question about recon-all

List overview All Threads
Download

newer

older

Creating age-adjusted z score maps...

Monte Carlo error (fwhm4 vs....

Jasmin Alves

31 May 2017 31 May '17

2:15 p.m.

Hello,

I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours.

Is it possible there is too much motion in the image? Or does FS6.0 possibly take longer to complete for some brains?

Thanks, Jasmin

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Attachments:

attachment.html (text/html — 1.2 KB)

Show replies by date

Douglas N Greve

31 May 31 May

3:07 p.m.

You probably have cerebellum or some extra cerebral structure attached to the brain. Check the wm.mgz

On 05/31/2017 02:15 PM, Jasmin Alves wrote:

...

Hello,

I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours.

Is it possible there is too much motion in the image? Or does FS6.0 possibly take longer to complete for some brains?

Thanks, Jasmin

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.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/

Bruce Fischl

3:28 p.m.

Hi Jasmin

typically that means there is a big topological defect, which definitely can be caused by motion. What is the last couple of lines of the recon-all.log file of one of the subjects? Can you upload an image we can look at?

cheers Bruce

On Wed, 31 May 2017, Jasmin Alves wrote:

...

Hello, I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours.

Is it possible there is too much motion in the image? Or does FS6.0 possibly take longer to complete for some brains?

Thanks, Jasmin

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Jasmin Alves

6:09 p.m.

Hi Bruce,

Thanks for the reply, below is a couple of sentences from the recon-all.log

reading initial pial vertex positions from white.preaparc...

mean border=65.6, 300 (300) missing vertices, mean dist 2.2 [2.0 (%0.1)->3.2 (%99.9))]

%21 local maxima, %44 large gradients and %29 min vals, 639 gradients ignored

perforing initial smooth deformation to move away from white surface

tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000

mom=0.00, dt=0.05.

I also attached a screenshot of the log.

Is there a place I should upload the files?

Thanks,

Jasmin

On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Jasmin

typically that means there is a big topological defect, which definitely can be caused by motion. What is the last couple of lines of the recon-all.log file of one of the subjects? Can you upload an image we can look at?

cheers Bruce

On Wed, 31 May 2017, Jasmin Alves wrote:

Hello,

...
I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours.

Is it possible there is too much motion in the image? Or does FS6.0 possibly take longer to complete for some brains?

Thanks, Jasmin

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m= WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM&s= kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4 BdRVo3y7hhYtM&s=D45vVuai1NqKbXaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Bruce Fischl

6:24 p.m.

you can put it on our ftp site:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

but at that point you might as well tar and gzip the entire subject dir and upload it On Wed, 31 May 2017, Jasmin Alves wrote:

...

Hi Bruce, Thanks for the reply, below is a couple of sentences from the recon-all.log

reading initial pial vertex positions from white.preaparc...

mean border=65.6, 300 (300) missing vertices, mean dist 2.2 [2.0 (%0.1)->3.2 (%99.9))]

%21 local maxima, %44 large gradients and %29 min vals, 639 gradients ignored

perforing initial smooth deformation to move away from white surface

tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000

mom=0.00, dt=0.05.

I also attached a screenshot of the log.

Is there a place I should upload the files?

Thanks,

Jasmin

On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jasmin
  typically that means there is a big topological defect, which
  definitely can be caused by motion. What is the last couple of
  lines of the recon-all.log file of one of the subjects? Can you
  upload an image we can look at?

  cheers
  Bruce


  On Wed, 31 May 2017, Jasmin Alves wrote:

        Hello,
        I have used FS6.0 to do recon-all on about 57
        brains, but for some reason,
        recon-all is not working on some brains, recon-all
        is not able to get past
        "Automatic topology fixer", after the command has
        been running for 24 hours.

         Is it possible there is too much motion in the
        image? Or does FS6.0
        possibly take longer to complete for some brains?

        Thanks,
        Jasmin 

        --
        Jasmin Alves
        Doctoral Candidate 
        Medical Biology Graduate Program 
        University of Southern California
        jalves@usc.edu 
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y 7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM&s=D45vVuai1NqKb XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Jasmin Alves

1 Jun 1 Jun

1:01 p.m.

