Re: [HCP-Users] A question about FDT 3.0

[Glasser, Matthew]

I guess maybe you need to post the results of fslhd on a bunch of files: /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Thalamus.nii.gz /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/nodif_brain_mask.nii.gz /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/merged_f1samples.nii.gz /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Cortex.nii.gz I don't recommend modifying the paths as they will be the way they were released in Q2 going forward, so you'll have to do a lot of modifying. Peace, Matt. From: Huang Su-Chun <claire0...@gmail.com> Date: Wednesday, July 17, 2013 6:29 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] A question about FDT 3.0 Yes, I modified the pathway a little bit. The folder contains one diffusion folder and one T1w folder, I use the ${StudyFolder}/${SubjectID}/Diffusion/data.nii.gz  as my diffusion data. I ran bedpostX on the data and the results looks quite convincing. So I want to move on to tractography. However, the same mistake message keep shows up and I am not sure what matrix it refers to? Do you have any clue where might be the wrong part? Thank you, Su 2013/7/17 Glasser, Matthew <glass...@wusm.wustl.edu> If it's Q2 data, shouldn't you be in ${StudyFolder}/${SubjectID}/T1w/Diffusion?  The Q1+Q2 release that we recently put out has the diffusion data in 1.25mm native volume (structural) space. Peace, Matt. From: Huang Su-Chun <claire0...@gmail.com> Date: Wednesday, July 17, 2013 6:03 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] A question about FDT 3.0 The data is a Q2 data, this is the waypoint txt: --------- /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Cortex.nii.gz ---------- and this is the fdt_log ----------------- set tool probtrackx set probtrack(bedpost_dir) /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX set probtrack(xfm)  set probtrack(mode) seedmask set probtrack(exclude_yn) 0 set probtrack(usereference_yn) 0 set probtrack(verbose_yn) 0 set probtrack(loopcheck_yn) 1 set probtrack(modeuler_yn) 0 set probtrack(curvature) 0.2 set probtrack(nsteps) 2000 set probtrack(steplength) 0.5 set probtrack(nparticles) 5000 set probtrack(fibthresh) 0.01 set probtrack(distthresh) 0.0 set probtrack(sampvox) 0.0 set probtrack(oneway_yn) 1 set probtrack(wayorder_yn) 0 set probtrack(waycond) AND set probtrack(reference) /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Thalamus.nii.gz set probtrack(output) /NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection set probtrack(waypoint_yn) 1  .fdt.data.targets.wf.tf.targets insert end /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Cortex.nii.gz ---------------------- Thank you very much! Su 2013/7/17 Glasser, Matthew <glass...@wusm.wustl.edu> Is this Q1 or Q2 data.  Can you also post the contents of waypoints.txt. Peace, Matt. From: Huang Su-Chun <claire0...@gmail.com> Date: Wednesday, July 17, 2013 5:59 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] A question about FDT 3.0 Just this: -------------------------------------------- /usr/share/fsl/5.0/bin/probtrackx2 -x /NAS_II/Public-Data/Parcellation/100307/Diffusion/Masks/MNI2DTI_shadowreg_L_Thalamus.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/merged -m /NAS_II/Public-Data/Parcellation/100307/Diffusion/data.bedpostX/nodif_brain_mask --dir=/NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection --waypoints=/NAS_II/Public-Data/Parcellation/100307/Diffusion/L_Thalamocortico_connection/waypoints.txt --waycond=AND  --------------------------------------------- 2013/7/17 Glasser, Matthew <glass...@wusm.wustl.edu> What is your probtrackx.log file say? Peace, Matt. From: Huang Su-Chun <claire0...@gmail.com> Date: Wednesday, July 17, 2013 5:45 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] A question about FDT 3.0 Hello all, I want to run probabilistic tracking on one of the HCP data, all the setting I put in is the same as usual (seed mask, waypoint masks, and output directory), however, the error message as follow keep shows up : Errors: Image Exception : #3 :: Mask of different size used in matrix () terminate called after throwing an instance of  'RBD_COMMOM :: BaseException' Anyone has any idea what's going on here? Did I miss something?  Thank you very much, Su -- Su-Chun Huang Research Scientist Integrated Brain Imaging Center Department of Radiology Seattle, WA 98105 206-687-0113 _______________________________________________ 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. -- Su-Chun Huang Research Scientist Integrated Brain Imaging Center Department of Radiology Seattle, WA 98105 206-687-0113   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. -- Su-Chun Huang Research Scientist Integrated Brain Imaging Center Department of Radiology Seattle, WA 98105 206-687-0113   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. -- Su-Chun Huang Research Scientist Integrated Brain Imaging Center Department of Radiology Seattle, WA 98195 phone: 206-687-0113   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