRI_test_retest_2subjects, qte_lte_pte, resdnn_weights, scil_b0, sherbrooke_3shell, stanford_hardi, stanford_labels, stanford_pve_maps, stanford_t1, syn_data, taiwan_ntu_dsi, target_tractogram_hcp, tissue_data I'll wait for DiPy 1.7 on Monday. -D Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz ________________________________ From: Koudoro, Serge <skoudoro@iu.edu> Sent: Saturday, April 22, 2023 11:00 AM To: Patterson, Dianne K - (dkp) <dkp@arizona.edu>; dipy@python.org <dipy@python.org> Subject: [EXT]Re: Error installing tutorial data External Email Dear Diana, Thank you for your feedback. Your problem will be fixed on Monday with the future new DIPY release (1.7). For now, you can use the following command line, it will fetch 97% of the tutorial data. You will be able to finalize the 3% this Monday. Command dipy_fetch DiB_217_lte_pte_ste DiB_70_lte_pte_ste bundle_atlas_hcp842 bundle_fa_hcp bundles_2_subjects cenir_multib cfin_multib evac_test evac_weights file_formats fury_surface gold_standard_io isbi2013_2shell ivim mni_template ptt_minimal_dataset qtdMRI_test_retest_2subjects qte_lte_pte resdnn_weights scil_b0 sherbrooke_3shell stanford_hardi stanford_labels stanford_pve_maps stanford_t1 syn_data synb0_test synb0_weights taiwan_ntu_dsi target_tractogram_hcp tissue_datalist Have a great week end Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro@iu.edu<mailto:skoudoro@indiana.edu> ________________________________ From: Patterson, Dianne K - (dkp) <dkp@arizona.edu> Sent: Saturday, April 22, 2023 7:34 PM To: dipy@python.org <dipy@python.org> Subject: [External] [DIPY] Error installing tutorial data You don't often get email from dkp@arizona.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai/> Mastodon: @dpat@scicomm.xyz
Dear Diana, Thank you for your feedback. Your problem will be fixed on Monday with the future new DIPY release (1.7). For now, you can use the following command line, it will fetch 97% of the tutorial data. You will be able to finalize the 3% this Monday. Command dipy_fetch DiB_217_lte_pte_ste DiB_70_lte_pte_ste bundle_atlas_hcp842 bundle_fa_hcp bundles_2_subjects cenir_multib cfin_multib evac_test evac_weights file_formats fury_surface gold_standard_io isbi2013_2shell ivim mni_template ptt_minimal_dataset qtdMRI_test_retest_2subjects qte_lte_pte resdnn_weights scil_b0 sherbrooke_3shell stanford_hardi stanford_labels stanford_pve_maps stanford_t1 syn_data synb0_test synb0_weights taiwan_ntu_dsi target_tractogram_hcp tissue_datalist Have a great week end Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro@iu.edu<mailto:skoudoro@indiana.edu> ________________________________ From: Patterson, Dianne K - (dkp) <dkp@arizona.edu> Sent: Saturday, April 22, 2023 7:34 PM To: dipy@python.org <dipy@python.org> Subject: [External] [DIPY] Error installing tutorial data You don't often get email from dkp@arizona.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai/> Mastodon: @dpat@scicomm.xyz
Thank you Serge and Eleftherios, You were do fast to reply! wow! I'm installing the 97% INFO:Fetched 22 / 31 Files WARNING:Skipped data name(s): dib_217_lte_pte_ste dib_70_lte_pte_ste evac_test evac_weights ptt_minimal_dataset qtdmri_test_retest_2subjects synb0_test synb0_weights tissue_datalist WARNING:Please, select between the following data names: DiB_217_lte_pte_ste, DiB_70_lte_pte_ste, bundle_atlas_hcp842, bundle_fa_hcp, bundles_2_subjects, cenir_multib, cfin_multib, file_formats, fury_surface, gold_standard_io, hbn, hcp, isbi2013_2shell, ivim, mni_template, qtdMRI_test_retest_2subjects, qte_lte_pte, resdnn_weights, scil_b0, sherbrooke_3shell, stanford_hardi, stanford_labels, stanford_pve_maps, stanford_t1, syn_data, taiwan_ntu_dsi, target_tractogram_hcp, tissue_data I'll wait for DiPy 1.7 on Monday. -D Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz ________________________________ From: Koudoro, Serge <skoudoro@iu.edu> Sent: Saturday, April 22, 2023 11:00 AM To: Patterson, Dianne K - (dkp) <dkp@arizona.edu>; dipy@python.org <dipy@python.org> Subject: [EXT]Re: Error installing tutorial data External Email Dear Diana, Thank you for your feedback. Your problem will be fixed on Monday with the future new DIPY release (1.7). For now, you can use the following command line, it will fetch 97% of the tutorial data. You will be able to finalize the 3% this Monday. Command dipy_fetch DiB_217_lte_pte_ste DiB_70_lte_pte_ste bundle_atlas_hcp842 bundle_fa_hcp bundles_2_subjects cenir_multib cfin_multib evac_test evac_weights file_formats fury_surface gold_standard_io isbi2013_2shell ivim mni_template ptt_minimal_dataset qtdMRI_test_retest_2subjects qte_lte_pte resdnn_weights scil_b0 sherbrooke_3shell stanford_hardi stanford_labels stanford_pve_maps stanford_t1 syn_data synb0_test synb0_weights taiwan_ntu_dsi target_tractogram_hcp tissue_datalist Have a great week end Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro@iu.edu<mailto:skoudoro@indiana.edu> ________________________________ From: Patterson, Dianne K - (dkp) <dkp@arizona.edu> Sent: Saturday, April 22, 2023 7:34 PM To: dipy@python.org <dipy@python.org> Subject: [External] [DIPY] Error installing tutorial data You don't often get email from dkp@arizona.