It is hard to keep track of these threads when they don’t contain the prior info below. I did find that you are not using FSL 6.0.1, so I would retry with that.
Matt. From: Qunjun Liang <liangqun...@foxmail.com<mailto:liangqun...@foxmail.com>> Date: Wednesday, April 10, 2019 at 9:24 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] An error about subcorticalprocessinginHCPfMRI-surface pipeline Hi Matt, I am very grateful for your kindness. After looked through files in working directory by fslinfo, I found a image, named T1_store.2.nii.gz, which I think is the first file be generated in wrong space (91x108x91). Given the name of the file, I traced back the command line in the fMRIvolume script. Finally, I found Line 126 in OneStepResampling.sh which is the command line to generate the file. #---------------- ${FSLDIR}/bin/flirt -interp spline -in ${T1wImage} -ref ${T1wImage} -applyisoxfm ${FinalfMRIResolution} -out ${WD}/${T1wImageFile}.${FinalfMRIResolution} #--------------- So I tested this command line independently using the image in its log file. Repeatedly, the result file was also generated in 91x108x91 space. I noticed that in this script, the fMRI image would be resampled reference to T1_store.2.nii.gz. I think because of the wrong space of T1_store.2.nii.gz, it also effected the fMRI resampling image. However, I notice a comment above Line 126 in OneStepResampling.sh. #------ NB: don't use FLIRT to do spline interpolation with -applyisoxfm for the 2mm and 1 mm cases because it dosen't know the peculiarities of the MNI template FOVs #------ I wonder if it give a cue to the problem? Sincerely, Qunjun ________________________________ 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
