It looks like you missed a space between recon-all and ‘-i’.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of behçet ayyildiz
Sent: Monday, February 13, 2023 9:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] bash: recon-all -İ : command not found

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Hi dear all,

I got the similar problem. I have freesurfer version 7.1.1 and when I was trying to run the "recon-all" it indicates me that the command not found. Here below you can find all that bash indicates. 

-------- freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /sw/freesurfer/7.1.1/

FSFAST_HOME       /sw/freesurfer/7.1.1/

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /sw/freesurfer/6.0.0//subjects

MNI_DIR           /sw/freesurfer/7.1.1//mni

FSL_DIR           /sw/fsl/6.0.5.1

drodriguez@causal:~$ cd ../../..

drodriguez@causal:/$ cd data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD/

drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ export SUBJECTS_DIR=`pwd`

drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ echo $SUBJECTS_DIR

/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD

drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ recon-all-i pat_CoDa85.nii -s pat_CoDa85 -all

bash: recon-all-i: command not found

thanks..

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Behçet Ayyıldız..