Hi Corinna,You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_ JNeurophysiol11_SplitLabels. zip?dl=0 Regards,ThomasOn Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer <corinnab83@gmail.com> wrote:Dear Dr. Yeo,Our research group is currently trying to segment the Yeo atlas into separate labels, but just came across this thread which indicates that you have already done this. Would you be willing to re-share the link to your previously extracted individual labels from your 7 and 17 networks?Thank you!CorinnaOn Thu, May 14, 2015 at 4:54 AM, Thomas Yeo <ythomas@csail.mit.edu> wrote:Hi Annie,
I have previously extracted individual regions from the 7 and 17
networks. You can download them here
(https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol ).11_SplitLabels.zip?dl=0
Please see the README in the folder for more explanations. There
should be a precuneus DMN region.
The 17 networks consist of 114 regions that have been previously published:
1) Krienen et al., Reconfigurable state-dependent functional coupling
modes cluster around a core functional architecture. Philosophical
Transactions of the Royal Society B, 369:20130526, 2014
2) Yeo et al., Functional connectivity during rested wakefulness
predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
2015
Hope this helps.
Cheers,
Thomas
On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 <poohann1122@gmail.com> wrote:
> Hello Dr. Yeo,
>
> Thank you for your previous help and reply. We've worked out the way to
> switch the resolution of parcellation and successfully extracted the
> anatomical information using your mask derived from iFC work.
>
> However, we came across a new problem to apply the cortical mask and need
> your kind help again. We aim to conduct a seed-based analysis to investigate
> structural covariance based on the network defined by iFC, and find your
> work of cortical parcellation conceptually perfectly suit our research
> question. Based on the current approach, however, it seemed that we could
> only extract the anatomical information from the whole well-defined network,
> but not the specific hub within the network (e.g., the anatomical
> information of the precuneus from the DMN). We wonder if you have any
> suggestion to resolve our problem, ie, to be specific, is there any way to
> only extract the discrete hub information rather than the whole network?
>
> We really appreciate your generous help. Thank you very much.
>
> p.s. This email would also forward to my senior colleague, Dr. Hsiang-Yuan
> Lin, who is a child and adolescent psychiatrist doing imaging research in
> Taiwan.
>
>
> 2015-05-13 19:15 GMT+08:00 陳昱潔 <poohann1122@gmail.com>:
>>
>> Hi Professor Yeo :
>>
>> Thank you for helping us so much!
>> After mris_anatomical_stat I tried aparcstats2table to extract the table.
>> But I failed with generating the table.
>>
>>
>> Best wishes,
>> Annie
______________________________>>
>> 2015-05-12 8:29 GMT-04:00 Thomas Yeo <ythomas@csail.mit.edu>:
>>
>>> Hi Annie,
>>>
>>> I assume this means 5202 is your subject ID? Maybe you should check if
>>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network s_N1000.annot
>>> exist?
>>>
>>> If so, you can run mris_anatomical_stats to generate statistics for
>>> the parcellation.
>>>
>>> Cheers,
>>> Thomas
>>>
>>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 <poohann1122@gmail.com> wrote:
>>> > Hi Professor Yeo :
>>> > After I rechecked the directory and run again mri_surf2surf
>>> > I got the result:
>>> > "Saving target data
>>> > Converting to target annot
>>> > Saving to target annot
>>> >
>>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network s_N1000.annot"
>>> > The file of 5202/label didn't come out with
>>> > lh.Yeo2011_7Networks_N1000.annot
>>> > But it seems succeed, right?
>>> > How can I get the stat of this parcellation ?
>>> >
>>> > Thank you very much!
>>> >
>>> > Best wishes,
>>> > Annie
>>> >
>>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo <ythomas@csail.mit.edu>:
>>> >
>>> >> Hi Annie,
>>> >>
>>> >> mri_surf2surf is complaining that it cannot write out the annotation.
>>> >>
>>> >> Just to clarify, is your subject called test_run_allindex? In other
>>> >> words, is the variable s equal to test_run_allindex?
>>> >>
>>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? If
>>> >> not, then you first need to create the directory first, and then
>>> >> mri_surf2surf can write the resulting annotation file into the
>>> >> directory.
>>> >>
>>> >> Cheers,
>>> >> Thomas
>>> >>
>>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 <poohann1122@gmail.com> wrote:
>>> >> > Hi Professor Yeo :
>>> >> >
>>> >> > We tried the code
>>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>>> >> >>> --sval-annot
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networ ks_N1000.annot
>>> >> >>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>>> >> > However there came an error of "could not write annot file
>>> >> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N10 00.annot
>>> >> > No such file or directory"
>>> >> > And we checked our individual subject's label there isn't
>>> >> > lh.Yeo2011_7Networks_N1000.annot
>>> >> > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into
>>> >> > our
>>> >> > subjects/label first?
