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

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[Freesurfer] Surface Problem

Z K zkaufman at nmr.mgh.harvard.edu
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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> Freesurfer mailing list
> Freesurfer at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 

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