glad it worked out
cheers
Bruce
On Fri, 21 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
Today I restarted my computer, and tried everything again. This time I
indeed used the full path in the -i and the sub_dir, and now it seems to
work!
Thanks for helping out.
Best,
Marja
On Fri, Oct 21, 201
Hi Bruce,
Today I restarted my computer, and tried everything again. This time I
indeed used the full path in the -i and the sub_dir, and now it seems to
work!
Thanks for helping out.
Best,
Marja
On Fri, Oct 21, 2016 at 4:35 AM, Bruce Fischl
wrote:
> Try using /Users/MarjaCaverle/Desktop/MR
Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
> On Oct 20, 2016, at 6:03 PM, Marja Caverlé wrote:
>
> /Users/MarjaCaverle/Desktop/MRI
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bash-3.2$ pwd
/Users/MarjaCaverle/Desktop/MRI
(this means that I am in the right one right?)
Not really someone near, furthermore, almost no one uses mac. I did some
analysis a few months back, and it worked just fine, but now I get these
errors. I intentionally did not update to Sierra yet, beca
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.
Furtherm
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 understa
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.ni
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
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
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
You need to provide the full path to it with the -i command. Then you can
use -sd and -s to specify where the output
should go. Make sure that the directory exists and is
writeable by you, as recon-all will create a subtree called
under it
cheers
Bruce
On Wed, 19 Oct 2016, Marja Cav
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 wrote:
>
> what directory is the file L001.nii.gz in?
>
> cheers
> Bruce
>
>> On Wed, 19 Oct 2
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
sa
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
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
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