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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
==================================== 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 ====================================
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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >
==================================== 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 ====================================
Hi again Christophe,
Yes thank you, this does makes things much more clear.
I still have a few questions:
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 nameI 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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >>
==================================== 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 - 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 ====================================
Hi Narly
My answers are included in the copy of your message :
- 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'.
?h.aparc.a2002s.annot corresponds to the 2002 atlas,
?h.aparc.a2005s.annot corresponds to the 2005 atlas, ?h.aparc.a2009s.annot corresponds to the 2009 atlas,
One of these atlases is included in the automated reconstruction of fs. Only one parcellation is output by default, and this default version depends of the fs release you are running : - I can't remember the fs release in witch ?h.aparc.a2005s.annot replaced ?h.aparc.a2002s.annot ; it was in 2005 (3.0.3 or anterior ?) ; Bruce or Nick could precisely tell you the version in which the change occurred - The ?h.aparc.a2009s.annot became the default sulco gyral atlas in the 4.5.0 version.
The gcs files used to automatically label the surface are located in the average directory of you fs home; for instance the 4.5.0 fs release includes the following gcs files : lh.atlas2002_simple.gcs, lh.atlas2005_simple.gcs, and lh.destrieux.simple.2009-07-29.gcs, respectively corresponding to the 2002, 2005 and 2009 "destrieux" atlases -I'm not sure if it is still possible to use the 2002 version with the actual reconstruction process : if I remember there was an important change in the reconstruction process in 2005 that obliged us to relabel the subjects used in the database ; Bruce : am I right?
- 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?
no idea ; Rahul will probably answer this one
- 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.
not that I know
cheers
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 anteriortransverse 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 nameI 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. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>>
==================================== 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 ====================================
Christophe Destrieux
Laboratoire d'Anatomie Faculté de Médecine, 10 Bd Tonnellé, 37032 Tours, France 33-2 47 36 61 36 - 33-6 60 47 67 01
Hello all,
Thanks Chistophe for your answers.
I have not heard back regading some of the other points.
I would like to know:
1) The fs release in which ?h.aparc.a2005s.annot replaced ?h.aparc.a2002s.annot. I assume it was before 2007 (I used version 3.0.5 in 2007).
2a) *** If it is possible to use the 2002 Destrieux atlas with either the present or with older (say version 3.0.5) versions of freesurfer? ****
Christophe seems to think that there was an important change in the reconstruction process in 2005 that obliged you to relabel the subjects used in the database.
2b) If this is possible, how can I go about it? I guess somewhere in the recon-all -all command I will need to specificy to use the 2002 and not the default atlas for that version (ie; the a2005 atlas for version 3.0.5).
3) Rahul: how does the Desikan parcellation define the transverse temporal gyrus (ie; does it include multiple transverse gyri or only the most anterior one in the case of duplication)? And has this definition changed between freesurfer versions 3.0.5 and 4.4? I have looked at the Desikan 2006 Neuroimage paper (desikan06-parcellation.pdf) but it does not specify exactly how the posterior boundary of the transverse gyrus was defined.
thanks in advance, best wishes, Narly.
Narly,
v3.0 uses the aparc.a2005s atlas.
to use the a2002s atlas in v3.0, edit the recon-all script and replace instances of '2005' with '2002', which only appear in the cortparc2 stage. i havent tried this, so i dont know if the atlas will work though.
Nick
On Tue, 2009-10-20 at 18:03 +0100, Narly A Golestani wrote:
Hello all,
Thanks Chistophe for your answers.
I have not heard back regading some of the other points.
I would like to know:
- The fs release in which ?h.aparc.a2005s.annot replaced
?h.aparc.a2002s.annot. I assume it was before 2007 (I used version 3.0.5 in 2007).
2a) *** If it is possible to use the 2002 Destrieux atlas with either the present or with older (say version 3.0.5) versions of freesurfer? ****
Christophe seems to think that there was an important change in the reconstruction process in 2005 that obliged you to relabel the subjects used in the database.
2b) If this is possible, how can I go about it? I guess somewhere in the recon-all -all command I will need to specificy to use the 2002 and not the default atlas for that version (ie; the a2005 atlas for version 3.0.5).
- Rahul: how does the Desikan parcellation define the transverse
temporal gyrus (ie; does it include multiple transverse gyri or only the most anterior one in the case of duplication)? And has this definition changed between freesurfer versions 3.0.5 and 4.4? I have looked at the Desikan 2006 Neuroimage paper (desikan06-parcellation.pdf) but it does not specify exactly how the posterior boundary of the transverse gyrus was defined.
thanks in advance, best wishes, Narly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick,
This does seem to work.
best wishes, Narly.
On Tue, 20 Oct 2009, Nick Schmansky wrote:
Narly,
v3.0 uses the aparc.a2005s atlas.
to use the a2002s atlas in v3.0, edit the recon-all script and replace instances of '2005' with '2002', which only appear in the cortparc2 stage. i havent tried this, so i dont know if the atlas will work though.
Nick
On Tue, 2009-10-20 at 18:03 +0100, Narly A Golestani wrote:
Hello all,
Thanks Chistophe for your answers.
I have not heard back regading some of the other points.
I would like to know:
- The fs release in which ?h.aparc.a2005s.annot replaced
?h.aparc.a2002s.annot. I assume it was before 2007 (I used version 3.0.5 in 2007).
2a) *** If it is possible to use the 2002 Destrieux atlas with either the present or with older (say version 3.0.5) versions of freesurfer? ****
Christophe seems to think that there was an important change in the reconstruction process in 2005 that obliged you to relabel the subjects used in the database.
2b) If this is possible, how can I go about it? I guess somewhere in the recon-all -all command I will need to specificy to use the 2002 and not the default atlas for that version (ie; the a2005 atlas for version 3.0.5).
- Rahul: how does the Desikan parcellation define the transverse
temporal gyrus (ie; does it include multiple transverse gyri or only the most anterior one in the case of duplication)? And has this definition changed between freesurfer versions 3.0.5 and 4.4? I have looked at the Desikan 2006 Neuroimage paper (desikan06-parcellation.pdf) but it does not specify exactly how the posterior boundary of the transverse gyrus was defined.
thanks in advance, best wishes, Narly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
==================================== Narly Golestani Institute of Cognitive Neuroscience 17 Queen Square London WC1N 3AR United Kingdom Tel: +44 (0)20 7679 7529 ====================================
freesurfer@nmr.mgh.harvard.edu
-
Christophe Destrieux -
Narly A Golestani -
Nick Schmansky