1) I would like to confirm that the '?h.aparc.a2005s.annot' parcellization
refers to the labels generated by the 2002, 2005, and 2009 atlases (and
that one can output their results to tables using 'aparcstats2table'
with the '--parc aparc.a2005s' option), but that which atlas is actually
used depends on the freesurfer release.  I'm not sure about this though
because in one of your last messages you mentioned that but both
atalases (atlas2002_simple.gcs and atlas2005_simple.gcs) were
distributed for a while, suggesting that they were used in parallel,
within a particular release of freesurfer (? maybe I misunderstood).
In any case I only see the following parcellation after running recon-all
-all with freesurfer 3.0.5 and 4.4: '?h.aparc.a2005s.annot'.

2) Do you know how the Desikan parcellation defines the transverse
temporal gyrus (ie; whether or not they include multiple transverse gyri,
or only the most anterior one in the case of duplication)?  And do you
know if this definition has changed between freesurfer versions 3.0.5 and
4.4?

3) Given that your atlas also reports some sulci, is there a way of
knowing whether an intermediate sulcus was detected at all or not
for a particular brain/hemisphere (eg; there should not be any detected
if there is only one transverse temporal gyrus).  In other words, I would
like to know when freesurfer detected multiple transverse gyri and when it
did not.

thanks again and best wishes,
Narly.


On Fri, 16 Oct 2009, Christophe Destrieux wrote:

I Narly

I can imagine you can get confused with the different atlases and

versions of the same atlas ; basically there are 2 main atlases:

   * one developed by Rahul Desikan that outputs the ?h.aparc.annot

     parcellation and which is gyral based (what you called 'the

     default'). For the temporal transverse 'complex' it only outputs a

     label : "?h_transversetemporal" [gyrus]

   * the other one that I developed creates the ?h.aparc.a20??s.annot.

     It is sulco-gyral based and we proposed several versions

     correcting mislabelling or anatomical problems (you know how picky

     the anatomists are !) : 2002, 2005, and now 2009. Each of them

     produces one sulcal and one gyral label for the temporal

     transverse 'complex'

         o 2002 : "S_temporal_transverse" and

           "G_temp_sup-G_temp_transv_and_interm_S" ; When several

           transverse temporal gyri were present they were grouped

           together in a common label with the sulcus limiting them

           (G_temp_sup-G_temp_transv_and_interm_S) ; The sulcus

           posterior to this large label was then labeled

           "S_temporal_transverse"

         o 2005: as I told you we changed the way we labeled this

           region : the transverse temporal sulcus

           ('S_temporal_transverse') limits the planum temporale

           (posteriorly) from the transverse temporal gyrus

           (anteriorly). We only included the most anterior transverse

           temporal gyrus in the corresponding label, the other ones

           being included in the planum temporale. Unfortunatly I

           simply forgot to change the name of this label that remained

           'G_temp_sup-G_temp_transv_and_interm_S'.In other words, the

           same name refers to labels differntly defined between 2002

           and 2005.

         o 2009: to fix this bug and to shorten the labels name for a

           better display on the interface, we finally kept 2 labels

           for the temporal transverse 'complex' :

           'S_temporal_transverse', and 'G_temp_sup-G_T_transv'. The

           latter exactly corresponding to the 2002 definition... but

           with a correct name

I attached a figure showing the differences between 2002, 2005 and 2009

versions. Of course the changes in the limits of the temporal transverse

gyrus also affected the limits of the planum temporale.

I hope I clarified the situation.

Hi Chrisophe,

Thanks very much for your answer but I'm not sure I understand.  I see the

below labels in the '?h.aparc.a2005s.annot' label files generated by

freesurfer version 4.4 as well as in those generated by freesurfer version

3.0.5:

'S_temporal_transverse'

'G_temp_sup-G_temp_transv_and_interm_S'

In the 'default' label file (ie; 'lh.cortex.label' and 'rh.aparc.annot')

of the output generated by both of these versions of freesurfer, I see

the following labels only: '?h_transversetemporal'.

In sum, I'm not sure how the atlases that you've mentioned below relate to

the 'default' versus '2005a' versions of the label files, and also how

they relate to different version of freesurfer.  If the

'atlas2002_simple.gcs' atlas is used to generate the 'default' labels (ie;

'?h.cortex.label'), then I'm not sure why I don't see the

'G_temp_sup-G_temp_transv_and_interm_S' amongst the labels

generated by freesurfer version 3.0.5.  I'm also not clear on how this

changed between versions 3.0.5 and 4.4 - I would expect to see different

labels between the 2 versions, but I don't.

