Why are the symbolic links creating a problem? Is it a mac thing?
On 1/24/2021 10:17 AM, Erika Nolan wrote:
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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 mailto: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 andrecon-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 mailto: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 https://secure-web.cisco.com/1jYW48mj_BY16q-EMax4fRk_hOnEV9Yg01sUZWrNAoPumiJQRF4jcS46_TjkdFfwJh0F1Sv24W8tn1UHAgsvDOfh2en7DB48GXPV4GDx33muLJDg7iLADhmrihvrvDgfOUZucbDFqt8mevsI6lll2lbgUrrPh8jA2f13a1vp2UlLuYdmAyywwbuPdvP230ixNpFBwoBg6WirphL4yeGkbm6pm2yPalIAf-Yn2S_MuTHZL2pPzO3wIrVYLmMq0Om2wd6vzOGUvoax2D9TgUt7tug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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