On Wed, Sep 28, 2011 at 5:21 PM, Douglas N Greve <g reve@nmr.mgh.harvard.edu> wrote:

The gcareg step depends on the talairach registration, so if that is changed, it thinks that the gcareg needs to change. If the gcareg needs to change, then the canorm needs to change, and so on. This does not mean that anything really needs to be updated. This is strictly looking at the time stamps and assuming that things have changed and need to be updated. If your results look ok, then there's no need to re-run.

Unfortunately, this does not tell us whether the surfaces themselves are up to date. You can do this with:
recon-all -vno-check -s subject
This looks at the number of vertices in each of the surfaces to make sure they are consistent.

doug

Michelle Umali wrote:

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 <mailto: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 <mailto: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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
>>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422>
>>>
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>>>
>>>
>>>
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>>
>>
>> >
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
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--
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