I defined the label on the inflated surface, I don't know what the
coordinates are mapped into when they are saved from tksurfer. I guess
the vertex numbers go through a lookup into the orig surface to get
those coordinates.
When I ran the label2label mapping a second time, using the results of
the first mapping, the results are identical! That confirms the
integrity of the mri_label2label process.
So, tksurfer is mapping coordinates to a different surface (orig) to the
surface used in mri_label2label (white). So, the coordinates of a label
saved from tksurfer cannot be compared with the output of
mri_label2label, even when the vertex indices are identical. There is
nothing in the .label file to indicate what surface it belongs to.
Thanks, Darren
Doug Greve wrote:
>
> Hmmm, I just tried this and did not have a problem. There's something
> funny going on here. The indices for both labels are the same, only the
> cooridnates are different. This means that the source label and the new
> label are using different surfaces. Are you sure you created the source
> label from the white surface? Can you take your new label and generate
> another new label in the same way?
>
> doug
>
>
>
>
> Darren Weber wrote:
>> This is an example of diff output for the test without the --trgsurf option:
>>
>>
>> endorphin.14> diff --side-by-side DLWeber_rh_ACC.label
>> DLWeber_surface_rh_ACC.label | head -
>> #!ascii label , from subject ucsf_wa #!ascii
>> label , from subject ucsf_wa
>> 660 660
>> 106091 3.122 21.824 57.650 0.000000 | 106091
>> 2.037 22.222 57.359 0.000000
>> 106981 7.056 22.926 59.092 0.000000 | 106981
>> 7.114 22.942 59.024 0.000000
>> 106982 6.147 22.676 59.500 0.000000 | 106982
>> 6.137 22.636 59.159 0.000000
>> 106983 5.178 22.521 58.995 0.000000 | 106983
>> 4.816 22.583 58.765 0.000000
>> 106984 4.149 22.523 58.728 0.000000 | 106984
>> 3.440 22.988 58.509 0.000000
>> 106985 3.138 22.925 58.465 0.000000 | 106985
>> 2.206 23.278 58.150 0.000000
>> 106991 7.153 22.847 58.153 0.000000 | 106991
>> 7.272 22.963 58.219 0.000000
>> 106992 6.603 22.649 58.357 0.000000 | 106992
>> 6.639 22.730 58.329 0.000000
>>
>>
>> Are these values just from different layers in the rh.<surf> data?
>>
>>
>> Thanks, Darren
>>
>>
>> Doug Greve wrote:
>>
>>> I think it should be the same. When the source and target subjs are
>>> the same, there should not be any resampling.
>>>
>>>
>>>
>>> On Tue, 11 Jul 2006, Bruce Fischl wrote:
>>>
>>>
>>>> It probably won't be the same as a cp in any case, as you will go
>>>> through some resampling steps.
>>>>
>>>> cheers,
>>>> Bruce
>>>> On Tue, 11 Jul 2006, Doug Greve wrote:
>>>>
>>>>
>>>>> The label coords as created by tksurfer should be that of the white
>>>>> surface, so you're really just changing the coords from that of white
>>>>> to that of pial. Can you try removing --trgsurf pial from your cmd
>>>>> and see if the labels are the same?
>>>>>
>>>>> doug
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Darren Weber wrote:
>>>>>
>>>>>
>>> Dear Doug et al.,
>>>
>>> I'm trying to test mri_label2label because we've observed some strange
>>> results in the download for:
>>>
>>> freesurfer-Linux-rh9-stable-pub-v3.0.2
>>>
>>> To test the program, I thought it would be sensible to map a label of
>>> one subject onto itself, with a different label filename for the
>>> output.
>>> So I created a large label in a subject rh inflated surface and
>>> saved it
>>> to X.label file. I then tried to run mri_label2label using the same
>>> srcsubject and target subject, with a different name for the target
>>> label, ie:
>>>
>>> mri_label2label \
>>> --srclabel $SUBJECTS_DIR/${srcsubject}/label/$label \
>>> --trglabel $SUBJECTS_DIR/${srcsubject}/label/$newlabel \
>>> --srcsubject ${srcsubject} \
>>> --trgsubject ${srcsubject} \
>>> --regmethod surface --hemi $hemi --trgsurf pial
>>>
>>> In effect, this should be equivalent to:
>>>
>>> cd $SUBJECTS_DIR/${srcsubject}/label/
>>> cp $label $newlabel
>>>
>>> That is, the label mapping onto the same subject surface should be
>>> identical. It is not. Can you please try to replicate this result? I
>>> would like to know if it is particular to the setup here. If you
>>> find a
>>> bug in mri_label2label, please forward a fix ASAP, as we are trying to
>>> complete some analysis that depends on mapping labels across subjects.
>>>
>>> Thanks, Darren
>>>
>>>
>>> --
>>>
>>> Darren L. Weber, Ph.D.
>>> Postdoctoral Scholar
>>>
>>> Dynamic Neuroimaging Laboratory,
>>> UCSF Department of Radiology,
>>> 185 Berry Street, Suite 350, Box 0946,
>>> San Francisco, CA 94107, USA.
>>>
>>> Tel: +1 415 353-9444
>>> Fax: +1 415 353-9421
>>> www: http://dnl.ucsf.edu/users/dweber
>>>
>>> "To explicate the uses of the brain seems as difficult
>>> a task as to paint the soul, of which it is commonly
>>> said, that it understands all things but itself."
>>> Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
--
Darren L. Weber, Ph.D.
Postdoctoral Scholar
Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.
Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
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