External Email - Use Caution        

Hi Erika,

As I understand it, FreeSurfer 7.1.1 is like an entirely different pipeline from FreeSurfer 6.0.
So discussing why one file is a regular file in one version and a symbolic link in another seems to be a moot point.
I think it's advisable that you and your colleagues standardize on one version and platform
if you're intending to work on each other's output files.

(But from the look of it, I think it's possible that they did this to facilitate some T2/Flair-related analyses.)

And about why that is happening to that one subject only, I think there could be misunderstandings.
For example both lh.pial and rh.pial are symbolic links for my bert.
Are you sure they aren't leftovers from old FreeSurfer 6 runs for example?

One way to check whether the output is from FreeSurfer 7 is to see which directory the "fsaverage" symbolic link points to.
At least in FreeSurfer 7, FreeSurfer creates that symbolic link next to the subject directory such as bert.
Mine is like this:

% ls -l fsaverage
lrwxrwxr-x  ... fsaverage@ -> /Applications/freesurfer/7.1.1/subjects/fsaverage

And I don't have a Linux PC to test this on, but I guess it won't be different there.
You can check that by running this command under Linux:

$ ls -l lh.pial
lrwxrwxr-x  ... lh.pial@ -> lh.pial.T1

Best,
Horsng Junn

On Jan 25, 2021, at 12:17 AM, Erika Nolan <erika.nolan@mail.mcgill.ca> wrote:

        External Email - Use Caution        

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
 
        External Email - Use Caution        

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:

        External Email - Use Caution        

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
<Screen Shot 2021-01-23 at 10.06.37 AM.png>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer