Hi,

I attached two SUMA images, each one corresponding to the folded grey matter surface of the left hemisphere of one subject. The region that should correspond to the superior temporal sulcus (STS) is shown in red. As you can see, anteriorly, cortex buried inside the sulcus, and only there, was correctly labeled as STS, whereas, posteriorly, cortex outside any sulcus was also labeled as STS.

thanks for your help goulven

On Nov 3, 2005, at 7:36 AM, Bruce Fischl wrote:

Hi Goulven,

could you send us an image with some arrows on it?

cheers, Bruce On Wed, 2 Nov 2005, Goulven Josse wrote:

...

Dear Freesurfers,

We have used the automated parcellation (Fischl et al, 2004) in several subjects and noticed in some cases labeling of the lateral part of a gyrus (i mean the part that's visible on the folded surface), as belonging to a sulcus. The example I have in mind is the labeling of a gyrus that could be the middle temporal or the angular gyrus as the posterior part of the superior temporal sulcus (STS). I figured the program could not find the correspondence between that particular gyrus and any labels and, since it happened to be close and, sometimes, between two branches of STS, it was labeled as such.

Or we made a mistake somewhere ... ?

Could anyone please comment on this ?

thanks !

Goulven Josse (U of Chicago)

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On Nov 3, 2005, at 10:59 AM, Doug Greve wrote:

To eliminate the possibility of a SUMA/FreeSurfer incompatibility, can you send pics displayed in tksurfer?

I attached them. For each hemisphere, the version without the label corresponding to STS is also shown, so that you can see a bit more clearly that the label covers areas that are not buried inside sulci.

Also, to clarify, this is a label for a subject shown on that subject (ie, you did not map the label from one subject to another)?

To the best of my knowledge, no.

thanks

thank you !

doug

We found the same result, in the same STS region, with different versions : the latest version in january of 2005 for Mac OSX 10.3 and the latest version (installed last week) for Linux / RedHat (again, we don't find this in all subjects).

We don't have a recon-all.log file, but i attached other log files coming from a subject processed with the version installed on the Linux / RedHat version. If necessary, we could re-run a subject in order to get a recon-all.log file.

goulven

On Nov 3, 2005, at 3:22 PM, Bruce Fischl wrote:

Hi Goulven,

can you send the recon-all.log file for one of these subjects? What version of freesurfer are you using?

Bruce

On Thu, 3 Nov 2005, Goulven Josse wrote:

...

On Nov 3, 2005, at 10:59 AM, Doug Greve wrote:

...

To eliminate the possibility of a SUMA/FreeSurfer incompatibility, can you send pics displayed in tksurfer?

I attached them. For each hemisphere, the version without the label corresponding to STS is also shown, so that you can see a bit more clearly that the label covers areas that are not buried inside sulci.

...

Also, to clarify, this is a label for a subject shown on that subject (ie, you did not map the label from one subject to another)?

To the best of my knowledge, no.

...

thanks

thank you !

...

doug

Hi Xiao,

I don't have a recon-all.log file because we used a homemade script implementing freesurfer commands. I attached the corresponding output log file, is this of any help?

If not, I was thinking of using recon-all but, if I understand correctly, it provides by default a parcellation that does not differentiate the very posterior part of the superior temporal sulcus from surrounding areas. Could you tell me how to use recon-all with another parcellation, i guess the one referenced in Fischl, 04, which labels the STS including its posterior portion ?: Destrieux CE, Halgren E, Dale AM, Fischl B, Sereno MI (1998) Variability of the human brain studied on the flattened cortical surface. Soc Neurosci Abstr 24:1164.

thanks a lot goulven

On Nov 3, 2005, at 5:06 PM, Xiao Han wrote:

Hi Goulven,

There should be a recon-all.log file under the $SUBJECTS_DIR/subject/script/ directory, if you processed the data using the "recon-all" script.

The log files you attached were produced by the tools to visuallize the results, not by the programs that create the label result. Thus we couldn't tell whether anything went wrong during the processing stage from them.

-Xiao

On Thu, 3 Nov 2005, Goulven Josse wrote:

...

We found the same result, in the same STS region, with different versions : the latest version in january of 2005 for Mac OSX 10.3 and the latest version (installed last week) for Linux / RedHat (again, we don't find this in all subjects).

We don't have a recon-all.log file, but i attached other log files coming from a subject processed with the version installed on the Linux / RedHat version. If necessary, we could re-run a subject in order to get a recon-all.log file.

goulven

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