Hi Bruce, Thanks for your quickly response. Sorry for my late.
I try to run FreeSurfer in a server. It was installed in my home share folder. Here is the setting environment information. Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/share/freesurfer FSFAST_HOME /home/share/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/share/freesurfer/subjects MNI_DIR /home/share/freesurfer/mni And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data. When I do a ls, I can’t see the share folder. Do you think I should install if under /home/ting instead of /home/share? Thanks a lot! Best, Ting On Jan 20, 2018, at 9:12 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > > Hi Ting > > that means $FREESURFER_HOME/bin is not in your path and you need to add it > (and make sure that the environment variable FREESURFER_HOME is set > properly). If it is, you can do: > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > Are you new to Linux also? If so, you might want to go through some basic > tutorials. > > cheers > Bruce > > On Fri, 19 Jan 2018, Ting Li wrote: > >> Hi Freesurfer Expert, >> >> I am very new to Freesurfer and have a very basic question. How to convert >> .nii files to nii.gz? I have tried the mri_convert subject_name.nii to >> subject_name.nii.gz directly. It gives me an error information that >> mri_convert: command not found. Thanks for your help! >> >> Best, >> Ting >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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