Thanks Bruce and Doug!
I can't find the lh.BA.annot in fsaverage/label folder (version 5.1):
lh.BA6.label lh.aparc.a2005s.annot
rh.BA44.label rh.PALS_B12_OrbitoFrontal.annot
lh.MT.label lh.aparc.a2009s.annot
rh.BA45.label rh.PALS_B12_Visuotopic.annot
lh.BA1.label lh.Medial_wall.label lh.aparc.annot
rh.BA4a.label rh.V1.label
lh.BA2.label lh.PALS_B12.labels.gii lh.aparc.label
rh.BA4p.label rh.V2.label
lh.BA3a.label lh.PALS_B12_Brodmann.annot lh.cortex.label
rh.BA6.label rh.aparc.a2005s.annot
lh.BA3b.label lh.PALS_B12_Lobes.annot
lh.entorhinal.label rh.MT.label
rh.aparc.a2009s.annot
lh.BA44.label lh.PALS_B12_OrbitoFrontal.annot rh.BA1.label
rh.Medial_wall.label rh.aparc.annot
lh.BA45.label lh.PALS_B12_Visuotopic.annot rh.BA2.label
rh.PALS_B12.labels.gii rh.aparc.label
lh.BA4a.label lh.V1.label rh.BA3a.label
rh.PALS_B12_Brodmann.annot rh.cortex.label
lh.BA4p.label lh.V2.label rh.BA3b.label
rh.PALS_B12_Lobes.annot rh.entorhinal.label
So, how can I be sure that the label I got from converting a volume ROI to a
surface label with mri_vol2surf is accurate? Is there a way other than visually
checking (in pial surface instead of in inflated in order to compare to a SPM
surface render) that it is in the same location?
many thanks again for your help,
Gari
On 2012-08-06, at 20:00, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Gari, can you check whether you have ?h.BA.annot in your subject/labels
> folder? this is an annotation of all the BA labels. They are
> non-overlapping; overlaps are resolved by the one with the most
> probability. I can't remember whether this made it into 5.1 or not.
> doug
>
> On 08/06/2012 01:18 PM, Bruce Fischl wrote:
>> Hi Gari
>>
>> they overlap as the labels represent every location that could possibly
>> be in either label. Unless we could predict them perfectly they have to
>> overlap, since they share a border. With 5.2 we will include different
>> default thresholds, but at the moment you have to do it yourself. You could
>> do a max probability in matlab, or load them in tksurfer and threshold them
>> manually to remove overlap.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote:
>>
>>> Hi Bruce,
>>> thanks for your answer.
>>>
>>> I am mapping a volume ROI (BA45) from SPM in MNI 152 space to fsaverage
>>> (the result is the red ROI). The problem is that:
>>> - when I load the BA45.label from FS in order to compare, they are not
>>> quite similar. My main problem is to know if the differences are acceptable
>>> or not and what method should I use to check the validity.
>>> - Secondary problem: when I load both the lh.BA45.label and lh.BA44.label,
>>> they overlap. I didn't create those labels, they are the ones that come in
>>> fsaverage/label. I don't understand how can they overlap (in the
>>> lh.aparc.annot or lh.aparc.a2009s.annot those areas don't overlap at all).
>>>
>>>
>>> Thanks again for your help,
>>> Gari
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 2012-08-06, at 15:27, Bruce Fischl<fis...@nmr.mgh.harvard.edu> wrote:
>>>
>>>> Hi Gari
>>>>
>>>> sorry, I'm a bit confused. Are you using the individual subject estimates
>>>> of 44 and 45 generated by FreeSurfer, or mapping them from MNI space? In
>>>> either case you can get overlap unless you pick the most probably label at
>>>> each point.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>> On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote:
>>>>
>>>>> Hi freesurfers experts,
>>>>> this is (please check attached image) the best I got when trying to map a
>>>>> volume ROI (BA45 in MarsBar = MNI_Frontal_Inf_Tri_L_roi) to freesurfer
>>>>> using mri_vol2surf.
>>>>> I used /freesurfer/average/mni152.register.dat instead of spmregister
>>>>> since the ROI was already in mni152 2mm, the registration was perfect
>>>>> -checked with tkregister2.
>>>>>
>>>>> - I obtained the red area of the image, which is outside of the
>>>>> ROI45.label. Considering that the source was not exactly the same, could
>>>>> I consider it acceptable for cortical thickness analysis?
>>>>> - Why are the 44 and 45 overlapping?
>>>>>
>>>>> Thank you very much and sorry for the multiple questions,
>>>>> Gari
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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