Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file
--erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing . . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hi Bruce,
As always thank you for your prompt reply.
For the morphological close operation, would you suggest using mris_fill on the surface ROI I created and then running mri_vol2surf again on the volume output by mris_fill?
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
p.s. you could remove many/most of these holes using a morphological close operation On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hello Freesurfer Developers and Community,
I am looking to map a ROI.nii based on the MNI152 template to the fsaverage pial surface.
I have used the following commands
Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl ‹12 ‹t1
Then
mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
The ROI appears to be in the right place however is very blotchy. Have I missed a step? Or is this correct?
See bellow a picture of the ROI highlighted in FSL and in tksurfer after mapped using the above.
Thank you for your support,
Best, Derek
[IMAGE]
__ ___
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .a
ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 b8
3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e f7
af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sdata =% 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c1 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3D&re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C61983 9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sdata=y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
________________________________________ Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file
--erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing . . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hi Bruce,
As always thank you for your prompt reply.
For the morphological close operation, would you suggest using mris_fill on the surface ROI I created and then running mri_vol2surf again on the volume output by mris_fill?
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
p.s. you could remove many/most of these holes using a morphological close operation On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hello Freesurfer Developers and Community,
I am looking to map a ROI.nii based on the MNI152 template to the fsaverage pial surface.
I have used the following commands
Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl ‹12 ‹t1
Then
mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
The ROI appears to be in the right place however is very blotchy. Have I missed a step? Or is this correct?
See bellow a picture of the ROI highlighted in FSL and in tksurfer after mapped using the above.
Thank you for your support,
Best, Derek
[IMAGE]
__ __ ___
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai l. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek .a
ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c 16 b8
3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3 D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C6 5e f7
af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sda ta =% 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail .n
mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek
.andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34 c1
6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ %3 D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .a
ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16 b8
3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C619 83
9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sdata =y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C527f8 01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdata=H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file --erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing. . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hi Bruce,
As always thank you for your prompt reply.
For the morphological close operation, would you suggest using mris_fill on the surface ROI I created and then running mri_vol2surf again on the volume output by mris_fill?
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
p.s. you could remove many/most of these holes using a morphological close operation On Fri, 28 Oct 2016, Andrews, Derek wrote:
> Hello Freesurfer Developers and Community, > > I am looking to map a ROI.nii based on the MNI152 template to the > fsaverage > pial surface. > > I have used the following commands > > Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl > ‹12 > ‹t1 > > Then > > mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh > > The ROI appears to be in the right place however is very blotchy. > Have I > missed a step? Or is this correct? > > See bellow a picture of the ROI highlighted in FSL and in tksurfer > after > mapped using the above. > > Thank you for your support, > > Best, Derek > > [IMAGE] > > > > > > > _____________________________________________________________________ > __ > __ > ___ > > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopment > > Department of Forensic and Neurodevelopmental Sciences > > Institute of Psychiatry, Psychology & Neuroscience, King's College > London > > Telephone: +44 (0)20 7848 5701 > Email: Derek.Andrews@kcl.ac.uk > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai l. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek .a
ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c 16 b8
3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3 D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C6 5e f7
af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sda ta =% 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail .n
mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek
.andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34 c1
6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ %3 D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .a
ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16 b8
3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C619 83
9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sdata =y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C527f8 01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdata=H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug that worked perfectly.
Is it possible then to go back to a .w from a label?
________________________________________ Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 16:10, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file --erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing. . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
Hi Bruce,
As always thank you for your prompt reply.
For the morphological close operation, would you suggest using mris_fill on the surface ROI I created and then running mri_vol2surf again on the volume output by mris_fill?
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
> p.s. you could remove many/most of these holes using a >morphological > close operation > On Fri, 28 Oct 2016, Andrews, Derek wrote: > >> Hello Freesurfer Developers and Community, >> >> I am looking to map a ROI.nii based on the MNI152 template to the >> fsaverage >> pial surface. >> >> I have used the following commands >> >> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat >>‹init-fsl >> ‹12 >> ‹t1 >> >> Then >> >> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi >>lh >> >> The ROI appears to be in the right place however is very blotchy. >> Have I >> missed a step? Or is this correct? >> >> See bellow a picture of the ROI highlighted in FSL and in tksurfer >> after >> mapped using the above. >> >> Thank you for your support, >> >> Best, Derek >> >> [IMAGE] >> >> >> >> >> >> >> >>___________________________________________________________________ >>__ >> __ >> __ >> ___ >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> >> Department of Forensic and Neurodevelopmental Sciences >> >> Institute of Psychiatry, Psychology & Neuroscience, King's College >> London >> >> Telephone: +44 (0)20 7848 5701 >> Email: Derek.Andrews@kcl.ac.uk >> >> >> >> _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > > >https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >ai > l. > nm > > > >r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd >er > ek > .a > > > >ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f3 >4c > 16 > b8 > > > >3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo >%3 > D& > re > served=0 > > > The information in this e-mail is intended only for the person to > whom > it > is > addressed. If you believe this e-mail was sent to you in error and > the > e-mail > contains patient information, please contact the Partners >Compliance > HelpLine at > > > >https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww >w. > pa > rt > > > >ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7 >C6 > 5e > f7 > > > >af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&s >da > ta > =% > 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If > the > e-mail was sent to you in error > but does not contain patient information, please contact the sender > and > properly > dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma il .n
mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd er ek
.andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f 34 c1
6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9j KQ %3 D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai l. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek .a
ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c 16 b8
3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C6 19 83
9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sda ta =y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C527 f8
01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdata =H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .andrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c1 6b83c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78Mk Q4mM%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78MkQ4mM %3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C727ae 8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=Z 6ZPFU4U6kIC4pGxlAgx4GDAqIiot74Pj8EgQKOeFRE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Apologies I meant from a label to a .mgh
Best, Derek
________________________________________ Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 17:35, "Andrews, Derek" derek.andrews@kcl.ac.uk wrote:
This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
Thank you Doug that worked perfectly.