I have another, related question: I would also like to know if there is a

way of seeing whether an intermediate sulcus was detected at all or not

for a particular brain/hemisphere (eg; there should not be any detected

if there is only one transverse temporal gyrus).  In other words, I would

like to know when freesurfer detected multiple transverse gyri and when it

did not.

thanks very much in advance,

and all the best,

Narly.

On Thu, 15 Oct 2009, Christophe Destrieux wrote:

Hi Narly

Hello Christophe, hello all,

I would like to know if the way that the transverse gyrus is labelled in

freesurfer, and specifically the fact that in the case of multiple

transverse gyri only the more anterior transverse temporal gyrus (ie;

Heschl's gyrus) is included, has changed across different releases of

freesurfer, or if it differs between the different atlases used by

freesurfer.  I ask this because I see a somewhat different pattern of

results in this part of the brain when comparing output generated by

freesurfer version 3.0.5 and version 4.4.

the changed occured in 2005; but both atalases (atlas2002_simple.gcs and

atlas2005_simple.gcs) were distributed for a while)

In the 2002 version the parcellation was indeed different :

   * When several transverse temporal gyri were present they were

     grouped together in a common label with the sulcus limiting them

     (G_temp_sup-G_temp_transv_and_interm_S)

   * The sulcus posterior to this label was then labeled

     "S_temporal_transverse"

I hope that it helped

More generally, I would like to know if there is any version of

freesurfer, or any atlas, that includes multiple transverse gyri when they

exist (ie; that does NOT exclude the more posterior one in cases of

multiple transverse gyri).

thanks in advance and best wishes,

Narly.

On Thu, 2009-08-06 at 20:57 +0200, Christophe Destrieux wrote:

Hi Narly

below are a few explanations on the transverse temporal gyrus in the

a2005 parcellation

At the superior aspect of the superior temporal gyrus:

* the transverse temporal *sulcus* limits the planum temporale

(posteriorly) from the transverse temporal gyrus (anteriorly); it

originates at the posterior segment of the lateral sulcus, runs

anterior and lateral and joins the lateral aspect of the temporal

lobe.

* The transverse temporal gyrus (or Heschl's gyrus) is just anterior

and parallel to the transverse temporal sulcus. Instead of a

single transverse temporal gyrus, several ?transverse? temporal

gyri bordered by intermediate sulci may be present. Only the more

anterior transverse temporal gyrus is labeled in Freesurfer, the

posterior ones being included in the planum temporale since they

where shown not to correspond to primary, but to secondary

auditory cortex

I hope that it helped

cheers

--

Christophe Destrieux

Laboratoire d'Anatomie - Facult? de M?decine - 10 Bd Tonnell?

37032 Tours - France

tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

Narly,

I'm forwarding this to Christophe Destrieux, cc'd, who I think can

answer your question about how that region is labelled.

It is not possible to do translucent viewing in tksurfer.  However, it

is possible in qdec.  Just use the load surface and load annotation menu

options.

Nick

On Thu, 2009-08-06 at 16:26 +0100, Narly A Golestani wrote:

Hello,

I would like to know more about the automatic labelling of the transverse

temporal gyrus is done.  I looked at the below article but don't see any

details about this structure.

https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf

I would for example like to know how the boundaries of this structure are

defined/determined.

Also, when using tksurfer to view labels ('import annotation'), is it

possible to make the 3D brain surface (and labels) translucent so that one

can more carefully view where this (medial-spanning) gyrus was identified?

thanks in advance,

Narly.

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====================================

Narly Golestani

Institute of Cognitive Neuroscience

17 Queen Square

London WC1N 3AR

United Kingdom

Tel: +44 (0)20 7679 7529

====================================

--

Christophe Destrieux

Laboratoire d'Anatomie - Facult? de M?decine - 10 Bd Tonnell?

37032 Tours - France

tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07

====================================

Narly Golestani

Institute of Cognitive Neuroscience

17 Queen Square

London WC1N 3AR

United Kingdom

Tel: +44 (0)20 7679 7529

====================================

--

Christophe Destrieux

Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé

37032 Tours - France

tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07

====================================
Narly Golestani
Institute of Cognitive Neuroscience
17 Queen Square
London WC1N 3AR
United Kingdom
Tel: +44 (0)20 7679 7529
====================================