>>> >> > What can we do ?
>>> >> > Thank you very much!
>>> >> >
>>> >> > Best wishes,
>>> >> > Annie
>>> >> >
>>> >> >
>>> >> > 2015-05-05 8:36 GMT-04:00 Thomas Yeo <ythomas@csail.mit.edu>:
>>> >> >
>>> >> >> Hi Annie,
>>> >> >>
>>> >> >> Please cc the freesurfer list when you reply because there might be
>>> >> >> other people more qualified to answer your question.
>>> >> >>
>>> >> >> Based on what you are saying, I think you can first use
>>> >> >> mri_surf2surf
>>> >> >> (with the "sval-annot" flag) to transform the 2011 functional
>>> >> >> networks
>>> >> >> .annot file from fsaverage space to the subject's native surface
>>> >> >> space. Type "mri_surf2surf --help" to see examples.
>>> >> >>
>>> >> >> You can then use mris_anatomical_stats to compute thickness
>>> >> >> statistics.
>>> >> >>
>>> >> >> Cheers,
>>> >> >> Thomas
>>> >> >>
>>> >> >> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 <poohann1122@gmail.com> wrote:
>>> >> >> > Dear Pro. Yeo:
>>> >> >> >
>>> >> >> > Very appreciate for your reply !
>>> >> >> >
>>> >> >> > We are trying to use your definition of the functional network
>>> >> >> > regions
>>> >> >> > to
>>> >> >> > re-parcellate our images
>>> >> >> > and get the regions of volume or cortical thickness for our study
>>> >> >> > interest
>>> >> >> > of structural network.
>>> >> >> > However, we did not want to re-run the first recon-all again due
>>> >> >> > to
>>> >> >> > it's
>>> >> >> > spending to much time.
>>> >> >> > And we are still can't find the way to solve this problem.
>>> >> >> > Thank you very much for helping us!
>>> >> >> >
>>> >> >> > Best wishes,
>>> >> >> > Annie Chen
>>> >> >> >
>>> >> >> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo <ythomas@csail.mit.edu>:
>>> >> >> >>
>>> >> >> >> Hi Yu-Chieh,
>>> >> >> >>
>>> >> >> >> I am cc-ing the freesurfer list who may help you with your
>>> >> >> >> issues.
>>> >> >> >>
>>> >> >> >> Can you explain what exactly you are trying do? The parcellation
>>> >> >> >> is
>>> >> >> >> released in different resolutions including fsaverage5. Why
>>> >> >> >> can't
>>> >> >> >> you
>>> >> >> >> just use the fsaverage5 parcellation?
>>> >> >> >>
>>> >> >> >> Cheers,
>>> >> >> >> Thomas
>>> >> >> >>
>>> >> >> >> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 <poohann1122@gmail.com>
>>> >> >> >> wrote:
>>> >> >> >> > Dear professor Yeo :
>>> >> >> >> >
>>> >> >> >> > My name is Yu-chieh Chen , I am a graduated student from
>>> >> >> >> > National
>>> >> >> >> > Taiwan
>>> >> >> >> > University of medical school, and my supervisor is professor
>>> >> >> >> > Susan
>>> >> >> >> > Shur-Fen
>>> >> >> >> > Gau from department of psychiatry, National Taiwan University
>>> >> >> >> > Hospital &
>>> >> >> >> > College of Medicine. We are very interesting about your paper
>>> >> >> >> > published
>>> >> >> >> > in
>>> >> >> >> > 2011 which using resting MRI to separate brain regions to
>>> >> >> >> > functional
>>> >> >> >> > networks. We'd like to use your percellation to re-separate
>>> >> >> >> > the
>>> >> >> >> > brain
>>> >> >> >> > regions based on your released data in Freesurfer(
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Y ).eo2011
>>> >> >> >> > And
>>> >> >> >> > use
>>> >> >> >> > these volume of brain regions for our study, however, there
>>> >> >> >> > comes
>>> >> >> >> > the
>>> >> >> >> > problem that we assumed that we can change the fsaverage into
>>> >> >> >> > fsaverage5,
>>> >> >> >> > thus we may get the new volume of the parcellation_Yeo. But it
>>> >> >> >> > is
>>> >> >> >> > not
>>> >> >> >> > work.
>>> >> >> >> > So I send this email for help. Last , I am very appreciate
>>> >> >> >> > your
>>> >> >> >> > kindness
>>> >> >> >> > and
>>> >> >> >> > very sorry for my inappropriate and rough.
>>> >> >> >> > Thank you very much for read this email and sorry for occupied
>>> >> >> >> > your
>>> >> >> >> > time.
>>> >> >> >> >
>>> >> >> >> > Best wishes,
>>> >> >> >> > Yu-chieh Chen
>>> >> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >
>>> >> >
>>> >
>>> >
>>
>>
>
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