Re: [HCP-Users] hcp_fix_multi_fix errors
Hi Matt, No, its 3.14. Is the latest (3.15, I believe) needed for the script? Best, Shankar From: Glasser, Matthew [glass...@wustl.edu] Sent: Wednesday, October 10, 2018 4:28 PM To: Shankar Tumati; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] hcp_fix_multi_fix errors Is this with the latest melodic? Matt. On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of Shankar Tumati" wrote: >Hi > >We get these seemingly random errors when implementing the >hcp_fix_multi_run code on the task data with some subjects. We need help >to figure it out. > >Below is the output for two of the subjects. It the same error in all >cases but with different column numbers. > >Thanks, >Shankar >- > >Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: >/usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o >day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall >--tr=0.72 --vn --dim=160 --verbose --debug -m >/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d >ay2_brain_mask > >Melodic Version 3.14 > >Melodic results will be in day2_hp2000.ica/filtered_func_data.ica > >START: setup >START: setup_misc >Mask provided : >/group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/d >ay2_brain_mask > >END: setup_misc > after setup_misc START: setup_classic >START: process_file > before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf >... done > after reading file day2_hp2000_vnf before est smoothness Estimating >data smoothness ... done > after smoothness before reshape after reshape Removing mean image >... before remmean after remmean done >END: process_file > after process_file Excluding voxels with constant value ... done > day2_hp2000.ica/filtered_func_data.ica/alldat > > > >An exception has been thrown >Logic error:- detected by Newmat: index error: requested index = 0 > >MatrixType = Rect # Rows = 1; # Cols = 1994 > >Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has >been run: return_code = 0 >-- >-- >-- > >Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: >/usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o >day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall >--tr=0.72 --vn --dim=139 --verbose --debug -m >/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d >ay1_brain_mask > >Melodic Version 3.14 > >Melodic results will be in day1_hp2000.ica/filtered_func_data.ica > >START: setup >START: setup_misc >Mask provided : >/group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/d >ay1_brain_mask > >END: setup_misc > after setup_misc START: setup_classic >START: process_file > before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf >... done > after reading file day1_hp2000_vnf before est smoothness Estimating >data smoothness ... done > after smoothness before reshape after reshape Removing mean image >... before remmean after remmean done >END: process_file > after process_file Excluding voxels with constant value ... done > day1_hp2000.ica/filtered_func_data.ica/alldat > > > >An exception has been thrown >Logic error:- detected by Newmat: index error: requested index = 0 > >MatrixType = Rect # Rows = 1; # Cols = 1882 > >Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has >been run: return_code = 0 > > >___ >HCP-Users mailing list >HCP-Users@humanconnectome.org >http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix_multi_fix errors
Hi We get these seemingly random errors when implementing the hcp_fix_multi_run code on the task data with some subjects. We need help to figure it out. Below is the output for two of the subjects. It the same error in all cases but with different column numbers. Thanks, Shankar - Wed Oct 10 13:40:11 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: /usr/local/fsl-5.0/bin/melodic -i day2_hp2000_vnf -o day2_hp2000.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.72 --vn --dim=160 --verbose --debug -m /group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/day2_brain_mask Melodic Version 3.14 Melodic results will be in day2_hp2000.ica/filtered_func_data.ica START: setup START: setup_misc Mask provided : /group/northoff/share/hcp_task_prep_fix/104416/MNINonLinear/Results/day2/day2_brain_mask END: setup_misc after setup_misc START: setup_classic START: process_file before reading file day2_hp2000_vnfReading data file day2_hp2000_vnf ... done after reading file day2_hp2000_vnf before est smoothness Estimating data smoothness ... done after smoothness before reshape after reshape Removing mean image ... before remmean after remmean done END: process_file after process_file Excluding voxels with constant value ... done day2_hp2000.ica/filtered_func_data.ica/alldat An exception has been thrown Logic error:- detected by Newmat: index error: requested index = 0 MatrixType = Rect # Rows = 1; # Cols = 1994 Wed Oct 10 14:41:57 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has been run: return_code = 0 -- Wed Oct 10 14:07:43 EDT 2018 - hcp_fix_multi_run - INFORM - melodic_cmd: /usr/local/fsl-5.0/bin/melodic -i day1_hp2000_vnf -o day1_hp2000.