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
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