Hi Bronwyn

can you send us the full command line you ran, screen output and recon-all.log? And maybe a description of where you are in the process? You already ran all the tps through the cross? And created the base?

cheers Bruce On Thu, 17 Aug 2017, Bronwyn Overs wrote:

Hi again list, Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below: [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554988 Aug  9 13:11 lh.qsphere.nofix -rw-rw-r-- 1 b.overs GroupID 4518556 Aug  9 13:35 lh.smoothwm -rw-rw-r-- 1 b.overs GroupID  501887 Aug  9 13:36 lh.smoothwm.BE.crv ... -rw-rw-r-- 1 b.overs GroupID 4507326 Jul 19 19:15 lh.sphere -rw-rw-r-- 1 b.overs GroupID 4507810 Jul 19 19:36 lh.sphere.reg -rw-rw-r-- 1 b.overs GroupID  501887 Aug  9 13:35 lh.sulc …

Kind regards,

Bronwyn Overs Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

  On 17 Aug 2017, at 2:39 pm, Bronwyn Overs <b.overs@neura.edu.au>
  wrote:

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASE ID_001/scripts

mris_register -curv -nosulc -norot/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif ../surf/lh.sphere.reg

using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg... reading template parameterization from/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.f ix/BASEID_001/surf/lh.smoothwm): surface doesn't match/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg

No such file or directory mrisReadTriangleFile failed.

No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem?

Kind regards,

Bronwyn Overs Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

Hi Bronwyn

I defer to Martin :) Bruce On Fri, 18 Aug 2017, Bronwyn Overs wrote:

Hi Bruce,

Please find attached both the command line output and the recon-all log. The command line I ran was: recon-all -long BASEID_001 TPID_001 -all

I have already run and reviewed the cross-sectional and base images for this subject and am now at the point of running the longitudinal image for the first time. This is one of 25 longitudinal images that exited with the same error.

Kind regards, Bronwyn Overs Research Assistant

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

...

On 18 Aug 2017, at 12:57 am, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Bronwyn

can you send us the full command line you ran, screen output and recon-all.log? And maybe a description of where you are in the process? You already ran all the tps through the cross? And created the base?

cheers Bruce On Thu, 17 Aug 2017, Bronwyn Overs wrote:

...

Hi again list, Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below: [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554988 Aug 9 13:11 lh.qsphere.nofix -rw-rw-r-- 1 b.overs GroupID 4518556 Aug 9 13:35 lh.smoothwm -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:36 lh.smoothwm.BE.crv ... -rw-rw-r-- 1 b.overs GroupID 4507326 Jul 19 19:15 lh.sphere -rw-rw-r-- 1 b.overs GroupID 4507810 Jul 19 19:36 lh.sphere.reg -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:35 lh.sulc … Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

 On 17 Aug 2017, at 2:39 pm, Bronwyn Overs <b.overs@neura.edu.au>
 wrote:

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASE ID_001/scripts mris_register -curv -nosulc -norot/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg... reading template parameterization from/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.f ix/BASEID_001/surf/lh.smoothwm): surface doesn't match/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

---

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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 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.

Hi Martin,

Thanks for your suggestion, I will try rerunning the base from scratch to see if this makes a difference. With regards to the base and time-point IDs, those included in the files I sent you were actually not the IDs we use. I did a find and replace to remove our actual IDs in case they could be used to identify the participant. We use our subject ID for the base ID (a ten digit number made up of the 3 digit site ID, 4 digit family ID, and 3 digit person ID), and the unique scan ID for the time-point ID (BAR_***, a 3 digit number assigned at the time of scanning). We have 1 or two timepoints per subject. Kind regards, Bronwyn Overs Research Assistant

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

On 25 Aug 2017, at 7:28 pm, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Bronwyn, I would guess that there has been a problem with the way you run the base. Take one case, copy the cross sectionals into a new directory and re-run the base from scratch. If your two time points are named like: TPID_001 and TPID_002 then the base command should be:

recon-all -base BASEID -tp TPID_001 -tp TPID_002 -all

this will create a directory called BASEID.

Then the longitudinal commands will be: recon-all -long TPID_001 BASEID -all and recon-all -long TPID_002 BASEID -all

I am a little irritated by the way you call your base (as it looks like you called it BASEID_001. If 001 is the subject ID, then this makes sense, but then the time point ID , TPID_001 does not. It is missing an index for the time point like TPID_001_01 for the first and TPID_001_02 for the next etc. Please let me know how you call your input data and base IDS. Also how many time points do you have per subject.

Best, Martin

Am 18.08.2017 um 03:01 schrieb Bruce Fischl:

...

Hi Bronwyn

I defer to Martin :) Bruce On Fri, 18 Aug 2017, Bronwyn Overs wrote:

...

Hi Bruce,

Please find attached both the command line output and the recon-all log. The command line I ran was: recon-all -long BASEID_001 TPID_001 -all

I have already run and reviewed the cross-sectional and base images for this subject and am now at the point of running the longitudinal image for the first time. This is one of 25 longitudinal images that exited with the same error.

Kind regards, Bronwyn Overs Research Assistant

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au http://neura.edu.au/ http://neura.edu.au/ https://twitter.com/neuraustralia https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe http://www.neura.edu.au/help-research/subscribe

...

On 18 Aug 2017, at 12:57 am, Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu wrote:

Hi Bronwyn

can you send us the full command line you ran, screen output and recon-all.log? And maybe a description of where you are in the process? You already ran all the tps through the cross? And created the base?

cheers Bruce On Thu, 17 Aug 2017, Bronwyn Overs wrote:

...

Hi again list, Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below: [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554988 Aug 9 13:11 lh.qsphere.nofix -rw-rw-r-- 1 b.overs GroupID 4518556 Aug 9 13:35 lh.smoothwm -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:36 lh.smoothwm.BE.crv ... -rw-rw-r-- 1 b.overs GroupID 4507326 Jul 19 19:15 lh.sphere -rw-rw-r-- 1 b.overs GroupID 4507810 Jul 19 19:36 lh.sphere.reg -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:35 lh.sulc … Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

 On 17 Aug 2017, at 2:39 pm, Bronwyn Overs <b.overs@neura.edu.au> <mailto:b.overs@neura.edu.au> 
 wrote: 

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASE ID_001/scripts mris_register -curv -nosulc -norot/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg... reading template parameterization from/usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.b uckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.f ix/BASEID_001/surf/lh.smoothwm): surface doesn't match/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh .sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine

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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.