Hello,
I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can read it with read_annotation.m and it seems correct. (The modification is simply a subdivision of the middletemporal to 32 subregion named : middletemporal_1 .middletemporal_32).
I copied this 'rh.myaparc.annot' file to /usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I did this because the original 'rh.aparc.annot' file was there.
When I run the mris_ca_label as done in the log file generated by recon-all command:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot ../label/rh.myaparc.annot
I have an error:
GCSAread(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot): file magic #28002 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
How can I do to use this annotation file? Is it necessary to have GCS file for parcellation? If yes how can I create it with this annotation file. I don't want to create my own atlas, I want to use the freesurfer atlas (35 entries) but just divide some of its regions.
If needed, I can send you my annotation file.
Thanks a lot
Hi Liela,
the .gcs file is constructed by training a classifier on multiple individual .annot files using mris_ca_train. And it is definitely needed for the auto-parcellation.
cheers, Bruce On Mon, 5 Mar 2007, Leila BH wrote:
Hello,
I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can read it with read_annotation.m and it seems correct. (The modification is simply a subdivision of the middletemporal to 32 subregion named : middletemporal_1 .middletemporal_32).
I copied this 'rh.myaparc.annot' file to /usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I did this because the original 'rh.aparc.annot' file was there.
When I run the mris_ca_label as done in the log file generated by recon-all command:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot ../label/rh.myaparc.annot
I have an error:
GCSAread(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot): file magic #28002 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
How can I do to use this annotation file? Is it necessary to have GCS file for parcellation? If yes how can I create it with this annotation file. I don't want to create my own atlas, I want to use the freesurfer atlas (35 entries) but just divide some of its regions.
If needed, I can send you my annotation file.
Thanks a lot
Hi,
In order to change the atlas (35 entries) by subdividing the mediotemporal into N rois, I tried first to manipulate the atlas annotation file, I constructed the gcs file and apply the mris_ca_label, the parcellation (plotted on inflated) is good but quite different from the one obtained using the original rh.curvature.buckner40.filled.desikan_killiany.gcs:
These are the command I used to construct and use my gcs (theoretically the same that rh.curvature.buckner40.filled.desikan_killiany.gcs)
mris_ca_train -t ./average/colortable_desikan_killiany.txt rh /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.aparc.annot fsaverage mydesik.gcs
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/mydesik.gcs ../label/rh.saaparcssmat.annot
In fact the output lines are :
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/mydesik.gcs...
reading color table from GCSA file....
average std = 0.1 using min determinant for regularization = 0.000
0 singular and 167 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 0 changed, 155533 examined...
000: 87 total segments, 52 labels (341 vertices) changed
001: 37 total segments, 2 labels (61 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 126 changed)
writing output to ../label/rh.saaparcssmat.annot...
writing colortable into annotation file...
classification took 0 minutes and 56 seconds.
While when I use directly the available gsc file it seems that there are much more iterations skipped in the command above:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany .gcs ../label/rh.saaparc.annot
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany .gcs...
reading color table from GCSA file....
average std = 35.0 0.3 using min determinant for regularization = 0.011
0 singular and 829 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 3991 changed, 155533 examined...
001: 950 changed, 16590 examined...
002: 204 changed, 5127 examined...
003: 49 changed, 1234 examined...
004: 15 changed, 308 examined...
005: 11 changed, 96 examined...
006: 5 changed, 54 examined...
007: 3 changed, 32 examined...
008: 1 changed, 15 examined...
009: 1 changed, 8 examined...
010: 0 changed, 6 examined...
000: 111 total segments, 76 labels (659 vertices) changed
001: 39 total segments, 4 labels (51 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 32 changed)
writing output to ../label/rh.saaparc.annot...
writing colortable into annotation file...
classification took 2 minutes and 53 seconds.
Do you know why the parcellations are quite different (between the original gcs file and the constructed gcs file from the original annotation file)? Why there are some steps skipped in mris_ca_label with my gcs file? And why there are '0 changed' in gibbs step?
Thank you very much for your help
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: lundi, 5. mars 2007 21:22 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use modified annotation file for parcellation
Hi Liela,
the .gcs file is constructed by training a classifier on multiple
individual .annot files using mris_ca_train. And it is definitely needed
for the
auto-parcellation.
cheers,
Bruce
On Mon, 5 Mar 2007, Leila BH wrote:
Hello,
I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can
read it with read_annotation.m and it seems correct. (The modification is
simply a subdivision of the middletemporal to 32 subregion named :
middletemporal_1 .middletemporal_32).
I copied this 'rh.myaparc.annot' file to
/usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I did
this
because the original 'rh.aparc.annot' file was there.
When I run the mris_ca_label as done in the log file generated by
recon-all
command:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
../label/rh.myaparc.annot
I have an error:
GCSAread(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot):
file magic #28002 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
How can I do to use this annotation file? Is it necessary to have GCS file
for parcellation? If yes how can I create it with this annotation file. I
don't want to create my own atlas, I want to use the freesurfer atlas (35
entries) but just divide some of its regions.
