Dear Bruce,
Thanks for your response. I will check it today.
Best, Ting
On Jan 21, 2018, at 10:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ting
if you can't see the share folder then you can't access our binaries. Maybe talk to your local sysadmins?
cheers Bruce On Sat, 20 Jan 2018, Ting Li wrote:
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 fischl@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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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.