Hi Anastasia!
The command in the recon-all.log is this one:
mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface
And I tried substituing BAxxx.label by BAxxx.thresh.label like this:
mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface
gave an error :
SUBJECTS_DIR /home/user/visao/Freesurfer/
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
No such file or directory
mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
Illegal seek
ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing.
Thank you!
Andreia
Quoting Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
> Hi Andreia - What you're rerunning is using BAxxx.label instead of
> BAxxx.thresh.label. So of course the results will be the same as before
> you copied over the BAxxx.thresh.label files, b/c these new files aren't
> being used in 5.0.
>
> You'll need to find the "BA labels" section in recon-all.log and rerun
> those commands yourself, changing every BAxxx.label to BAxxx.thresh.label.
>
> Hope this helps,
> a.y
>
> On Mon, 25 Mar 2013, _andreia_@sapo.pt wrote:
>
>> Hello list!
>>
>> Any suggestions on what I may be doing wrong?
>>
>> Thanks!
>> Andreia
>>
>>
>>
>> ----- Mensagem encaminhada de _andreia_@sapo.pt -----
>> Data: Sun, 24 Mar 2013 19:11:13 +0000
>> De: _andreia_@sapo.pt
>> Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume
>> Para: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>, freesurfer
>> <freesurfer@nmr.mgh.harvard.edu>
>> Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>>
>> Hi all,
>>
>> I want to study Brodmann Areas cortical thickness, surface area and
>> volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage
>> and run the recon-all BA labels command. Now I run aparcstats2table
>> and get a table with the values but they are the same as before
>> running the BAxxx.threshold.label.
>>
>> So, everything is working but the values haven't changed. Am I missing
>> something? Do I need to run any other command so to the threshold have
>> effect?
>>
>> Andreia
>>
>>
>> Quoting Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>
>>> Sounds like centos4 is probably the safest bet for you, although you
>>> should ask the list this question.
>>>
>>> Sorry, I don't know what values you want to get in a table.
>>>
>>> On Sat, 23 Mar 2013, _andreia_@sapo.pt wrote:
>>>
>>>> Ah ok! Anyway, I'm thinking of working with 5.2, should I download
>>>> the version for centOS 4 then?
>>>>
>>>> After running the new BAxxx.thresh.label files how can I get the
>>>> values in a table?
>>>>
>>>>
>>>>
>>>>
>>>> Quoting Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>>
>>>>> It doesn't matter. You just need to use those .label files from
>>>>> the fsaverage directory in the 5.2 distritbution. You don't need
>>>>> to run any of the executables from the 5.2 distribution.
>>>>>
>>>>> On Sat, 23 Mar 2013, _andreia_@sapo.pt wrote:
>>>>>
>>>>>> I'm using Centos5, which file should I download? The one for
>>>>>> CentOS 6 or > 4?
>>>>>>>> Quoting Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>>>>>> You'll need to go to the section of recon-all.log under the
>>>>>>> heading "BA > > labels". You'll need to rerun the commands in
>>>>>>> that section, but instead > > of using the BAxxx.label files, us
>>>>>>> the BAxxx.thresh.label files, which > > you'll find in the
>>>>>>> fsaverage subject dir in the 5.2 distribution.
>>>>>>>>> On Sat, 23 Mar 2013, _andreia_@sapo.pt wrote:
>>>>>>>>>> Hello Anastasia,
>>>>>>>>> How should I proceed to get the different BAs measures
>>>>>>> output with > > > > FS > 5.0?
>>>>>>>>> Thank you very much!
>>>>>>>>> Andreia
>>>>>>>>>> Quoting Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
>>>>>>>>>> The thresholded labels are in the 5.2 version of
>>>>>>> fsaverage > > > > > under:
>>>>>>>>> $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
>>>>>>>>>>> On Sat, 23 Mar 2013, Bruce Fischl wrote:
>>>>>>>>>>>> Anastasia?
>>>>>>>>>> On Sat, 23 Mar 2013, _andreia_@sapo.pt wrote:
>>>>>>>>>>>> Ok, that was my guess... I am running against a
>>>>>>> deadline, > > > > > > > any > > > > > news on
>>>>>>>>>>> automatically computing the correct threshold script?
>>>>>>> Will I > > > > > > be > > > > able to
>>>>>>>>>>> use it in 5.0?
>>>>>>>>>>>>> Thanks you!
>>>>>>>>>>>>> Andreia
>>>>>>>>>>>>>>> Quoting Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
>>>>>>>>>>>>>> yes. Surface area will be the affected much
>>>>>>> more than > > > > > > > > > > > > > > > > thickness (and >
>>>>>>>>> > volume of > > > > > > > > > course scales with area)
>>>>>>>>>>>>> On Fri, 22 Mar 2013, _andreia_@sapo.pt wrote:
>>>>>>>>>>>>>> Hi Bruce,
>>>>>>>>>>>>>>> Thank you for the quick response!
>>>>>>>>>>>>>>> In the meanwhile, does that also apply to
>>>>>>> cortical > > > > > > > > > > > > > > > > > > thickness >
>>>>>>>>>>>> and > > > > > > > > > > > > volume?
