Question on saving interim files when generating an fsavearge

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Re: [Freesurfer] Creating custom...

West, John D.

14 Feb 2017 14 Feb '17

9:43 a.m.

Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

John D. West, M.S. Principal Systems Analyst | Center for Neuroimaging Indiana University School of Medicine

355 West 16th Street | GH 4100 Indianapolis, IN 46202 317-963-7510 jdwest@iupui.edumailto:jdwest@iupui.edu

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Douglas N Greve

15 Feb 15 Feb

5:28 p.m.

New subject: Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir.

On 02/14/2017 09:43 AM, West, John D. wrote:

...

Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

*John D. West, M.S.*

Principal Systems Analyst | Center for Neuroimaging

Indiana University School of Medicine

**

355 West 16^th Street | GH 4100

Indianapolis, IN 46202

317-963-7510

jdwest@iupui.edu mailto:jdwest@iupui.edu

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

West, John D.

1 Mar 1 Mar

2:48 p.m.

New subject: Question on saving interim files when generating an fsavearge

Hi Douglas.

Thanks for the reply. Forgive me for not responding quickly.

It turns out what we really want is the interim files that are saved during recon-all if you add the -qcache option. Is there any way to generate those files after running recon-all without having to run recon-all again in its entirety? We would also be ok with running the sub command manually if we could know what the command line would be.

Thanks so much. -John

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 15, 2017 5:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir.

On 02/14/2017 09:43 AM, West, John D. wrote:

...

Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

*John D. West, M.S.*

Principal Systems Analyst | Center for Neuroimaging

Indiana University School of Medicine

**

355 West 16^th Street | GH 4100

Indianapolis, IN 46202

317-963-7510

jdwest@iupui.edu mailto:jdwest@iupui.edu

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Douglas N Greve

2 Mar 2 Mar

11:19 a.m.

New subject: Question on saving interim files when generating an fsavearge

Just run it with -qcache only and it will only do qcache

On 03/01/2017 02:48 PM, West, John D. wrote:

...

Hi Douglas.

Thanks for the reply. Forgive me for not responding quickly.

It turns out what we really want is the interim files that are saved during recon-all if you add the -qcache option. Is there any way to generate those files after running recon-all without having to run recon-all again in its entirety? We would also be ok with running the sub command manually if we could know what the command line would be.

Thanks so much. -John

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 15, 2017 5:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir.

On 02/14/2017 09:43 AM, West, John D. wrote:

...
Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

*John D. West, M.S.*

Principal Systems Analyst | Center for Neuroimaging

Indiana University School of Medicine

**

355 West 16^th Street | GH 4100

Indianapolis, IN 46202

317-963-7510

jdwest@iupui.edu mailto:jdwest@iupui.edu

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

West, John D.

7 Mar 7 Mar

10:27 a.m.

New subject: Question on saving interim files when generating an fsavearge

Perfect! Thanks so much Douglas! Any idea how long that will take?

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 02, 2017 11:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

Just run it with -qcache only and it will only do qcache

On 03/01/2017 02:48 PM, West, John D. wrote:

...

Hi Douglas.

Thanks for the reply. Forgive me for not responding quickly.

It turns out what we really want is the interim files that are saved during recon-all if you add the -qcache option. Is there any way to generate those files after running recon-all without having to run recon-all again in its entirety? We would also be ok with running the sub command manually if we could know what the command line would be.

Thanks so much. -John

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 15, 2017 5:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir.

On 02/14/2017 09:43 AM, West, John D. wrote:

...
Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

*John D. West, M.S.*

Principal Systems Analyst | Center for Neuroimaging

Indiana University School of Medicine

**

355 West 16^th Street | GH 4100

Indianapolis, IN 46202

317-963-7510

jdwest@iupui.edu mailto:jdwest@iupui.edu

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Douglas Greve

10:36 a.m.

New subject: Question on saving interim files when generating an fsavearge

Not sure, but probably on the order of 30min/subject

On 3/7/17 10:27 AM, West, John D. wrote:

...

Perfect! Thanks so much Douglas! Any idea how long that will take?

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 02, 2017 11:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

Just run it with -qcache only and it will only do qcache

On 03/01/2017 02:48 PM, West, John D. wrote:

...
Hi Douglas.

Thanks for the reply. Forgive me for not responding quickly.

It turns out what we really want is the interim files that are saved during recon-all if you add the -qcache option. Is there any way to generate those files after running recon-all without having to run recon-all again in its entirety? We would also be ok with running the sub command manually if we could know what the command line would be.

Thanks so much. -John

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 15, 2017 5:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on saving interim files when generating an fsavearge

There is not a flag to do this, but you could edit the scripts so that it does not delete the tmpdir.

On 02/14/2017 09:43 AM, West, John D. wrote:

...
Hello.

We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us?

Thanks for your help.

*John D. West, M.S.*

Principal Systems Analyst | Center for Neuroimaging

Indiana University School of Medicine

**

355 West 16^th Street | GH 4100

Indianapolis, IN 46202

317-963-7510

jdwest@iupui.edu mailto:jdwest@iupui.edu

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

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Douglas Greve
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