Re: [Freesurfer] convert nii to nii.gz

2018-01-22 Thread Ting Li
Dear Bruce, Thanks for your response. I will check it today. Best, Ting > On Jan 21, 2018, at 10:41 AM, Bruce Fischl 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, Ti

Re: [Freesurfer] convert nii to nii.gz

2018-01-21 Thread Bruce Fischl
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

Re: [Freesurfer] convert nii to nii.gz

2018-01-20 Thread Ting Li
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

Re: [Freesurfer] convert nii to nii.gz

2018-01-20 Thread Bruce Fischl
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 so

[Freesurfer] convert nii to nii.gz

2018-01-19 Thread Ting Li
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! Bes