I’d like Tim’s input on where to upload if you don’t have your own convenient spot.
Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 10:58 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while yes, it happened for each of my subjects. these are the input files for the command - temp_subject_smooth.dtseries.nii, temp_template.dlabel.nii where should i upload them to? On Sun, 31 Mar 2019 at 18:56, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: We need the input files to the command that is taking too long. Also, does the problem happen reproducibly? Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 10:53 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while so ive connected to our server and visually examined the rfMRI_REST_AP.nii.gz file, the output from the fMRIVolume pipeline, and it looks great. where would you like me to upload the files, and which files exactly, other than temp_subject_smooth.dtseries.nii, temp_template.dlabel.nii and the registered volume? thanks, Shachar On Sun, 31 Mar 2019 at 18:37, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Perhaps you should upload the various input files to the specific wb_command command somewhere so we can test them if this issue is reproducible (i.e. is not a random thing from bad RAM or something like that). Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 10:32 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while Its 500 time points. I'll have a look at the volume input tommorow when I get back to the office. I ran them serially, the fmri pipelines.. Cheers Shachar On Sun, Mar 31, 2019, 18:13 Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu> wrote: How many volumes and did you look at the data being input yet? This code didn’t change so we don’t expect any difference. Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 10:10 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while hey matt, this is the call to the pipeline: /root/hcppilelines/HCPpipelines-master/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh --path=/root/hcppilelines/piano_hcp/working_directory --subject=101 --fmriname=rfMRI_REST_AP --lowresmesh=32 --fmrires=2 --smoothingFWHM=4 --grayordinatesres=2 --regname=MSMSulc the TR is 0.75, and the resolution is 2 mm isometric. as i wrote, this went smoothly with the previous release of the pipelines, and resulted in data that looked great thanks, Shachar On Sun, 31 Mar 2019 at 17:53, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How did you call fMRISurface and what kind of data is this in terms of spatial and temporal resolution? Do the input and template data line up and look reasonable? Matt From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 8:27 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while some further information that might be useful - the output file rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the target folder. but the command won't stop "running" On Sun, 31 Mar 2019 at 16:13, Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote: Dear experts, while running the fMRISurface pipeline (using the latest pipeline release) I encountered an issue where the subcortical-processing script takes a really long while (now running for more than 6 hours). this is the command on which it is stuck ${CARET7DIR}/wb_command -cifti-resample ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii COLUMN ${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 10 rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii the wb_command version is 1.3.2 there is no error being raise or anything. its still running, but its ages... the thing is, when running the older version of the pipeline (but the same workbench version), there was no problem. any ideas? ill report later on if it completes the command eventually.... thanks, Shachar _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. On Mar 31, 2019 18:13, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How many volumes and did you look at the data being input yet? This code didn’t change so we don’t expect any difference. Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 10:10 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while hey matt, this is the call to the pipeline: /root/hcppilelines/HCPpipelines-master/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh --path=/root/hcppilelines/piano_hcp/working_directory --subject=101 --fmriname=rfMRI_REST_AP --lowresmesh=32 --fmrires=2 --smoothingFWHM=4 --grayordinatesres=2 --regname=MSMSulc the TR is 0.75, and the resolution is 2 mm isometric. as i wrote, this went smoothly with the previous release of the pipelines, and resulted in data that looked great thanks, Shachar On Sun, 31 Mar 2019 at 17:53, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How did you call fMRISurface and what kind of data is this in terms of spatial and temporal resolution? Do the input and template data line up and look reasonable? Matt From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Sunday, March 31, 2019 at 8:27 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while some further information that might be useful - the output file rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the target folder. but the command won't stop "running" On Sun, 31 Mar 2019 at 16:13, Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote: Dear experts, while running the fMRISurface pipeline (using the latest pipeline release) I encountered an issue where the subcortical-processing script takes a really long while (now running for more than 6 hours). this is the command on which it is stuck ${CARET7DIR}/wb_command -cifti-resample ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii COLUMN ${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii COLUMN ADAP_BARY_AREA CUBIC ${ResultsFolder}/${NameOffMRI}_temp_atlas.dtseries.nii -volume-predilate 10 rm -f ${ResultsFolder}/${NameOffMRI}_temp_subject_smooth.dtseries.nii the wb_command version is 1.3.2 there is no error being raise or anything. its still running, but its ages... the thing is, when running the older version of the pipeline (but the same workbench version), there was no problem. any ideas? ill report later on if it completes the command eventually.... thanks, Shachar _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ________________________________ 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. ________________________________ 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
