Hi Bruce,

I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist.
---
bash-3.2$ recon-all -i L001.nii -subjid L1 -all
ERROR: cannot find L001.nii
Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all
ERROR: SUBJECTS_DIR /Desktop/MRI does not exist.
bash-3.2$ export SUBJECTS_DIR=/Documents/MRI
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all
ERROR: SUBJECTS_DIR /Documents/MRI does not exist.
bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all
ERROR: cannot find L001.nii.gz
Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---

Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it.

It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out.

Thank you!

Best,

Marja

On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Marja

can you send us the command you ran and the full screen output and the recon-all.log file?

thanks
Bruce

On Wed, 19 Oct 2016, Marja Caverlé wrote:

Dear all,

When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be
found. Any idea what is going wrong?

Best,

Marja


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