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]>: > I don’t think three dots is valid. > > Peace, > > Matt. > > From: "[email protected]" <[email protected]> > Date: Wednesday, October 19, 2016 at 5:04 PM > > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[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]> wrote: > > You could also need to run the add path parts of the command. > > Peace, > > Matt. > > From: nailin yao <[email protected]> > Date: Wednesday, October 19, 2016 at 4:02 PM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[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]>: > >> 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]> >> Date: Monday, October 17, 2016 at 2:58 PM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[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]>: >> >>> Is this compiled matlab or not compiled? >>> >>> Peace, >>> >>> Matt. >>> >>> From: <[email protected]> on behalf of nailin yao < >>> [email protected]> >>> Date: Monday, October 17, 2016 at 11:13 AM >>> To: "[email protected]" <[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_hp2 >>> 000.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] >>> 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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