If needed, I can send you my annotation file.
Thanks a lot
Leila,
Looking at your commands, when you create your own mydesikan.gcs atlas file, it is trained on one subject, so that atlas does not contain the same 'database' of probabilistic information as does the ?.curvature.buckner40.filled.desikan_killiany.gcs atlas distributed with freesurfer. That atlas is trained on 40 subjects. You will notice that the default atlas is quite a bit larger file than the mydesikan.gcs file that you created. This is why the parcellation you see when mris_ca_label is conducted using your atlas is similar but not identical to labeling performed against the default atlas.
If you want to create your own parcellation atlas focusing on just the mediotemporal area, you need to create your own training set of manually labeled subjects. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
in particular the example here:
http://surfer.nmr.mgh.harvard.edu/fswiki/mris_5fca_5ftrain
However, I have my doubts on how well this will work, since the parcellation scheme is based on the cortical curv info (mapped to sphere.reg), so I don't think it will work well for a small region. Bruce would know the answer to this.
Nick
On Tue, 2007-03-13 at 15:57 +0100, Leila BH wrote:
Hi,
In order to change the atlas (35 entries) by subdividing the mediotemporal into N rois, I tried first to manipulate the atlas annotation file, I constructed the gcs file and apply the mris_ca_label, the parcellation (plotted on inflated) is good but quite different from the one obtained using the original rh.curvature.buckner40.filled.desikan_killiany.gcs:
These are the command I used to construct and use my gcs (theoretically the same that rh.curvature.buckner40.filled.desikan_killiany.gcs)
mris_ca_train -t ./average/colortable_desikan_killiany.txt rh /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.aparc.annot fsaverage mydesik.gcs
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/mydesik.gcs ../label/rh.saaparcssmat.annot
In fact the output lines are :
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/mydesik.gcs...
reading color table from GCSA file....
average std = 0.1 using min determinant for regularization = 0.000
0 singular and 167 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 0 changed, 155533 examined...
000: 87 total segments, 52 labels (341 vertices) changed
001: 37 total segments, 2 labels (61 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 126 changed)
writing output to ../label/rh.saaparcssmat.annot...
writing colortable into annotation file...
classification took 0 minutes and 56 seconds.
While when I use directly the available gsc file it seems that there are much more iterations skipped in the command above:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.gcs ../label/rh.saaparc.annot
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.gcs...
reading color table from GCSA file....
average std = 35.0 0.3 using min determinant for regularization = 0.011
0 singular and 829 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 3991 changed, 155533 examined...
001: 950 changed, 16590 examined...
002: 204 changed, 5127 examined...
003: 49 changed, 1234 examined...
004: 15 changed, 308 examined...
005: 11 changed, 96 examined...
006: 5 changed, 54 examined...
007: 3 changed, 32 examined...
008: 1 changed, 15 examined...
009: 1 changed, 8 examined...
010: 0 changed, 6 examined...
000: 111 total segments, 76 labels (659 vertices) changed
001: 39 total segments, 4 labels (51 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 32 changed)
writing output to ../label/rh.saaparc.annot...
writing colortable into annotation file...
classification took 2 minutes and 53 seconds.
Do you know why the parcellations are quite different (between the original gcs file and the constructed gcs file from the original annotation file)? Why there are some steps skipped in mris_ca_label with my gcs file? And why there are ‘0 changed’ in gibbs step?
Thank you very much for your help
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: lundi, 5. mars 2007 21:22 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use modified annotation file for parcellation
Hi Liela,
the .gcs file is constructed by training a classifier on multiple
individual .annot files using mris_ca_train. And it is definitely needed
for the
auto-parcellation.
cheers,
Bruce
On Mon, 5 Mar 2007, Leila BH wrote:
Hello,
I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot'
I can
read it with read_annotation.m and it seems correct. (The
modification is
simply a subdivision of the middletemporal to 32 subregion named :
middletemporal_1 .middletemporal_32).
I copied this 'rh.myaparc.annot' file to
/usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I
did this
because the original 'rh.aparc.annot' file was there.
When I run the mris_ca_label as done in the log file generated by
recon-all
command:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
../label/rh.myaparc.annot
I have an error:
GCSAread
(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot):
file magic #28002 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
How can I do to use this annotation file? Is it necessary to have
GCS file
for parcellation? If yes how can I create it with this annotation
file. I
don't want to create my own atlas, I want to use the freesurfer
atlas (35
entries) but just divide some of its regions.
If needed, I can send you my annotation file.
Thanks a lot
--
No virus found in this incoming message.
Checked by AVG Free Edition.
