Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, February 14, 2019 3:28:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
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
You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Thursday, February 14, 2019 3:28:44 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] surface cortical lesions mask --> annotation file ??? not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file.
As I tried to use FreeSurferColorLUT.txt I got a list of all regions I did not need.
What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?
Thank you,
Vale
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Thursday, February 14, 2019 3:37:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Thursday, February 14, 2019 3:28:44 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] surface cortical lesions mask --> annotation file ??? not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
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 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
you have to create your own. Use FreeSurferColorsLUT.txt as your template
On 2/15/19 1:08 PM, Barletta, Valeria wrote:
Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file.
As I tried to use FreeSurferColorLUT.txt I got a list of all regions I did not need.
What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?
Thank you,
Vale
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, February 14, 2019 3:37:28 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Thursday, February 14, 2019 3:28:44 PM *To:* freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] surface cortical lesions mask --> annotation file ??? not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ok I did and inserted only this:
#No. Label Name: R G B A
1 Left-Cerebral-Exterior 70 130 180 0
since I binarized the lesion masks and when creating the label I assigned value 1 (with the option --id 1). Is it correct? Thanks, Vale ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, February 15, 2019 1:56:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
you have to create your own. Use FreeSurferColorsLUT.txt as your template
On 2/15/19 1:08 PM, Barletta, Valeria wrote:
Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file.
As I tried to use FreeSurferColorLUT.txt I got a list of all regions I did not need.
What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?
Thank you,
Vale
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, February 14, 2019 3:37:28 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Thursday, February 14, 2019 3:28:44 PM *To:* freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] surface cortical lesions mask --> annotation file ??? not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, if you only have one label. You will probably want to change the name to Lesion or somthing. You can also change the color by changing the RGB
On 2/15/19 2:01 PM, Barletta, Valeria wrote: Ok I did and inserted only this:
#No. Label Name: R G B A
1 Left-Cerebral-Exterior 70 130 180 0
since I binarized the lesion masks and when creating the label I assigned value 1 (with the option --id 1). Is it correct? Thanks, Vale ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Friday, February 15, 2019 1:56:50 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
you have to create your own. Use FreeSurferColorsLUT.txt as your template
On 2/15/19 1:08 PM, Barletta, Valeria wrote:
Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file.
As I tried to use FreeSurferColorLUT.txt I got a list of all regions I did not need.
What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?
Thank you,
Vale
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, February 14, 2019 3:37:28 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
You can make separate labels (mri_cor2label with --surf option), then use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
Yes sure, I need to extract values from discrete cortical lesions, but I have masks of all lesions together projected to the cortical surface.
I have a script that can provide me values for every single lesion separately, but this script works on annotation files.
Is it possible to create an annotation file for the lesion masks? They are in .mgh format
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Thursday, February 14, 2019 3:28:44 PM *To:* freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] surface cortical lesions mask --> annotation file ??? not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to the surface.
Do you know whether this is possible?
Thank you,
Valeria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Barletta, Valeria -
Greve, Douglas N.,Ph.D.