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.camailto: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 <Screen Shot 2021-01-23 at 10.06.37 AM.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1AEInMUr5P4kCOFGAG26B5BQs3yE-oWWCfm-IbnKq1iMQzW...https://secure-web.cisco.com/1jYW48mj_BY16q-EMax4fRk_hOnEV9Yg01sUZWrNAoPumiJQRF4jcS46_TjkdFfwJh0F1Sv24W8tn1UHAgsvDOfh2en7DB48GXPV4GDx33muLJDg7iLADhmrihvrvDgfOUZucbDFqt8mevsI6lll2lbgUrrPh8jA2f13a1vp2UlLuYdmAyywwbuPdvP230ixNpFBwoBg6WirphL4yeGkbm6pm2yPalIAf-Yn2S_MuTHZL2pPzO3wIrVYLmMq0Om2wd6vzOGUvoax2D9TgUt7tug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Why are the symbolic links creating a problem? Is it a mac thing?

On 1/24/2021 10:17 AM, Erika Nolan 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 mailto: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 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

They would be different. V7 works differently than previous versions in this way to allow for cases where the pial is placed using T2 instead of T1

On 1/26/2021 8:32 AM, Erika Nolan wrote:

External Email - Use Caution

Goodmorning Dr. Greve,

Thank you for responding.

The symbolic links should not be a problem if  the .pial and .pialT1 files are essentially the same.

If they were to come out as distinct files ( .pial not being a symbolic link for .pialT1), would both the .pial surface and the .pialT1 surface be the same, when opened in freeview?

Thank you for your help,

Erika Nolan

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, January 25, 2021 10:36:21 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview Why are the symbolic links creating a problem? Is it a mac thing?

On 1/24/2021 10:17 AM, Erika Nolan 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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Horsng Junn hsjunn@gmail.com mailto:hsjunn@gmail.com *Sent:* January 23, 2021 7:31 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer