patch for ribbon mgz failure

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Maria Gloria Rossetti

30 Aug 2017 30 Aug '17

6:32 a.m.

Hi freesurfer team,

I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use.

Any advice?

Thanks! Gloria

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Douglas N Greve

5 Sep 5 Sep

12:09 p.m.

Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats)

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:

...

Hi freesurfer team,

I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use.

Any advice?

Thanks! Gloria

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

Maria Gloria Rossetti

6 Sep 6 Sep

7:53 a.m.

New subject: patch for ribbon mgz failure. SAME ERROR

Hi Doug,

As you suggested, I copied the mri_segstats patch (mri_segstats.centos6_x86_64 because my system is centos6) to my freesurfer/bin location and reran the pipeline. However, I'm getting the same issue. Autorecon2 seems unable to create the ribbon.mgz file. Do you have any other suggestions for fixing this error? Attached you can find the recon-all.log file

Thanks, Gloria

Da: "Douglas N Greve" greve@nmr.mgh.harvard.edu A: "freesurfer" freesurfer@nmr.mgh.harvard.edu Inviato: Martedì, 5 settembre 2017 18:09:31 Oggetto: Re: [Freesurfer] patch for ribbon mgz failure

Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats)

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:

...

Hi freesurfer team,

I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use.

Any advice?

Thanks! Gloria

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

Douglas Greve

2:02 p.m.

New subject: patch for ribbon mgz failure. SAME ERROR

what happens if you run

recon-all -s subject -cortribbon

does it create the ribbon.mgz?

On 9/6/17 7:53 AM, Maria Gloria Rossetti wrote:

...

Hi Doug,

As you suggested, I copied the mri_segstats patch (mri_segstats.centos6_x86_64 because my system is centos6) to my freesurfer/bin location and reran the pipeline. However, I'm getting the same issue. Autorecon2 seems unable to create the ribbon.mgz file. Do you have any other suggestions for fixing this error? Attached you can find the recon-all.log file

Thanks, Gloria

*Da: *"Douglas N Greve" greve@nmr.mgh.harvard.edu *A: *"freesurfer" freesurfer@nmr.mgh.harvard.edu *Inviato: *Martedì, 5 settembre 2017 18:09:31 *Oggetto: *Re: [Freesurfer] patch for ribbon mgz failure

Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats)

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:

...
Hi freesurfer team,

I got the same error described here:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html

...
and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats

...
but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use.

Any advice?

Thanks! Gloria

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

Maria Gloria Rossetti

8 Sep 8 Sep

3:24 a.m.

New subject: patch for ribbon mgz failure. SAME ERROR

Yes it does. I ran -cortribbon first then reran autorecon-all (instead of -autorecon2). Now it finished "without error". However I'm still confused why do I get the error when I run -autorecon2 (a freesurfer newbie over here)

Best, Gloria

Da: "Douglas Greve" greve@nmr.mgh.harvard.edu A: "freesurfer" freesurfer@nmr.mgh.harvard.edu Inviato: Mercoledì, 6 settembre 2017 20:02:22 Oggetto: Re: [Freesurfer] patch for ribbon mgz failure. SAME ERROR

what happens if you run

recon-all -s subject -cortribbon does it create the ribbon.mgz?

On 9/6/17 7:53 AM, Maria Gloria Rossetti wrote:

Hi Doug,

Thanks, Gloria

Da: "Douglas N Greve" greve@nmr.mgh.harvard.edu A: "freesurfer" freesurfer@nmr.mgh.harvard.edu Inviato: Martedì, 5 settembre 2017 18:09:31 Oggetto: Re: [Freesurfer] patch for ribbon mgz failure

Use the mri_segstats from this URL that is appropriate for your system (eg, if you're running centos6, the download that patch and copy it to mri_segstats)

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/

On 08/30/2017 06:32 AM, Maria Gloria Rossetti wrote:

...

Hi freesurfer team,

I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use.

Any advice?

Thanks! Gloria

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 _______________________________________________ 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.

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Douglas Greve
Douglas N Greve
Maria Gloria Rossetti