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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