On 10 Dec 2016, at 22:50, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Anand

I can't help you getting permission - that you have to sort out with your IT staff or whomever owns the desktop

cheers
Bruce
On Sat, 10 Dec 2016, anand iyer wrote:

Thanks for your prompt reply.
I still cant figure it out.
All the DICOM files for T1 brain volume are on a folder on the desktop.
How do i get permission to a dir?
I’d be grateful for your reply.
Thanks,
Anand
Anand Iyer

     On 10 Dec 2016, at 22:23, Bruce Fischl
     <fischl@nmr.mgh.harvard.edu> wrote:
Hi Anand
you will need write permissions to a dir, after which you can just
run:
recon-all \
-i <path to a single dicom file in the right series> \
-s <subject id> \
-sd <dir for all your subjects> \
-all
No need to convert to nifti or anything
cheers
Bruce
On Sat, 10 Dec 2016, anand iyer wrote:

     I wonder if anybody could help please?
     1. I have converted DICOM to NIFTI and then when I try to
     apply mri_convert
     command to change it to .mgz; i cant locate the converted
     file!
     2. When I try and create directories of the patient within
     subjects
     subfolder; it says ‘permission denied’. I then used the
     sudo command to
     prepare directories.But then i cant move .mgz file (which
     is not found) into
     the mri subfolder of the patient.
     3. Thus i cannot apply the command recon-all.
     Is there any easy way to get the DICOM to load on to
     freesurfer without all
     this hassle?
     I am grateful for your help.
     Anand
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