External Email - Use Caution

Dear Falk,

Thank you very much for your email and explanation. It is working now. I wonder how I could set the smoothing for autorecon3 as to run recon -all -all I had the options: -qcache -openmp 8

Kind regards, Rosalia

On Fri, Oct 19, 2018 at 2:06 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

    External Email - Use Caution

Dear Rosalina,

you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and everything will run nicely. You should not include the -i flag again if you want to continue processing your data, as this flag tells FreeSurfer to create a new subject folder (which already exists and therefore give an error).

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 11:11 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear FreeSurfer team,

I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2*

It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows:

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls brainmask.auto.mgz nu.mgz rawavg.mgz brainmask.mgz orig T1.mgz mri_nu_correct.mni.log orig.mgz talairach_with_skull.log mri_nu_correct.mni.log.bak orig_nu.mgz transforms rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $

Best regards,

Rosalia

---

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

External Email - Use Caution

Dear Falk,

Thank you very much. Once last question: what would happen if I did run -autorecon1 without the flags: *-qcache -openmp 8’ *and I use them in autorecon2 or 3?

Best regards, Rosalia

On Fri, Oct 19, 2018 at 2:34 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

    External Email - Use Caution

Dear Rosalia,

You can specify all flags in every call of recon-all. If this flags does not change any commands, they will simply be ignored.

In your case, to first run autorecon1, overwrite the brainmask and continue with autorecon2 and 3, you can do the following:

1.  Run ‘recon-all -autorecon1 -i <your input> -s <your subject ID>
   

-qcache -openmp 8’

2.  Delete brainmaskmgz and use your brain mask created in BET with
   

mri_mask on the T1.mgz and name the output brainmask.mgz

3.  Run ‘recon-all -autorecon2 -autorecon3 -s <your subject ID>
   

-qcache -openmp 8’

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 14:10 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear Falk,

Thank you very much for your email and explanation. It is working now.

I wonder how I could set the smoothing for autorecon3 as to run recon -all -all I had the options: -qcache -openmp 8

Kind regards,

Rosalia

On Fri, Oct 19, 2018 at 2:06 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

•    External Email - Use Caution        *
  
  

Dear Rosalina,

you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and everything will run nicely. You should not include the -i flag again if you want to continue processing your data, as this flag tells FreeSurfer to create a new subject folder (which already exists and therefore give an error).

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 11:11 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear FreeSurfer team,

I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2*

It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows:

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls brainmask.auto.mgz nu.mgz rawavg.mgz brainmask.mgz orig T1.mgz mri_nu_correct.mni.log orig.mgz talairach_with_skull.log mri_nu_correct.mni.log.bak orig_nu.mgz transforms rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $

Best regards,

Rosalia

---

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

---

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

External Email - Use Caution

Dear Falk,

I understand. I will do exactly the same for all the participants. Thank you very much for all your helpful and kind explanations.

Best regards, Rosalia

On Fri, Oct 19, 2018 at 3:13 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

    External Email - Use Caution

Dear Rosalia,

When you use the openmp flag, you should make sure to use it always in the same for all subjects in your study, as otherwise you may introduce a bias (in your case either use it for autorecon1, autorecon2, and autorecon3 or use it for autorecon2 and autorecon3 only). With regards to the qcache flag, it is of no concern, as it does not affect anything in autorecon1 (as far as I know).

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 14:40 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear Falk,

Thank you very much.

Once last question: what would happen if I did run -autorecon1 without the flags: *-qcache -openmp 8’ *and I use them in autorecon2 or 3?

Best regards,

Rosalia

On Fri, Oct 19, 2018 at 2:34 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

•    External Email - Use Caution        *
  
  

Dear Rosalia,

You can specify all flags in every call of recon-all. If this flags does not change any commands, they will simply be ignored.

In your case, to first run autorecon1, overwrite the brainmask and continue with autorecon2 and 3, you can do the following:

1.  Run ‘recon-all -autorecon1 -i <your input> -s <your subject ID>
   

-qcache -openmp 8’

2.  Delete brainmaskmgz and use your brain mask created in BET with
   

mri_mask on the T1.mgz and name the output brainmask.mgz

3.  Run ‘recon-all -autorecon2 -autorecon3 -s <your subject ID>
   

-qcache -openmp 8’

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 14:10 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear Falk,

Thank you very much for your email and explanation. It is working now.

I wonder how I could set the smoothing for autorecon3 as to run recon -all -all I had the options: -qcache -openmp 8

Kind regards,

Rosalia

On Fri, Oct 19, 2018 at 2:06 PM Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

•    External Email - Use Caution        *
  
  

Dear Rosalina,

you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and everything will run nicely. You should not include the -i flag again if you want to continue processing your data, as this flag tells FreeSurfer to create a new subject folder (which already exists and therefore give an error).

Best,

Falk

*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta Aguayo *Gesendet:* Freitag, 19. Oktober 2018 11:11 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* [Freesurfer] Problems to run -autorecon2

•    External Email - Use Caution        *
  
  

Dear FreeSurfer team,

I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2*

It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows:

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls brainmask.auto.mgz nu.mgz rawavg.mgz brainmask.mgz orig T1.mgz mri_nu_correct.mni.log orig.mgz talairach_with_skull.log mri_nu_correct.mni.log.bak orig_nu.mgz transforms rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $

Best regards,

Rosalia

---

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

---

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

---

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