Hi Bruce,

I uploaded two subjects directories to the FTP site.

Thanks, Jasmin

On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

you can put it on our ftp site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer. nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQ UTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHL ug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=SWUWcgct6 aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e= but at that point you might as well tar and gzip the entire subject dir and upload it

On Wed, 31 May 2017, Jasmin Alves wrote:

Hi Bruce,

...
Thanks for the reply, below is a couple of sentences from the recon-all.log

reading initial pial vertex positions from white.preaparc...

mean border=65.6, 300 (300) missing vertices, mean dist 2.2 [2.0 (%0.1)->3.2 (%99.9))]

%21 local maxima, %44 large gradients and %29 min vals, 639 gradients ignored

perforing initial smooth deformation to move away from white surface

tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000

mom=0.00, dt=0.05.

I also attached a screenshot of the log.

Is there a place I should upload the files?

Thanks,

Jasmin

On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Jasmin
  typically that means there is a big topological defect, which
  definitely can be caused by motion. What is the last couple of
  lines of the recon-all.log file of one of the subjects? Can you
  upload an image we can look at?

  cheers
  Bruce


  On Wed, 31 May 2017, Jasmin Alves wrote:

        Hello,
        I have used FS6.0 to do recon-all on about 57
        brains, but for some reason,
        recon-all is not working on some brains, recon-all
        is not able to get past
        "Automatic topology fixer", after the command has
        been running for 24 hours.

         Is it possible there is too much motion in the
        image? Or does FS6.0
        possibly take longer to complete for some brains?

        Thanks,
        Jasmin

        --
        Jasmin Alves
        Doctoral Candidate
        Medical Biology Graduate Program
        University of Southern California
        jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3 vl8MelA4BdRVo3y 7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0 KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM& s=D45vVuai1NqKb XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m= XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=qabnnnfyc7W50hRGrdQ_ 49og8Z3BoC4WMLHMqOnyev4&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nr T1lSDT4_ooLOM&s=PcQnCYSjsxdh7viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Bruce Fischl

2:15 p.m.

Hi Jasmin

actually things look pretty reasonble given the degree of motion corruption. Is it still running? I would expect it to finish ok. I doubt you can get realiable thickness estimates off this kind of data, but you should be able to do e.g. fMRI analysis.

There were a bunch of big defects so the topology fixing took a lot longer than usual, but it did complete

cheers Bruce

On Thu, 1 Jun 2017, Jasmin Alves wrote:

...

Hi Bruce, I uploaded two subjects directories to the FTP site.

Thanks, Jasmin

On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can put it on our ftp site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard .edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7C Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_oo LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e= but at that point you might as well tar and gzip the entire subject dir and upload it On Wed, 31 May 2017, Jasmin Alves wrote:
        Hi Bruce,
        Thanks for the reply, below is a couple of sentences
        from the recon-all.log 

        reading initial pial vertex positions from
        white.preaparc...

        mean border=65.6, 300 (300) missing vertices, mean
        dist 2.2 [2.0 (%0.1)->3.2
        (%99.9))]

        %21 local maxima, %44 large gradients and %29 min
        vals, 639 gradients
        ignored

        perforing initial smooth deformation to move away
        from white surface

        tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2,
        l_surf_repulse=1.000,
        l_tspring=1.000, l_nspring=0.500, l_intensity=0.200,
        l_curv=1.000

        mom=0.00, dt=0.05.


        I also attached a screenshot of the log. 


        Is there a place I should upload the files?


        Thanks,

        Jasmin 


        On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Jasmin

              typically that means there is a big
        topological defect, which
              definitely can be caused by motion. What is
        the last couple of
              lines of the recon-all.log file of one of the
        subjects? Can you
              upload an image we can look at?

              cheers
              Bruce


              On Wed, 31 May 2017, Jasmin Alves wrote:

                    Hello,
                    I have used FS6.0 to do recon-all on
        about 57
                    brains, but for some reason,
                    recon-all is not working on some brains,
        recon-all
                    is not able to get past
                    "Automatic topology fixer", after the
        command has
                    been running for 24 hours.

                     Is it possible there is too much motion
        in the
                    image? Or does FS6.0
                    possibly take longer to complete for
        some brains?

                    Thanks,
                    Jasmin 

                    --
                    Jasmin Alves
                    Doctoral Candidate 
                    Medical Biology Graduate Program 
                    University of Southern California
                    jalves@usc.edu 



        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y
        7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=


        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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM&s=D45vVuai1NqKb
        XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e=  . 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.




        --
        Jasmin Alves
        Doctoral Candidate 
        Medical Biology Graduate Program 
        University of Southern California
        jalves@usc.edu 
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4 _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=PcQnCYSjsxdh7 viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Jasmin Alves

6:47 p.m.

Hi Bruce,

So it does not matter that the recon-all.done script never appeared in the script folder? Or that the isrunning.lh+rh script is still in the folder?

I plan to run the hippocampal subfield analysis on these folders, so I am wondering if the subfield analysis can still function without the recon-all.done script being in the folder.

Thanks, Jasmin

On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Jasmin

actually things look pretty reasonble given the degree of motion corruption. Is it still running? I would expect it to finish ok. I doubt you can get realiable thickness estimates off this kind of data, but you should be able to do e.g. fMRI analysis.

There were a bunch of big defects so the topology fixing took a lot longer than usual, but it did complete

cheers Bruce

On Thu, 1 Jun 2017, Jasmin Alves wrote:

Hi Bruce,

...
I uploaded two subjects directories to the FTP site.

Thanks, Jasmin

On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

...
wrote: you can put it on our ftp site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer. nmr.mgh.harvard .edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0N U5BOUHhpN0H8p7C Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR 4K7nrT1lSDT4_oo LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e= but at that point you might as well tar and gzip the entire subject dir and upload it On Wed, 31 May 2017, Jasmin Alves wrote:
        Hi Bruce,
        Thanks for the reply, below is a couple of sentences
        from the recon-all.log

        reading initial pial vertex positions from
        white.preaparc...

        mean border=65.6, 300 (300) missing vertices, mean
        dist 2.2 [2.0 (%0.1)->3.2
        (%99.9))]

        %21 local maxima, %44 large gradients and %29 min
        vals, 639 gradients
        ignored

        perforing initial smooth deformation to move away
        from white surface

        tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2,
        l_surf_repulse=1.000,
        l_tspring=1.000, l_nspring=0.500, l_intensity=0.200,
        l_curv=1.000

        mom=0.00, dt=0.05.


        I also attached a screenshot of the log.


        Is there a place I should upload the files?


        Thanks,

        Jasmin


        On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Jasmin

              typically that means there is a big
        topological defect, which
              definitely can be caused by motion. What is
        the last couple of
              lines of the recon-all.log file of one of the
        subjects? Can you
              upload an image we can look at?

              cheers
              Bruce


              On Wed, 31 May 2017, Jasmin Alves wrote:

                    Hello,
                    I have used FS6.0 to do recon-all on
        about 57
                    brains, but for some reason,
                    recon-all is not working on some brains,
        recon-all
                    is not able to get past
                    "Automatic topology fixer", after the
        command has
                    been running for 24 hours.

                     Is it possible there is too much motion
        in the
                    image? Or does FS6.0
                    possibly take longer to complete for
        some brains?

                    Thanks,
                    Jasmin

                    --
                    Jasmin Alves
                    Doctoral Candidate
                    Medical Biology Graduate Program
                    University of Southern California
                    jalves@usc.edu



        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3 vl8MelA4BdRVo3y
        7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=


        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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0

KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM& s=D45vVuai1NqKb
        XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e=  . 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.




