Dear Bruce,

Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested):

bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all
ERROR: cannot find /Documents/MRI/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 15:39:16 CEST 2016

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




On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it

cheers
Bruce




 On Wed, 19 Oct 2016, Marja Caverle wrote:

I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI.

Marja Caverlé

On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

what directory is the file L001.nii.gz in?

cheers
Bruce

On Wed, 19 Oct 2016, Marja Caverlé wrote:

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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