you probably aren't in the MRI dir. What does the command:
pwd
return? And are there any mac-savvy users that can help you out nearby?
cheers
Bruce
On Thu, 20 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
After downloading, I have put the files in those folders, and I can see them. Furthermore, when I go to
the folder and then do the ls command, they are listed as being there. however the command looking for
all files with the .nii extension says there are no files there. I don't understand how this is
possible, do you?
Thanks for helping out.
ls: /Desktop/MRI/L001.nii.gz: No such file or directory
bash-3.2$ ls -l /Desktop/MRI/*.nii*
ls: /Desktop/MRI/*.nii*: No such file or directory
bash-3.2$ ls
L001.nii.gz S1 S13 S4 S8
L1 S1.nii S13.nii S4.nii S8.nii
bash-3.2$ cd ..
bash-3.2$ cd ..
bash-3.2$ ls
20151020volunteer Library
Applications Movies
Desktop Music oasys.log
Desktop.feat OneDrive simdir
Desktop.ica Pictures simdir-
Documents Public simdir--
Downloads ibt_application.log simdir---
Dropbox ibtsa.log summary.txt
Google Drive matlab
bash-3.2$ cd Desktop
bash-3.2$ ls
ARCsleep TIMID printscreens
MRI Uren.xlsx
bash-3.2$ cd MRI
bash-3.2$ ls
L001.nii.gz S1 S13 S4 S8
L1 S1.nii S13.nii S4.nii S8.nii
bash-3.2$
On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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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