        --
        Jasmin Alves
        Doctoral Candidate
        Medical Biology Graduate Program
        University of Southern California
        jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLa JXR4K7nrT1lSDT4 _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0 KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM& s=PcQnCYSjsxdh7 viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_ W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa5KKP-s&s= hRwIqSvnivcn2Fq_clewi1C8D05Qw2smP28HsGHKtMk&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W- Ibh0SCMa2DLmtX9mHsa5KKP-s&s=KRfTs08CU2sbLAvfTwDIKa8PfD-d0mzHuBoqZbLgtsU&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Bruce Fischl

6:52 p.m.

Hi Jasmin

how long did you wait? Is the process still running? The last step in the log is not a very long one. Maybe someone/something killed your job prematurely? I see no reason in the log that it wouldn't have finished

Bruce

On Thu, 1 Jun 2017, Jasmin Alves wrote:

...

Hi Bruce, So it does not matter that the recon-all.done script never appeared in the script folder? Or that the isrunning.lh+rh script is still in the folder?

I plan to run the hippocampal subfield analysis on these folders, so I am wondering if the subfield analysis can still function without the recon-all.done script being in the folder.

Thanks, Jasmin

On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jasmin
  actually things look pretty reasonble given the degree of motion
  corruption. Is it still running? I would expect it to finish ok.
  I doubt you can get realiable thickness estimates off this kind
  of data, but you should be able to do e.g. fMRI analysis.

  There were a bunch of big defects so the topology fixing took a
  lot longer than usual, but it did complete

  cheers
  Bruce


  On Thu, 1 Jun 2017, Jasmin Alves wrote:

        Hi Bruce,
        I uploaded two subjects directories to the FTP
        site. 

        Thanks,
        Jasmin 

        On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              you can put it on our ftp site:
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7C

Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_oo
             
        LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e=
              but at that point you might as well tar and
        gzip the entire
              subject dir and upload it
              On Wed, 31 May 2017, Jasmin Alves wrote:

                    Hi Bruce,
                    Thanks for the reply, below is a couple
        of sentences
                    from the recon-all.log 

                    reading initial pial vertex positions
        from
                    white.preaparc...

                    mean border=65.6, 300 (300) missing
        vertices, mean
                    dist 2.2 [2.0 (%0.1)->3.2
                    (%99.9))]

                    %21 local maxima, %44 large gradients
        and %29 min
                    vals, 639 gradients
                    ignored

                    perforing initial smooth deformation to
        move away
                    from white surface

                    tol=1.0e-04, sigma=2.0, host=hpc17,
        nav=16, nbrs=2,
                    l_surf_repulse=1.000,
                    l_tspring=1.000, l_nspring=0.500,
        l_intensity=0.200,
                    l_curv=1.000

                    mom=0.00, dt=0.05.


                    I also attached a screenshot of the
        log. 


                    Is there a place I should upload the
        files?


                    Thanks,

                    Jasmin 


                    On Wed, May 31, 2017 at 12:28 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          Hi Jasmin

                          typically that means there is a
        big
                    topological defect, which
                          definitely can be caused by
        motion. What is
                    the last couple of
                          lines of the recon-all.log file of
        one of the
                    subjects? Can you
                          upload an image we can look at?

                          cheers
                          Bruce


                          On Wed, 31 May 2017, Jasmin Alves
        wrote:

                                Hello,
                                I have used FS6.0 to do
        recon-all on
                    about 57
                                brains, but for some reason,
                                recon-all is not working on
        some brains,
                    recon-all
                                is not able to get past
                                "Automatic topology fixer",
        after the
                    command has
                                been running for 24 hours.

                                 Is it possible there is too
        much motion
                    in the
                                image? Or does FS6.0
                                possibly take longer to
        complete for
                    some brains?

                                Thanks,
                                Jasmin 

                                --
                                Jasmin Alves
                                Doctoral Candidate 
                                Medical Biology Graduate
        Program 
                                University of Southern
        California
                                jalves@usc.edu 



                   
        _______________________________________________
                    Freesurfer mailing list
                    Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y
                   
        7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=


                    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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM&s=D45vVuai1NqKb
                    XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e=  . 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.




