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

External Email - Use Caution 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/6.0.5.1http://secure-web.cisco.com/1b6lBSvADA5qf11yxQY9P7xlbCh-dBqyDDUCcL025cYmtFA99nnLP3QBl_JhmMZ3Jkt3p-B14XTsTfP8o1YDI72xOJLtxh32-aWGhSIxD_a5IQPcvLN3AVykaSzSv9JVsOKRLMSccJOZSxAGjfYpwcTdu8QF2BIhLwE-9nTER7sUplins99gLLb9lEc9N9tR08_DguvnQMjDH9Be4CGSZvFzuu3xE0YzBhR5mhi2eMiPonoGXUHz_EaqrUWEof1G_zF9ZNzDIhFFad1-fD58-Ywi8YYdzhA5IsZDxPM87PpmQDY2iQSGqBXCN6Ine1vzaj6MYuC4xxx9iHzbgDLFvQGk2UTyxP_zNqOqoFSvhAqs/http%3A%2F%2F6.0.5.1

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..

-- Behçet Ayyıldız..