External Email - Use Caution
Hello FreeSurfer Developers,
Thank you for your work ! I am new to Freesurfer and I apologize if my question
is naive but I cannot find a solution in any of the online resources.
I successfully set up Freesurfer and I am now attempting to run recon-all on a
.nii file ("s44891-153636-00001-00192-1.nii") on a MacOs Big Sur. To do so, I
run the command below, where "S001" is the subject name and
"/Users/giorgio/Documents/MATLAB/spm12/Group
0/S001/scans/struct/s44891-153636-00001-00192-1.nii " is the path to the .nii
image file:
..$ recon-all -s S001 -i /Users/giorgio/Documents/MATLAB/spm12/Group
0/S001/scans/struct/s44891-153636-00001-00192-1.nii -all
However, I get the following error:
"ERROR: You cannot give recon-all a folder as input. It must be an image file.
If you have multiple files, you need multiple -i flags.
Darwin macbook-pro.home 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22
21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 recon-all -s
S001 exited with ERRORS at Mon May 24 15:50:32 CEST 2021"
My input volume is a .nii, an image file, and I copied its pathway
automatically so I do not think there are mistakes in the pathway to the image:
do you see why is it considered as a folder? Can you help me troubleshoot?
Thank you!
Best,
Giorgio
PS I have already tried to restart the program, to change directory on
terminal, to convert manually the files to .mgz, or to move the .nii file in
the freesurfer home (which gives the following error: ERROR: You are trying to
re-run an existing subject with (possibly) new input data (-i). If this is
truly new input data, you should delete the subject folder and re-run, or
specify a different subject name. If you are just continuing an analysis of an
existing subject, then omit all -i flags.)_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