                    --
                    Jasmin Alves
                    Doctoral Candidate 
                    Medical Biology Graduate Program 
                    University of Southern California
                    jalves@usc.edu 



        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4
        _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e=


        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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=PcQnCYSjsxdh7

viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa 5KKP-s&s=hRwIqSvnivcn2Fq_clewi1C8D05Qw2smP28HsGHKtMk&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa5KKP-s&s=KRfTs08CU2sbL AvfTwDIKa8PfD-d0mzHuBoqZbLgtsU&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Jasmin Alves

6:55 p.m.

Hi Bruce,

I waited 24 hours, and then the job, at that point it was killed by the computing center I use. They have a max analysis time of 24 hours. Perhaps the last steps are not being reached due to the large topological defects, however I never encountered this problem before with FS5.3, what do you recommend?

Thanks, Jasmin

On Thu, Jun 1, 2017 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Jasmin

how long did you wait? Is the process still running? The last step in the log is not a very long one. Maybe someone/something killed your job prematurely? I see no reason in the log that it wouldn't have finished

Bruce

On Thu, 1 Jun 2017, Jasmin Alves wrote:

Hi Bruce,

...
So it does not matter that the recon-all.done script never appeared in the script folder? Or that the isrunning.lh+rh script is still in the folder?

I plan to run the hippocampal subfield analysis on these folders, so I am wondering if the subfield analysis can still function without the recon-all.done script being in the folder.

Thanks, Jasmin

On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

...
wrote: Hi Jasmin
  actually things look pretty reasonble given the degree of motion
  corruption. Is it still running? I would expect it to finish ok.
  I doubt you can get realiable thickness estimates off this kind
  of data, but you should be able to do e.g. fMRI analysis.

  There were a bunch of big defects so the topology fixing took a
  lot longer than usual, but it did complete

  cheers
  Bruce


  On Thu, 1 Jun 2017, Jasmin Alves wrote:

        Hi Bruce,
        I uploaded two subjects directories to the FTP
        site.

        Thanks,
        Jasmin

        On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              you can put it on our ftp site:
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer. nmr.mgh.harvard

.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0N U5BOUHhpN0H8p7C

Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR 4K7nrT1lSDT4_oo
        LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e=
              but at that point you might as well tar and
        gzip the entire
              subject dir and upload it
              On Wed, 31 May 2017, Jasmin Alves wrote:

                    Hi Bruce,
                    Thanks for the reply, below is a couple
        of sentences
                    from the recon-all.log

                    reading initial pial vertex positions
        from
                    white.preaparc...

                    mean border=65.6, 300 (300) missing
        vertices, mean
                    dist 2.2 [2.0 (%0.1)->3.2
                    (%99.9))]

                    %21 local maxima, %44 large gradients
        and %29 min
                    vals, 639 gradients
                    ignored

                    perforing initial smooth deformation to
        move away
                    from white surface

                    tol=1.0e-04, sigma=2.0, host=hpc17,
        nav=16, nbrs=2,
                    l_surf_repulse=1.000,
                    l_tspring=1.000, l_nspring=0.500,
        l_intensity=0.200,
                    l_curv=1.000

                    mom=0.00, dt=0.05.


                    I also attached a screenshot of the
        log.


                    Is there a place I should upload the
        files?


                    Thanks,

                    Jasmin


                    On Wed, May 31, 2017 at 12:28 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          Hi Jasmin

                          typically that means there is a
        big
                    topological defect, which
                          definitely can be caused by
        motion. What is
                    the last couple of
                          lines of the recon-all.log file of
        one of the
                    subjects? Can you
                          upload an image we can look at?

                          cheers
                          Bruce


                          On Wed, 31 May 2017, Jasmin Alves
        wrote:

                                Hello,
                                I have used FS6.0 to do
        recon-all on
                    about 57
                                brains, but for some reason,
                                recon-all is not working on
        some brains,
                    recon-all
                                is not able to get past
                                "Automatic topology fixer",
        after the
                    command has
                                been running for 24 hours.

