Hi Soumya Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce
> On Jul 22, 2014, at 8:01 PM, "soumyabrata.dey" > <soumyabrata....@knights.ucf.edu> wrote: > > Hi All, > > I am new to freeSurfer and need your guidance for some of the doubts I have. > > I have installed freeSurfer in a windows 7 machine using virtualBox. I am > trying to process some of my own sMRI data using freeSurfer software. The > data is skull-stripped and has cerebellum. The format of the data is NIFTI > (.hdr, .img). I am having some problem with running the recon-all command on > the data as I am getting the error message saying <filename>.hdr is not found > (I have also tried with inputting .img file). > > My questions are: > > Is recon-all compatible with .hdr .img file format? I know it should run > with .dcm and .nii files. If not what are my option? > Do I need to set up any environment variable for the -i option of the > recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the > full path of the input file. Also, I tried with moving to the directory of > input file and run the command from there. > Thanks for your help, > Soumya. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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