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Hi Varun,

 

I’m not sure what issue that you have been running into. Can you send your recon-all.log?

 

In general, you need to

1. set environment variable SUBJECTS_DIR to some directory that you have write permission

2. pass full path to T1 image to -i <full_path_to_T1_image>

 

Best,

 

Yujing

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Varun Chandran
Sent: Wednesday, June 21, 2023 10:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Pial and White surface maps are not found

 

        External Email - Use Caution        

Hi FS experts,

 

It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light on this issue?

 

command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache

 

 

                                                            thanks,

 

best,

Varun

 

--

Varun Arunachalam Chandran, PhD

Postdoctoral Research Associate,

Faculty of biology, medicine and health,

School of health sciences,

University of Manchester,

United Kingdom.

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