                                 Is it possible there is too
        much motion
                    in the
                                image? Or does FS6.0
                                possibly take longer to
        complete for
                    some brains?

                                Thanks,
                                Jasmin

                                --
                                Jasmin Alves
                                Doctoral Candidate
                                Medical Biology Graduate
        Program
                                University of Southern
        California
                                jalves@usc.edu




        _______________________________________________
                    Freesurfer mailing list
                    Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3 vl8MelA4BdRVo3y
        7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=


                    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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0

KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM& s=D45vVuai1NqKb
                    XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e=  . 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.




                    --
                    Jasmin Alves
                    Doctoral Candidate
                    Medical Biology Graduate Program
                    University of Southern California
                    jalves@usc.edu



        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLa JXR4K7nrT1lSDT4
        _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e=


        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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0

KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM& s=PcQnCYSjsxdh7

viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm r.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv i0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W- Ibh0SCMa2DLmtX9mHsa 5KKP-s&s=hRwIqSvnivcn2Fq_clewi1C8D05Qw2smP28HsGHKtMk&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part ners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc _gI&r=LH_W279i0 KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa5KKP-s& s=KRfTs08CU2sbL AvfTwDIKa8PfD-d0mzHuBoqZbLgtsU&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7_ ZUjRDEh6wPdCaB71enVHBAjTp0Ls22m4shTklqMFM&s=om73zSBAd4AgvHfAtEX5Uw7Ynllfrx Fe3tWrKskbnJQ&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7_ZUjRDEh6wPdCaB71enVHBAjTp0Ls22 m4shTklqMFM&s=43K8iWeiOMMDjdT7FFtr6P-c0TL8xs9ZfG885jPhj6k&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Bruce Fischl

6:58 p.m.

oh, yes, I think that is probably your problem. The left/right topology fixing alone took more than 10 hours I think, so probably you got to 24 and they killed it. If they gave you 48 or even 30 it might have finished On Thu, 1 Jun 2017, Jasmin Alves wrote:

...

Hi Bruce, I waited 24 hours, and then the job, at that point it was killed by the computing center I use. They have a max analysis time of 24 hours. Perhaps the last steps are not being reached due to the large topological defects, however I never encountered this problem before with FS5.3, what do you recommend?

Thanks, Jasmin

On Thu, Jun 1, 2017 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jasmin

  how long did you wait? Is the process still running? The last
  step in the log is not a very long one. Maybe someone/something
  killed your job prematurely? I see no reason in the log that it
  wouldn't have finished

  Bruce


  On Thu, 1 Jun 2017, Jasmin Alves wrote:

  Hi Bruce,
  So it does not matter that the recon-all.done script never
  appeared in the
  script folder? Or that the isrunning.lh+rh script is still
  in the folder? 

  I plan to run the hippocampal subfield analysis on these
  folders, so I am
  wondering if the  subfield analysis can still function
  without the
  recon-all.done script being in the folder.

  Thanks,
  Jasmin  

  On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu>
  wrote:
        Hi Jasmin

        actually things look pretty reasonble given the
  degree of motion
        corruption. Is it still running? I would expect it
  to finish ok.
        I doubt you can get realiable thickness estimates
  off this kind
        of data, but you should be able to do e.g. fMRI
  analysis.

        There were a bunch of big defects so the topology
  fixing took a
        lot longer than usual, but it did complete

        cheers
        Bruce


        On Thu, 1 Jun 2017, Jasmin Alves wrote:

              Hi Bruce,
              I uploaded two subjects directories to the FTP
              site. 

              Thanks,
              Jasmin 

              On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl
              <fischl@nmr.mgh.harvard.edu>
              wrote:
                    you can put it on our ftp site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7C

Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_oo

                   
             
  LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e=
                    but at that point you might as well tar
  and
              gzip the entire
                    subject dir and upload it
                    On Wed, 31 May 2017, Jasmin Alves wrote:

                          Hi Bruce,
                          Thanks for the reply, below is a
  couple
              of sentences
                          from the recon-all.log 

                          reading initial pial vertex
  positions
              from
                          white.preaparc...

                          mean border=65.6, 300 (300)
  missing
              vertices, mean
                          dist 2.2 [2.0 (%0.1)->3.2
                          (%99.9))]

                          %21 local maxima, %44 large
  gradients
              and %29 min
                          vals, 639 gradients
                          ignored

                          perforing initial smooth
  deformation to
              move away
                          from white surface

                          tol=1.0e-04, sigma=2.0,
  host=hpc17,
              nav=16, nbrs=2,
                          l_surf_repulse=1.000,
                          l_tspring=1.000, l_nspring=0.500,
              l_intensity=0.200,
                          l_curv=1.000

                          mom=0.00, dt=0.05.


                          I also attached a screenshot of
  the
              log. 


                          Is there a place I should upload
  the
              files?


                          Thanks,

                          Jasmin 


                          On Wed, May 31, 2017 at 12:28 PM,
  Bruce
              Fischl
                          <fischl@nmr.mgh.harvard.edu>
                          wrote:
                                Hi Jasmin

                                typically that means there
  is a
              big
                          topological defect, which
                                definitely can be caused by
              motion. What is
                          the last couple of
                                lines of the recon-all.log
  file of
              one of the
                          subjects? Can you
                                upload an image we can look
  at?

                                cheers
                                Bruce


                                On Wed, 31 May 2017, Jasmin
  Alves
              wrote:

                                      Hello,
                                      I have used FS6.0 to
  do
              recon-all on
                          about 57
                                      brains, but for some
  reason,
                                      recon-all is not
  working on
              some brains,
                          recon-all
                                      is not able to get
  past
                                      "Automatic topology
  fixer",
              after the
                          command has
                                      been running for 24
  hours.

                                       Is it possible there
  is too
              much motion
                          in the
                                      image? Or does FS6.0
                                      possibly take longer
  to
              complete for
                          some brains?

                                      Thanks,
                                      Jasmin 

                                      --
                                      Jasmin Alves
                                      Doctoral Candidate 
                                      Medical Biology
  Graduate
              Program 
                                      University of Southern
              California
                                      jalves@usc.edu 



                         
             
  _______________________________________________
                          Freesurfer mailing list
                          Freesurfer@nmr.mgh.harvard.edu

https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y

                         
             
  7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e=


                          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

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3vl8MelA4BdRVo3y7hhYtM&s=D45vVuai1NqKb

                          XaPiyL_IyC3_nb4RC-eDYCmlpRSVF4&e= 
  . 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.




                          --
                          Jasmin Alves
                          Doctoral Candidate 
                          Medical Biology Graduate Program 
                          University of Southern California
                          jalves@usc.edu 



             
  _______________________________________________
              Freesurfer mailing list
              Freesurfer@nmr.mgh.harvard.edu

https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4

             
  _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e=


              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

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=PcQnCYSjsxdh7

  viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e=  . 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.




  --
  Jasmin Alves
  Doctoral Candidate 
  Medical Biology Graduate Program 
  University of Southern California
  jalves@usc.edu 



  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu

https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e

du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8

p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa

  5KKP-s&s=hRwIqSvnivcn2Fq_clewi1C8D05Qw2smP28HsGHKtMk&e=


  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

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli

anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0

KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa5KKP-s&s=KRfTs08CU2sbL

AvfTwDIKa8PfD-d0mzHuBoqZbLgtsU&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7_ZUjRDEh6wPdCaB71enVHBAjTp0Ls22m4shT klqMFM&s=om73zSBAd4AgvHfAtEX5Uw7YnllfrxFe3tWrKskbnJQ&e=

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=7_ZUjRDEh6wPdCaB71enVHBAjTp0Ls22m4shTklqMFM&s=43K8iWeiOMMDj dT7FFtr6P-c0TL8xs9ZfG885jPhj6k&e= . 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.

-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu

3288

Age (days ago)

3289

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

10 comments

3 participants

tags (0)

participants (3)

Bruce Fischl
Douglas N Greve
Jasmin Alves