Hi Marja
you need to figure out where the input files are! How do you know they are there? Can you run:
ls -l /Desktop/MRI/*.nii*
cheers
Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.nii.gz
ls: /Documents/MRI/L001.nii.gz: No such file or directory
bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz
ls: /Desktop/MRI/L001.nii.gz: No such file or directory
Even though, the niftis are really there.
Best,
Marja
On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
what does:
ls -l /Documents/MRI/L001.nii.gz
show?
On Wed, 19 Oct 2016, Marja Caverlé wrote:
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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