Hey Doug and Freesurfers,
At the bottom is the output showing what steps didn't run.

1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1:

 I made edits with talairach registration edits with tkregister2 and  ran recon-all -all -label_v1. 
After that,with tkmedit  I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1.

 2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch?  Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag?

Thanks.
Michelle

FreeSurfer:/media/sf_windows/
subjects> recon-all -s ld07 -make all -dontrun
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Subject 'ld07': make -n all
recon-all -s /media/sf_windows/subjects/ld07 -gcareg
recon-all -s /media/sf_windows/subjects/ld07 -canorm
recon-all -s /media/sf_windows/subjects/ld07 -careg -careginv
recon-all -s /media/sf_windows/subjects/ld07 -rmneck
recon-all -s /media/sf_windows/subjects/ld07 -skull-lta
recon-all -s /media/sf_windows/subjects/ld07 -calabel
recon-all -s /media/sf_windows/subjects/ld07 -normalization2
recon-all -s /media/sf_windows/subjects/ld07 -maskbfs
recon-all -s /media/sf_windows/subjects/ld07 -segmentation
recon-all -s /media/sf_windows/subjects/ld07 -fill
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -tessellate
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -tessellate
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth1
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth1
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate1
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate1
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -qsphere
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -qsphere
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -fix
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -fix
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth2
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth2
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -sphere
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -sphere
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -surfreg
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -surfreg
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -jacobian_white
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -jacobian_white
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -avgcurv
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -avgcurv
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc2
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc2
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats2
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats2
recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortribbon
recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortribbon
recon-all -s /media/sf_windows/subjects/ld07 -segstats
recon-all -s /media/sf_windows/subjects/ld07 -aparc2aseg
recon-all -s /media/sf_windows/subjects/ld07 -wmparc
- Hide quoted text -

 

On Wed, Sep 28, 2011 at 11:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
> Hi Michelle, this almost surely means that the surfaces are out-of-synch.
> You can try
> recon-all -s subject -make all -dontrun
> on one of your subjects.
>
> If everything is in synch, then it should print
>  make: Nothing to be done for `all'.
>
> If not, it should print out the steps that it would have run (if not for the
> -dontrun option).
>
> doug
>
> Michelle Umali wrote:
>>
>> Hi Doug,
>> I get the same MRISripZeros() and MRIScopyMRI Surf/src mismatch error
>> when I use -sphere and not -occip in fieldsign-sess.
>>
>> What else should I try?
>>
>> Thank you.
>> Michelle
>>
>>
>> On Tue, Sep 27, 2011 at 8:51 PM, Douglas N Greve
>> <greve@nmr.mgh.harvard.edu> wrote:
>>  
>>>
>>> Is the occip patch out of synch with the subject? Does it run if you use
>>> -sphere instead of -occip?
>>> doug
>>>
>>> Michelle Umali wrote:
>>>    
>>>>
>>>> Dear Freesurfers,
>>>> This is related to my retinotopy analysis tksurfer-sess dimension
>>>> mismatch error message.
>>>>
>>>> So another subject had these errors come up during fieldsign-sess
>>>> selxavg3-sess -a rtopy.self.lh -s sjXX -force
>>>> (which ran without error)
>>>>
>>>> then I ran fieldsign
>>>> fieldsign-sess -a rtopy.self.lh -occip -s sjXX
>>>>
>>>> and got:
>>>> ERROR: MRISripZeros(): dimension mismatch
>>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
>>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
>>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
>>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
>>>>
>>>> What may have caused this?
>>>>
>>>> Thanks.
>>>> Michelle
>>>> _______________________________________________
>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>>
>>>
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>>> is
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>>>    
>>
>> _______________________________________________
>> Freesurfer mailing list
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>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>