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&In-Reply-To=%3C253ef8e4-8ac6-18e9-86f7-f2945cbeba69%40nmr.mgh.harvard.edu%3E Wed Jun 21 16:28:19 EDT 2017

* Previous message: [Freesurfer] Surface Problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html * Messages sorted by: [ date ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#52613 [ thread ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html#52613 [ subject ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.html#52613 [ author ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html#52613

Search archives:

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$

Freesurfer mailing list

Freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

* Previous message: [Freesurfer] Surface Problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html * Messages sorted by: [ date ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#52613 [ thread ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html#52613 [ subject ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.html#52613 [ author ]https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html#52613

More information about the Freesurfer mailing listhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer