External Email - Use Caution Dear R.,
Thanks for your reply. My apologies if I did not totally get your point – I moved the Sub-132 folder to Home directory and typed in the command as you suggested. However, I still got the error as follows: developer@developer-VirtualBox:~$ export SUBJECTS_DIR=/home/developer developer@developer-VirtualBox:~$ 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 `(' developer@developer-VirtualBox:~$ ls Desktop ExternalHD.txt license.txt Pictures Templates Documents fsl_507 matlab Public Videos Downloads guest_shared Music Sub-132 developer@developer-VirtualBox:~$ cd Sub-132 developer@developer-VirtualBox:~/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 `(' developer@developer-VirtualBox:~/Sub-132$ Would you please kindly advise? Thank you so much! Best regards, Krystal From: fsbuild<mailto:fsbu...@contbay.com> Sent: Friday, May 6, 2022 11:31 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: krystaly<mailto:kryst...@hku.hk> Subject: Re: [Freesurfer] Recon-all Hello Krystally, Try putting the directory Sub-132 under your userid’s home directory, i.e., /home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point to it. With the directory Sub-132 specified on your command line, you could then try, $ export SUBJECTS_DIR=/home/developer - R. On May 5, 2022, at 21:53, krystaly <kryst...@hku.hk> wrote: 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 (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html<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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1xj1_o_Dxx7BcPTE610em1PQ9XT8fSa1h2dPfddJJ9kOyd5GDf5nLyGsiYltzNH6XbavCx-Ao7m7pST3JE3Amq9XuAHY3bRAFrKt7AVnquOWzADLY7nMPAa8db2zBTXC8xqvfq-Ltpq7xr4nCJmoVIBH8GR8eyk7hOIcrWxinu93ysM2MkHGANy5OgSq5lgWdymT9qnn5_rXBtC9Iz4QiUzE0j5aFwr9t2wReaGM0soiMR02AxsL1bbyUY4zh93czc2OR0_AA6ZjazirWddIhP8ln43Upj64qtF2m6Pz6lAKT0FSfwLlB6KcXBlcFxywwSRQ2bGB3BTmLYRbJthwIow/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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