-n 2 tells it to use 2 feature dimensions (sulc and curv) -t <fname> tells it to use the color LUT in <fname> On Fri, 16 Dec 2005, Fornito, Alexander wrote:

Hi, I'm also trying to create my own custom atlas, but can't seem to create an annotation file. I load my files in tksurfer, than click the "Export annotation" option and save the file. When I then try to re-import the annotation, nothing appears, and I get the message:

% surfer: WARNING: no labels imported; annotation was empty

Any help is much appreciated!

PS - Greg, I noticed that you used -n and -t in your command line. What do these flags refer to? I can't seem to get options in the usage.

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greg Harris Sent: Thu 15/12/2005 4:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Defining one's own atlas in FreeSurfer

By snooping in the log files in scripts/ and considering the instruction to train and then label with commands such as

mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs

which prepares the way for

mris_ca_label ${SUBJECT} rh sphere.reg /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs

it becomes evident that the -autorecon3 step applies the MGH standard parcellation atlas from

/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs

and thus, the "standard" atlas is known as "curvature.buckner40.filled.desikan_killiany".

When we evaluate our own atlas, we compare hand-traced labels with the labels produced by mris_ca_label.

Now my question: Is there a way we could access the training data for "curvature.buckner40.filled.desikan_killiany", so we can compare how mris_ca_label approximates the MGH atlas's gold standard with how it approximates the Iowa atlas's gold standard?

We are curious how many subjects went into the standard atlas at mris_ca_train, too. Is there a paper (a pdf?) where this is reported?

Greg Harris University of Iowa Psychiatry Brain Imaging Lab

---

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---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

yes, sulc represents large scale structure of the folding patterns and preferences deep folds over shallow ones, while curv is a differential measure (mean curvature) and is much noiser. The sulc alignment comes first and aligns the major folds, then the curv alignment moves secondary folds such as the hand area into alignment where they are consistent.

Don't know why you can't create a .annot file. I'm waiting for Kevin to respond. You could try sending us the subject with the .annot file and we can take a look, or maybe the .xdebug_tksurfer file has some clue?

cheers, Bruce

On Fri, 16 Dec 2005, Fornito, Alexander wrote:

Hi Bruce, Is there a reason why use sulc and curv together would be better than one alone? Also, any ideas as to why I can't create my annotations? Thanks again for your help, Alex

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 16/12/2005 11:34 AM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer

-n 2 tells it to use 2 feature dimensions (sulc and curv) -t <fname> tells it to use the color LUT in <fname> On Fri, 16 Dec 2005, Fornito, Alexander wrote:

...

Hi, I'm also trying to create my own custom atlas, but can't seem to create an annotation file. I load my files in tksurfer, than click the "Export annotation" option and save the file. When I then try to re-import the annotation, nothing appears, and I get the message:

% surfer: WARNING: no labels imported; annotation was empty

Any help is much appreciated!

PS - Greg, I noticed that you used -n and -t in your command line. What do these flags refer to? I can't seem to get options in the usage.

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greg Harris Sent: Thu 15/12/2005 4:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Defining one's own atlas in FreeSurfer

By snooping in the log files in scripts/ and considering the instruction to train and then label with commands such as

mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs

which prepares the way for

mris_ca_label ${SUBJECT} rh sphere.reg /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs

it becomes evident that the -autorecon3 step applies the MGH standard parcellation atlas from

/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs

and thus, the "standard" atlas is known as "curvature.buckner40.filled.desikan_killiany".

When we evaluate our own atlas, we compare hand-traced labels with the labels produced by mris_ca_label.

Now my question: Is there a way we could access the training data for "curvature.buckner40.filled.desikan_killiany", so we can compare how mris_ca_label approximates the MGH atlas's gold standard with how it approximates the Iowa atlas's gold standard?

We are curious how many subjects went into the standard atlas at mris_ca_train, too. Is there a paper (a pdf?) where this is reported?

Greg Harris University of Iowa Psychiatry Brain Imaging Lab

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Bruce, I;d like to take up your offer of sending a subject with the annot file, as I'm quite stuck. Where can I upload it to? I can't seem to find the link on the wiki. Also, I only retained the mri, surf, and label subdirectories, although the tar is still quite big (~125 MB). Are there specific files that you need? Cheers, Alex

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 16/12/2005 12:25 PM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer

yes, sulc represents large scale structure of the folding patterns and preferences deep folds over shallow ones, while curv is a differential measure (mean curvature) and is much noiser. The sulc alignment comes first and aligns the major folds, then the curv alignment moves secondary folds such as the hand area into alignment where they are consistent.

Don't know why you can't create a .annot file. I'm waiting for Kevin to respond. You could try sending us the subject with the .annot file and we can take a look, or maybe the .xdebug_tksurfer file has some clue?

cheers, Bruce

On Fri, 16 Dec 2005, Fornito, Alexander wrote:

Hi Bruce, Is there a reason why use sulc and curv together would be better than one alone? Also, any ideas as to why I can't create my annotations? Thanks again for your help, Alex

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 16/12/2005 11:34 AM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer

-n 2 tells it to use 2 feature dimensions (sulc and curv) -t <fname> tells it to use the color LUT in <fname> On Fri, 16 Dec 2005, Fornito, Alexander wrote:

...

Hi, I'm also trying to create my own custom atlas, but can't seem to create an annotation file. I load my files in tksurfer, than click the "Export annotation" option and save the file. When I then try to re-import the annotation, nothing appears, and I get the message:

% surfer: WARNING: no labels imported; annotation was empty

Any help is much appreciated!

PS - Greg, I noticed that you used -n and -t in your command line. What do these flags refer to? I can't seem to get options in the usage.

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greg Harris Sent: Thu 15/12/2005 4:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Defining one's own atlas in FreeSurfer

By snooping in the log files in scripts/ and considering the instruction to train and then label with commands such as

mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs

which prepares the way for

mris_ca_label ${SUBJECT} rh sphere.reg /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs

it becomes evident that the -autorecon3 step applies the MGH standard parcellation atlas from

/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs

and thus, the "standard" atlas is known as "curvature.buckner40.filled.desikan_killiany".

When we evaluate our own atlas, we compare hand-traced labels with the labels produced by mris_ca_label.

Now my question: Is there a way we could access the training data for "curvature.buckner40.filled.desikan_killiany", so we can compare how mris_ca_label approximates the MGH atlas's gold standard with how it approximates the Iowa atlas's gold standard?

We are curious how many subjects went into the standard atlas at mris_ca_train, too. Is there a paper (a pdf?) where this is reported?

Greg Harris University of Iowa Psychiatry Brain Imaging Lab

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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