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Hi Horsng, 

Thank you for you response. I am confused as to why AFAIK is happening to me, while this is not the case in FreeSurfer 6.0, and also the subject Bert in 7.1.1. My colleagues have also run the same subject and it is also not happening to them: the only difference is that they are not using a Mac.

Erika

_____________________________

Erika Nolan 

Ph.D. Candidate

Clinical Psychology, Department of Psychology


Montreal Neurological Institute
McGill University
Montreal, Canada
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Horsng Junn <hsjunn@gmail.com>
Sent: January 23, 2021 7:31 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview
 

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Hi Erika,

Disclaimer: I’m not one of the developers of FreeSurfer so this is not the definitive answer.

AFAIK, it’s designed that way from the beginning and isn’t a problem in itself.
For example I’m using FreeSurfer 7.1.1 and my recon-all script is like this:

at lines 3895~3899:
    set pial = ../surf/$hemi.pial.T1
    set cmd = (mris_place_surface --adgws-in $ads --seg $aseg --threads $OMP_NUM_THREADS\
      --wm $wm --invol $bfs --$hemi  --i $inputsurf --o $pial \
      --pial --nsmooth 0 --rip-label $cortexha --pin-medial-wall $cortex \
      --aparc $aparc --repulse-surf $white  --white-surf $white)

and at 3918:
    cd ../surf; ln -sf $hemi.pial.T1 $hemi.pial; cd ../mri

So the script specifically creates {lh|rh}.pial.T1 as a regular file
and then it symbolically links {lh|rh}.pial to that file.

If you somehow always need {lh|rh}.pial to be a regular file,
you can modify the line at 3918 like this for example:
     cd ../surf; cp -f $hemi.pial.T1 $hemi.pial; cd ../mri

Best,
Horsng Junn

On Jan 24, 2021, at 12:22 AM, Erika Nolan <erika.nolan@mail.mcgill.ca> wrote:

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Hello everyone, 

I am new using FreeSurfer and would really appreciate your help with an issue I am encountering when running recon-all (using: recon-all -subject subjectname -i filename.nii -all and recon-all -s TEST2 -i 103515_t1_final.nii -3T -mprage -hires -all). 

I am using HCP data.

Although my white surface reconstruction seems fine, I am having an issue with the gray matter reconstruction: the rh.pial and lh.pial come out as alias files (see attached screenshot) and when I open them in Freeview they open as rh.pialT1 and lh.pialT1 instead! 

How do I rectify this situation? 

Thank you for your help,

Erika
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