External Email - Use Caution Dear Freesurfer experts,
I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (https://secure-web.cisco.com/1UHVC1FSZYmyuNB9-Imz9busENdngVDz-sSAkkWD-mKGV9WnletKDmDav6XNh4DeufrnDsxlVSaMuIYqWMnp2hLM3OoPum_g7pP6r7ilayKRTXVKkLWOtldS6xNiyHXQfxvgCt2ouIPS3x05icPfPrnunp8pV6-x_Y36h3uUGIUqJG1UNdnKWioAtAuKXqMznQXSN7bza3kVliqHiLrq_py0C20DDvg8QgE1r3G6er-TK6ddpq77V4-sP1ET_Q9B5rvXkUnePAZOS1CrQxQ5HnCUZ2nWU25otZlabWPg6h8kvqC1D4Sdc_e1pI1HYOYRvTWDcoE6ZK3169cipg_2BFg/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_03_ReconAll.html). Before running the command, I have converted DICOM files into NIFTI files. I, then, moved the nii files to Desktop at FS. They are in the folder named “Sub-132”. However, I got the following errors: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all bash: syntax error near unexpected token `(' To make another attempt, I tried to process with another T1 image, and I got the following error: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_T1_COR_5_0.5__250_i00002.nii -all mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied cp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file or directory. I reckoned that the T1 images could not be processed with only 1 plane. Would you please kindly advise on merging 3-plane T1 images into one comprehensive T1-weighter image for further processing? Or would you please let me know what went wrong in this case? Thanks. Best regards, Krystal
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