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