Hi  Yujing

Thank you very much for your quick reply. Yes, I used a directory path to set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the 'recon-all' command line. However, it was not very helpful to obtain the pial and white surface maps and exited with some errors as shown in the recon-all.log (please see the file attached). Now, I'll try running the same command by entering the full path name of the directory as you suggested.

                                                                                                                                 thanks again,

best,

Varun

On Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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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

 

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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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Varun Arunachalam Chandran, PhD

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Faculty of biology, medicine and health,

School of health sciences,

University of Manchester,

United Kingdom.

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