You also need the GIFTI toolbox installed for Matlab: http://www.artefact.tk/software/matlab/gifti/
Peace, Matt. From: nailin yao <[email protected]<mailto:[email protected]>> Date: Wednesday, October 19, 2016 at 6:58 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] hcp_fix bug Hi Matt, "... " in last Email refer to /home/fas/glahn/ny87/software/workbench/bin_linux64/ So before running fix_3_clean, I've set WBC='/home/fas/glahn/ny87/software/workbench/bin_linux64/wb_command' and CIFTI='/home/fas/glahn/ny87/software/workbench' , which have ciftiopen.m stored. However, I still met the problem as mentioned before. Do you know what could be wrong? Thank you! Best, Nailin 2016-10-19 19:29 GMT-04:00 Glasser, Matthew <[email protected]<mailto:[email protected]>>: I don’t think three dots is valid. Peace, Matt. From: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Wednesday, October 19, 2016 at 5:04 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] hcp_fix bug Hi Matt, I added all the paths needed in fix_3_clean, but still get the error. Is it possible because I add WBC as .../wb_command ? Best, Nailin Sent from my iPhone On Oct 19, 2016, at 5:46 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: You could also need to run the add path parts of the command. Peace, Matt. From: nailin yao <[email protected]<mailto:[email protected]>> Date: Wednesday, October 19, 2016 at 4:02 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] hcp_fix bug Hi Matt, I tried to run fix_3_clean on matlab directly, and met the error message below: fix_3_clean('.fix',0,1,2000) TR = 0.7200 /bin/bash: -cifti-convert: command not found Undefined function 'gifti' for input arguments of type 'char'. Error in ciftiopen (line 31) cifti = gifti([tmpfile '.gii']); Error in fix_3_clean (line 40) BO=ciftiopen('Atlas.dtseries.nii',WBC); Do you know why? Thank you very much! Best, Nailin 2016-10-17 20:12 GMT-04:00 Glasser, Matthew <[email protected]<mailto:[email protected]>>: Is it a reproducible error? What happens if you try running the fix_3_clean function with the parameters mentioned below? Peace, Matt. From: nailin yao <[email protected]<mailto:[email protected]>> Date: Monday, October 17, 2016 at 2:58 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] hcp_fix bug Hi Matt, It's not compiled matlab. Best, Nailin 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <[email protected]<mailto:[email protected]>>: Is this compiled matlab or not compiled? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> Date: Monday, October 17, 2016 at 11:13 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] hcp_fix bug Hi , I received the bug report when running hcp_fix for the last step: running FIX FIX Feature extraction for Melodic output directory: rfMRI_REST1_LR_nonlin_norm_hp2000.ica create edge masks run FAST registration of standard space masks extract features FIX Classifying components in Melodic directory: rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file: /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and threshold 10 FIX Applying cleanup using cleanup file: rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 1 sh: line 1: 24221 Bus error (core dumped) /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06'); addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1 Does anyone know what's the problem? Thank you very much! Best, Nailin -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University ________________________________ 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. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University ________________________________ 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. ________________________________ 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. -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University ________________________________ 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
