External Email - Use Caution

Got it!

Thank you very much :)

Rosie

El sáb., 19 jun. 2021 20:28, tibor.auer@gmail.com escribió:

    External Email - Use Caution

Hi Rosie,

You need to specify the SUBJECTS_DIR variable to tell FreeSurfer where to create the subject’s directory with the processed data.

If you use BASH:

*export SUBJECTS_DIR=/home/rosalia/Desktop/ARTICO*

will result in creation of /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii

BWT, I recommend leaving the “.nii” from the subject name. I.e.:

            *recon-all -s sub-003_ses-BSL -i

/home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all*

Kind regards,

Tibor

*Auer, Tibor M.D. Ph.D.*

*Research Fellow*

*School of Psychology, Faculty of Health and Medical Sciences*

University of Surrey, Guildford GU2 7XH

T.Auer@surrey.ac.uk

@TiborAuer https://secure-web.cisco.com/1PaDmiPK_zpKGV09Ns4MXxcyukpyuJVixFPFm-5dz_6gga8EdRO3MKspMeVB4chJ6aHayJLVarhb1By59t50V59zj6HZNKBDeogyGJpOtonSt_msbVaWbCGS7dNVcI5tlETATFo1NKP7NApX-XlgOiv9Cue5tm6lRnNqC3iDJe5HpmM5e_sy8MnpTsHc9bYXh_auioyVPWvw02kO8odM13cKZHD8bDN_IM2-NKkt7d3m5GfS7qciB6G_dyX-S3S4kZa8_Lfp4liFSJhycNC90_Q/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Ftwitter.com%252FTiborAuer%26data%3D04%257C01%257Ct.auer%2540surrey.ac.uk%257C5f32dba325f5422f5c5a08d8becc029f%257C6b902693107440aa9e21d89446a2ebb5%257C0%257C0%257C637469131016806177%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DwkpejqTmmo%252Fe4JA9QIaA6Z3%252BzipbFY%252FCEmRXC9UvKJs%253D%26reserved%3D0

*Feladó:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *E személy nevében: *Rosalia Dacosta Aguayo *Küldve:* 19 June 2021 12:36 *Címzett:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Tárgy:* [Freesurfer] Running Freesurfer in the Desktop

•    External Email - Use Caution        *
  
  

Dear Freesurfer's team,

I am trying to run FreeSurfer recon-all -all in a folder placed *on my Desktop* and I am having some trouble.

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt: No such file or directory.

I would greatly appreciate your help.

Kind regards,

Rosie

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