Dear freesurfer,
I saw the issue below online and wondered whether it got solved?
I have the “if: Missing file name.” error when testing my installation with
recon-all -i sample-002.nii.gz -s bert -all
attached my recon-all file.
Thank you for your help and best regards,
Laeitita
[Freesurfer] Surface Problem
Z K zkaufman at nmr.mgh.harvard.edu
<mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Surface%20Problem=%3C253ef8e4-8ac6-18e9-86f7-f2945cbeba69%40nmr.mgh.harvard.edu%3E>
Wed Jun 21 16:28:19 EDT 2017
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Can you send me your recon-all script to my email address (not to the
list). I suspect it has been modified.
On 06/21/2017 02:04 PM, Michael Davies wrote:
> Hello, i have been trying to regenerate the surface on one of my
> subjects but keep having a problem where the terminal is saying there is
> a missing file name. Do you have any suggestions please?
>
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer_v6.0.0
> FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5
> bash-4.1$ recon-all -autorecon-pial -s Subj5
> if: Missing file name.
> bash-4.1$
>
>
>
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