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.72 --vn --dim=139 --verbose --debug -m /group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/day1_brain_mask Melodic Version 3.14 Melodic results will be in day1_hp2000.ica/filtered_func_data.ica START: setup START: setup_misc Mask provided : /group/northoff/share/hcp_task_prep_fix/130114/MNINonLinear/Results/day1/day1_brain_mask END: setup_misc after setup_misc START: setup_classic START: process_file before reading file day1_hp2000_vnfReading data file day1_hp2000_vnf ... done after reading file day1_hp2000_vnf before est smoothness Estimating data smoothness ... done after smoothness before reshape after reshape Removing mean image ... before remmean after remmean done END: process_file after process_file Excluding voxels with constant value ... done day1_hp2000.ica/filtered_func_data.ica/alldat An exception has been thrown Logic error:- detected by Newmat: index error: requested index = 0 MatrixType = Rect # Rows = 1; # Cols = 1882 Wed Oct 10 14:57:27 EDT 2018 - hcp_fix_multi_run - INFORM - melodic has been run: return_code = 0 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] MSMAll
Hello, After running the hcp_fix_multi_run.sh script on the task data, a folder for concatenated files is created and a .ica folder is created in each task folder. However, MSMAllPipeline.sh script tries to find /filtered_func_data.ica/melodic_mix, which is present only in the Concat folder. When the script is run on the Concat folder, the output is a _MSMAll_hp2000_clean_vn.dtseries.nii file within a new output folder. Is this the correct output? Should we use the MSMAll.sh (not MSMAllpipeline.sh) instead and then apply DeDriftAndResamplePipeline.sh to get _MSMAll_hp2000_clean.dtseries.nii file for each task separately? Thank you Shankar Tumati Mind, Brain Imaging and Neuroethics lab University of Ottawa ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] MSMAll
Hello, After running the hcp_fix_multi_run.sh script on the task data, a folder for concatenated files is created and a .ica folder is created in each task folder. However, MSMAllPipeline.sh script tries to find /filtered_func_data.ica/melodic_mix, which is present only in the Concat folder. When the script is run on the Concat folder, the output is a _MSMAll_hp2000_clean_vn.dtseries.nii file within a new output folder. Is this the correct output? Should we use the MSMAll.sh (not MSMAllpipeline.sh) instead and then apply DeDriftAndResamplePipeline.sh to get _MSMAll_hp2000_clean.dtseries.nii file for each task separately? Thank you Shankar Tumati Mind, Brain Imaging and Neuroethics lab University of Ottawa ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] FIX denoised 3T task data release?
Hello, We were implementing the hcp_fix_multi_run script on the HCP 3T task data. Although the script is running, it is resource intensive. It seemed from a previous thread that FIX was implemented on the task data: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06605.html I was wondering if HCP plans to release fix denoised task data soon? Also, Is the MMP atlas available in 59k space? Thank you Shankar Tumati Mind, Brain Imaging and Neuroethics lab University of Ottawa ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Three Postdoctoral or PhD positions in Stochastic Signal Processing/Computational Modelling fMRI/EEG
Three postdoctoral (or graduate) positions are available at the Mind, Brain Imaging & Neuroethics lab. The candidates should have strong background in brain imaging (fMRI, MRS, EEG/MEG, TMS) and preferably strong education in neuroscience/brain imaging, engineering, physics, and/or computational neuroscience for data analyses. The project focuses on resting state and its interaction with task-evoked activity in relation to mental features like self and consciousness in both healthy and psychiatric subjects where neuronal, electrophysiological and biochemical measures will be obtained. A specific focus will be on novel ways of dynamic and non-linear analyses of the brain imaging data in conjunction with computational modeling and signal processing analyses. Part of the project will be carried out in China at Zhejiang University in Hangzhou/China and, in part, in Ottawa/Canada as the PI has affiliations with both places. Hence, Chinese skills are of advantage but not a prerequisite for application. More information about our work can be found on the website: www.georgnorthoff.com For PhD candidates. Graduation at University of Ottawa (PhD) under the supervision of Dr. G. Northoff is possible. Salary for the postdoctoral candidates depends on qualifications and will be around 35.000 CAD to 70.000 CAD. Outstanding candidates may also qualify for faculty position in China. Candidates shall contact: Dr. G. Northoff: georg.north...@theroyal.ca (website: www.georgnorthoff.com) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Neighbors of a vertex
Hello experts, I would like to get a list of neighbors of each vertex in a 32k surface file. How can I do this with workbench? If not with workbench, is there another way to get this info? Thank you. Best, Shankar ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
