External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to preprocesss a t1.nii.gz image in freesurfer with recon-all. I'm following the tutorial for linux in https://secure-web.cisco.com/1LNJqjy9_CcjRF6N2vjvepp4rKUty6HrwT4CmaUGa6hhi_5....
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export FREESURFER_HOME=/usr/local/freesurfer (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/eduardo/fsl
I'm getting the following error when I run the command:
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all
ERROR:
/home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or directory.
This error is strange for me. I don't know why it is showing "\301rea de Trabalho/" if the correct name of the directory is "Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the terminal.
Please, can anybody help how to fix this bug? I've looked for similar bug reports. Probably it is something simple, but I couln't found how to solve the problem.
1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 3) uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Best regards
External Email - Use Caution
Running the command in another directory I got another error:
(base) eduardo@eduardo-X555UB:/usr/local/freesurfer/subjects$ recon-all -i /home/eduardo/Área\ de\ Trabalho/Grant_Tractography/t1.nii.gz -s Grant_sub -all Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in <module> file.write(arg + '\n') UnicodeEncodeError: 'ascii' codec can't encode character '\udcc1' in position 14: ordinal not in range(128) ERROR: could not configure recon-all parameters
On Thu, Feb 18, 2021 at 9:20 PM Eduardo Bergonzoni Junqueira < dubergonzoni@usp.br> wrote:
Hello FreeSurfer Developers,
I'm attempting to preprocesss a t1.nii.gz image in freesurfer with recon-all. I'm following the tutorial for linux in https://secure-web.cisco.com/1LBFicwqnDaueJTJnse4_mduoj4rvakBKEqip8Dc7cnNhQx....
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export FREESURFER_HOME=/usr/local/freesurfer (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/eduardo/fsl
I'm getting the following error when I run the command:
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all
ERROR:
/home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or directory.
This error is strange for me. I don't know why it is showing "\301rea de Trabalho/" if the correct name of the directory is "Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the terminal.
Please, can anybody help how to fix this bug? I've looked for similar bug reports. Probably it is something simple, but I couln't found how to solve the problem.
- FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
- Platform: Ubuntu 20.04.1
- uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Best regards
My guess is that the problem is the spaces in the folder name. Try removing those spaces and see if it works
On 2/18/2021 7:29 PM, Eduardo Bergonzoni Junqueira wrote:
External Email - Use Caution
Running the command in another directory I got another error:
(base) eduardo@eduardo-X555UB:/usr/local/freesurfer/subjects$ recon-all -i /home/eduardo/Área\ de\ Trabalho/Grant_Tractography/t1.nii.gz -s Grant_sub -all Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in
<module> file.write(arg + '\n') UnicodeEncodeError: 'ascii' codec can't encode character '\udcc1' in position 14: ordinal not in range(128) ERROR: could not configure recon-all parameters
On Thu, Feb 18, 2021 at 9:20 PM Eduardo Bergonzoni Junqueira <dubergonzoni@usp.br mailto:dubergonzoni@usp.br> wrote:
Hello FreeSurfer Developers, I'm attempting to preprocesss a t1.nii.gz image in freesurfer with recon-all. I'm following the tutorial for linux in*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall <https://secure-web.cisco.com/1LBFicwqnDaueJTJnse4_mduoj4rvakBKEqip8Dc7cnNhQxdHNr6cnY9hYnO3ObSTXt7iYRQbzd7mcgkqlJjee7GRozXHxSm0X-skycoRDwa4SLEwQ4044yZZt3pw8kSNkAMzCdMZgS38iFYuUYzBha4DICiqc5tomfmUfmqGpV8ifrCHkHJTx-_c_L8-mk_A0uivnGquvWTC4ZMk2UWZE46RRaNTL5hz0_1-3yOKJzbmKPZcFBs_5jMoexz7_V3B/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinuxInstall>. (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export FREESURFER_HOME=/usr/local/freesurfer (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/eduardo/fsl I'm getting the following error when I run the command: (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all ERROR: /home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or directory. This error is strange for me. I don't know why it is showing "\301rea de Trabalho/" if the correct name of the directory is "Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the terminal. Please, can anybody help how to fix this bug? I've looked for similar bug reports. Probably it is something simple, but I couln't found how to solve the problem. 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 3) uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Best regards
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Douglas N. Greve -
Eduardo Bergonzoni Junqueira