Version: 7.1.413 / Virus Database: 268.18.7/710 - Release Date: 04.03.2007
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you describe your goal in detail? On Tue, 13 Mar 2007, Nick Schmansky wrote:
Leila,
Looking at your commands, when you create your own mydesikan.gcs atlas file, it is trained on one subject, so that atlas does not contain the same 'database' of probabilistic information as does the ?.curvature.buckner40.filled.desikan_killiany.gcs atlas distributed with freesurfer. That atlas is trained on 40 subjects. You will notice that the default atlas is quite a bit larger file than the mydesikan.gcs file that you created. This is why the parcellation you see when mris_ca_label is conducted using your atlas is similar but not identical to labeling performed against the default atlas.
If you want to create your own parcellation atlas focusing on just the mediotemporal area, you need to create your own training set of manually labeled subjects. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
in particular the example here:
http://surfer.nmr.mgh.harvard.edu/fswiki/mris_5fca_5ftrain
However, I have my doubts on how well this will work, since the parcellation scheme is based on the cortical curv info (mapped to sphere.reg), so I don't think it will work well for a small region. Bruce would know the answer to this.
Nick
On Tue, 2007-03-13 at 15:57 +0100, Leila BH wrote:
Hi,
In order to change the atlas (35 entries) by subdividing the mediotemporal into N rois, I tried first to manipulate the atlas annotation file, I constructed the gcs file and apply the mris_ca_label, the parcellation (plotted on inflated) is good but quite different from the one obtained using the original rh.curvature.buckner40.filled.desikan_killiany.gcs:
These are the command I used to construct and use my gcs (theoretically the same that rh.curvature.buckner40.filled.desikan_killiany.gcs)
mris_ca_train -t ./average/colortable_desikan_killiany.txt rh /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.aparc.annot fsaverage mydesik.gcs
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/mydesik.gcs ../label/rh.saaparcssmat.annot
In fact the output lines are :
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/mydesik.gcs...
reading color table from GCSA file....
average std = 0.1 using min determinant for regularization = 0.000
0 singular and 167 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 0 changed, 155533 examined...
000: 87 total segments, 52 labels (341 vertices) changed
001: 37 total segments, 2 labels (61 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 126 changed)
writing output to ../label/rh.saaparcssmat.annot...
writing colortable into annotation file...
classification took 0 minutes and 56 seconds.
While when I use directly the available gsc file it seems that there are much more iterations skipped in the command above:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.gcs ../label/rh.saaparc.annot
$Id: mris_ca_label.c,v 1.16.2.1 2006/05/02 21:41:01 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.gcs...
reading color table from GCSA file....
average std = 35.0 0.3 using min determinant for regularization = 0.011
0 singular and 829 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
000: 3991 changed, 155533 examined...
001: 950 changed, 16590 examined...
002: 204 changed, 5127 examined...
003: 49 changed, 1234 examined...
004: 15 changed, 308 examined...
005: 11 changed, 96 examined...
006: 5 changed, 54 examined...
007: 3 changed, 32 examined...
008: 1 changed, 15 examined...
009: 1 changed, 8 examined...
010: 0 changed, 6 examined...
000: 111 total segments, 76 labels (659 vertices) changed
001: 39 total segments, 4 labels (51 vertices) changed
002: 35 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 32 changed)
writing output to ../label/rh.saaparc.annot...
writing colortable into annotation file...
classification took 2 minutes and 53 seconds.
Do you know why the parcellations are quite different (between the original gcs file and the constructed gcs file from the original annotation file)? Why there are some steps skipped in mris_ca_label with my gcs file? And why there are ÿÿ0 changedÿÿ in gibbs step?
Thank you very much for your help
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: lundi, 5. mars 2007 21:22 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use modified annotation file for parcellation
Hi Liela,
the .gcs file is constructed by training a classifier on multiple
individual .annot files using mris_ca_train. And it is definitely needed
for the
auto-parcellation.
cheers,
Bruce
On Mon, 5 Mar 2007, Leila BH wrote:
Hello,
I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot'
I can
read it with read_annotation.m and it seems correct. (The
modification is
simply a subdivision of the middletemporal to 32 subregion named :
middletemporal_1 .middletemporal_32).
I copied this 'rh.myaparc.annot' file to
/usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I
did this
because the original 'rh.aparc.annot' file was there.
When I run the mris_ca_label as done in the log file generated by
recon-all
command:
mris_ca_label chuv44 rh ../surf/rh.sphere.reg
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
../label/rh.myaparc.annot
I have an error:
GCSAread
(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot):
file magic #28002 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from
/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot
How can I do to use this annotation file? Is it necessary to have
GCS file
for parcellation? If yes how can I create it with this annotation
file. I
don't want to create my own atlas, I want to use the freesurfer
atlas (35
entries) but just divide some of its regions.
If needed, I can send you my annotation file.
Thanks a lot
--
No virus found in this incoming message.
Checked by AVG Free Edition.
Version: 7.1.413 / Virus Database: 268.18.7/710 - Release Date: 04.03.2007
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Leila BH -
Nick Schmansky