Re: [HCP-Users] Help with dtifit on participants

[Glasser, Matthew]

That probably didn’t matter because it appeared you were using absolute paths.  The use of () and && was what I was unsure of. Peace, Matt. From: <Chiu>, "Bryan (PHTH)" <bryan.c...@ubc.ca> Date: Monday, May 4, 2015 at 4:35 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] Help with dtifit on participants Hi, Thanks again for your help. Your version of the script ends up running and I think mine would not run nicely because I would not 'cd' back to the top at the end of the loop. Regards, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia From: Chiu, Bryan (PHTH) Sent: Monday, May 04, 2015 1:51 PM To: Glasser, Matthew; mha...@wustl.edu; hcp-users@humanconnectome.org Subject: RE: [HCP-Users] Help with dtifit on participants Hi, Thanks for the help. I'm going to go with Matt's script first before consulting IT. I have reason to believe it isn't an issue that can be solved by IT because when I navigate to each participant individually and run the same code I have no issues at all. Kind Regards, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia From: Glasser, Matthew [glass...@wusm.wustl.edu] Sent: Monday, May 04, 2015 1:40 PM To: Chiu, Bryan (PHTH); hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Help with dtifit on participants I would write it like this: Subjlist=“YOUR LIST OF SUBJECT IDS SEPARATED BY SPACES" StudyFolder=“YOUR_STUDYFOLDER_THAT_CONTAINS_SUBJECT_FOLDERS_HERE” for Subject in ${Subjlist} ; do #Loop over subject IDs   DIR=`pwd` #Save the current directory   cd ${StudyFolder}/${Subject}/T1w/Diffusion #cd into diffusion directory   dtifit -k data.nii.gz -o data_dtifit -m nodif_brain_mask.nii.gz -r bvecs -b bvals --gradnonlin=grad_dev.nii.gz #Run DTIFIT   cd ${DIR} #Go back to current directory done Peace, Matt. From: <Chiu>, "Bryan (PHTH)" <bryan.c...@ubc.ca> Date: Monday, May 4, 2015 at 3:31 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Help with dtifit on participants Hi, I am trying to run dtifit on the HCP data through FSL, using the following bash script: for dir in /mnt/win/HCP/*;     do         (cd $dir/T1w/Diffusion && dtifit -k data -o data_dtifit -m nodif_brain_mask -r bvecs -b bvals);     done Except it won't run to completion; it will instead hang indefinitely after completing the first participant and the NAS I am connected to appears to hang on this connection. I have done some troubleshooting on this but I am completely stumped. This is my first attempt at bash scripting and FSLDTI. Any help would be appreciated, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia _______________________________________________ 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.   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