>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>> Andreia
>>>>>>>>>>>>>>> Quoting Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
>>>>>>>>>>>>>>>> Hi Andreia
>>>>>>>>>>>>>>>>> the issue is that the BA labels contain
>>>>>>> every > > > > > > > > > > > > point > > > > > > > > > >
>>>>>>> that > > > > > > > > > > > > > > > > > > > > has any > > >
>>>>>>> non-zero
>>>>>>>>>>>>>> probability (no matter how small!) of being in
>>>>>>> that > > > > > > > > > label. > > > > > > > So > > > > >
>>>>>>> the > > > > > > > > > > > > total
>>>>>>>>>>>>>> label area is almost certainly always bigger
>>>>>>> than the > > > > > > > > > > > > > > > > actual > > > > >
>>>>>>> BA. > > > > > > > > > > > > Anastasia
>>>>>>>>>>>>>> has some scripts for automatically computing
>>>>>>> the > > > > > > > > > correct > > > > > > > > > > > >
>>>>>>> threshold, > > > > > > > > > > > > and I
>>>>>>>>>>>>>> believe she and Nick integrated them into 5.2
>>>>>>> so that > > > > > > > > > the > > > > > > > stats > > > >
>>>>>>>> are
>>>>>>>>>>>>>> computed both thresholded and unthresholded, >
>>>>>>>>>>>>>>> hopefully > > > > > > > they can > > > >
>>>>>>>> >>>>>>>>>>>> comment.
>>>>>>>>>>>>>> Bruce
>>>>>>>>>>>>>>>>>>>>>>> On Fri, 22 Mar 2013, > > > >
>>>>>>>>>>>>>>>>>>>>> _andreia_@sapo.pt
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>> Hi all,
>>>>>>>>>>>>>>>>>>> I'm using FS 5.0 and some time ago I
>>>>>>> was > > > > > > > > > > > > > > told by > > > > > > > > > >
>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>
>>>>>>> Bruce that I had > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>>>>>>>> to
>>>>>>>>>>>>>>> threshold the BA in order to have an
>>>>>>> approximate > > > > > > > > > > area > > > > > > > > when
>>>>>>>>>>>>>> >>>>>>>>>>>>> overlaying
>>>>>>>>>>>>>>> in the inflated surface. To get surface area
>>>>>>> values > > > > > > > > > > I > > > > > > > > also > > > >
>>>>>>>>> need to > > > > > > > > > > > > > > use
>>>>>>>>>>>>>>> the label_area and put a threshold
>>>>>>>>>>>>>>> having the possibility to choose the surface
>>>>>>> that I > > > > > > > > > > > > > > > > > > want, > > > >
>>>>>>>>> either > > > > > > > > > > > > > > white
>>>>>>>>>>>>>>> or pial.
>>>>>>>>>>>>>>>>>>> But I can also get the BA stats in a
>>>>>>> table > > > > > > > > > > > > > > for > > > > > > > > > > >
>>>>>>>> all > > > > > > > > > > > > > > > > > > > > > > > >
>>>>>>> subjects and > > > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>>>>>> areas
>>>>>>>>>>>>>>> using either mris_anatomical_stats (on each
>>>>>>> label) > > > > > > > > > > or > > > > > > > > usinga > >
>>>>>>>>>>> >>>>>>>>>>>>>> script by
>>>>>>>>>>>>>>> Jamaan to get the table (since I already
>>>>>>> have the > > > > > > > > > > > > > > > > > > ?.BA.stats >
>>>>>>>>>>>> >>>>>>>>>>>>>> files),
>>>>>>>>>>>>>>> right?
>>>>>>>>>>>>>>>>>>> My question is, which is the
>>>>>>> better/correct > > > > > > > > > > > > > > way > > > > > > >
>>>>>>>>>>>> to > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>> get the > > > > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>> >>>> thickness
>>>>>>>>>>>>>>> and surface area values of the BA to export
>>>>>>> for > > > > > > > > > > > > > > > > > > statistical > > >
>>>>>>>>>>> >>>>>>>>>>>>> analysis
>>>>>>>>>>>>>>> since there are the thresolds issue.
>>>>>>>>>>>>>>>>>>> I want to study mainly cortical
>>>>>>> thickness > > > > > > > > > > > > > > and > > > > > > > > >
>>>>>>>>>> surface > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>> area but > > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>>>>>>> also
>>>>>>>>>>>>>>> look also at the volume (which is
>>>>>>> surface-based, > > > > > > > > > > thus
>>>>>>>>>>>>>>> thickness*surface are will not be = volume
>>>>>>> since > > > > > > > > > > they > > > > > > > > are an > >
>>>>>>>>>>> >>>>>>>>>>>>> > average
>>>>>>>>>>>>>>> from each label, right?).
>>>>>>>>>>>>>>>>>>> I' not sure of which approach to
>>>>>>> follow > > > > > > > > > > > > > > now... > > > > > > > > >
>>>>>>>>>> Does > > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>> it depend on > > > > > > > > > > > > > > > > > > > > > >
>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>> measure I'll be using?
>>>>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>>>> Andreia
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>>>>>>>>>>>>>
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