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Dear DiPy, I am following the instructions for DiPy 2023 and installing the tutorial data. The process seems to get quite far (3.6 GB) but then gets an error. Rerunning the command gets the same error, though nicely reports what is going on (see below) Environment Mac OS Monterey 12.6.3 Miniconda conda --version conda 22.11.1 conda list dipy # packages in environment at /Users/dpat/opt/miniconda3/envs/dipy: # # Name Version Build Channel dipy 1.6.0 pypi_0 pypi python --version Python 3.10.2 Conda Install Details `conda create -n dipy` `conda activate dipy` `conda install -c conda-forge dipy` `conda install -c conda-forge fury` `conda clean --all` Command dipy_fetch all Error (Scroll down) (dipy) [saci:dipy: 4121] $ dipy_fetch all INFO:------------------------------------------ INFO:Fetching at DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 166.3 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_217_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Data size is approximately 51.1 MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/DiB_70_lte_pte_ste INFO:------------------------------------------ INFO:Fetching at bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Data size is approximately 300MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_atlas_hcp842 INFO:------------------------------------------ INFO:Fetching at bundle_fa_hcp INFO:------------------------------------------ INFO:Data size is approximately 230kb INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_fa_hcp INFO:------------------------------------------ INFO:Fetching at bundles_2_subjects INFO:------------------------------------------ INFO:Data size is approximately 234MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/exp_bundles_and_maps INFO:------------------------------------------ INFO:Fetching at cenir_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cenir_multib INFO:------------------------------------------ INFO:Fetching at cfin_multib INFO:------------------------------------------ INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/cfin_multib INFO:This data was provided by Brian Hansen and Sune Jespersen More details about the data are available in their paper: https://www.nature.com/articles/sdata201672 INFO:------------------------------------------ INFO:Fetching at file_formats INFO:------------------------------------------ INFO:Data size is approximately 25MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/bundle_file_formats_example INFO:------------------------------------------ INFO:Fetching at fury_surface INFO:------------------------------------------ INFO:Data size is approximately 11MB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/fury_surface INFO:------------------------------------------ INFO:Fetching at gold_standard_io INFO:------------------------------------------ INFO:Data size is approximately 47.KB INFO:Dataset is already in place. If you want to fetch it again please first remove the folder /Users/dpat/.dipy/gold_standard_io INFO:------------------------------------------ INFO:Fetching at hbn INFO:------------------------------------------ Traceback (most recent call last): File "/Users/dpat/opt/miniconda3/envs/dipy/bin/dipy_fetch", line 7, in <module> run_flow(FetchFlow()) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/flow_runner.py", line 89, in run_flow return flow.run(**args) File "/Users/dpat/opt/miniconda3/envs/dipy/lib/python3.10/site-packages/dipy/workflows/io.py", line 185, in run fetcher_function() TypeError: fetch_hbn() mi Solutions Attempted I initially tried installing in the Mac's native zshell with my active conda environment. After that failed, I switched to a bash shell, just in case. I get the same error message for both shells. In every case, I am in my dipy environment. I tried creating a separate environment using pip instead of conda for install. That did not get far. I have repeated the command, with equivalent results. Thoughts? Thank you, Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp@arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai/> Mastodon: @dpat@scicomm.xyz
participants (2)
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Koudoro, Serge -
Patterson, Dianne K - (dkp)