Is it possible then to go back to a .w from a label?
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 16:10, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file --erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing. . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
> Hi Bruce, > > As always thank you for your prompt reply. > > For the morphological close operation, would you suggest using > mris_fill > on the surface ROI I created and then running mri_vol2surf again on > the > volume output by mris_fill? > > Best, Derek > > > ________________________________________ > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopment > Department of Forensic and Neurodevelopmental Sciences > Institute of Psychiatry, Psychology & Neuroscience, King's College > London > > Telephone: +44 (0)20 7848 5701 > Email: Derek.Andrews@kcl.ac.uk > > > > > > On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu > wrote: > >> p.s. you could remove many/most of these holes using a >>morphological >> close operation >> On Fri, 28 Oct 2016, Andrews, Derek wrote: >> >>> Hello Freesurfer Developers and Community, >>> >>> I am looking to map a ROI.nii based on the MNI152 template to the >>> fsaverage >>> pial surface. >>> >>> I have used the following commands >>> >>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat >>>‹init-fsl >>> ‹12 >>> ‹t1 >>> >>> Then >>> >>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi >>>lh >>> >>> The ROI appears to be in the right place however is very blotchy. >>> Have I >>> missed a step? Or is this correct? >>> >>> See bellow a picture of the ROI highlighted in FSL and in >>>tksurfer >>> after >>> mapped using the above. >>> >>> Thank you for your support, >>> >>> Best, Derek >>> >>> [IMAGE] >>> >>> >>> >>> >>> >>> >>> >>>__________________________________________________________________ >>>_ >>>__ >>> __ >>> __ >>> ___ >>> >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's >>>College >>> London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews@kcl.ac.uk >>> >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> >> >>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2F >>m >>ai >> l. >> nm >> >> >> >>r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7C >>d >>er >> ek >> .a >> >> >> >>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f >>3 >>4c >> 16 >> b8 >> >> >> >>3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcu >>o >>%3 >> D& >> re >> served=0 >> >> >> The information in this e-mail is intended only for the person to >> whom >> it >> is >> addressed. If you believe this e-mail was sent to you in error and >> the >> e-mail >> contains patient information, please contact the Partners >>Compliance >> HelpLine at >> >> >> >>https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fw >>w >>w. >> pa >> rt >> >> >> >>ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk% >>7 >>C6 >> 5e >> f7 >> >> >> >>af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0& >>s >>da >> ta >> =% >> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . >>If >> the >> e-mail was sent to you in error >> but does not contain patient information, please contact the >>sender >> and >> properly >> dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > > >https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >a >il > .n > > >mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7C >d >er > ek > > >.andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416 >f >34 > c1 > > >6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9 >j >KQ > %3 > D&reserved=0 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma i l. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cde r ek .a
ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34 c 16 b8
3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ% 3 D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww . pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C 6 19 83
9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sd a ta =y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.p a rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C52 7 f8
01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdat a =H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cdere k .andrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c 1 6b83c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78M k Q4mM%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n m r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek. a ndrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b 8 3c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78MkQ4m M %3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.par t ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C727a e 8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b83c724071654356%7C0&sdata= Z 6ZPFU4U6kIC4pGxlAgx4GDAqIiot74Pj8EgQKOeFRE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7Ca19b19ca9e5141130af508d407fdac90%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=CNW89no5rQuTihVAY8XW7XCTWugQ3FabP29yUsn28h0%3D&re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7Ca19b1 9ca9e5141130af508d407fdac90%7C8370cf1416f34c16b83c724071654356%7C0&sdata=q s3kPvmF1HaaRYygrshVeobomCboo8B16cJW6qLT%2Bio%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
use mri_label2label with the --outmask option
On 11/8/16 12:37 PM, Andrews, Derek wrote:
Apologies I meant from a label to a .mgh
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 17:35, "Andrews, Derek" derek.andrews@kcl.ac.uk wrote:
This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
Thank you Doug that worked perfectly.
Is it possible then to go back to a .w from a label?
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 16:10, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
> Hi Derek > > I think the dev version of mri_label2label supports > open/close/dilate/erode > operations: > > mri_label2label --help > USAGE: mri_label2label.bin > > --srclabel input label file > > --erode N erode the label N times before writing > --open N open the label N times before writing > --close N close the label N times before writing > --dilate N dilate the label N times before writing > . > . > . > > if your version doesn't have these operations let us know and we can > get > you an updated one > > cheers > Bruce > > > > On Fri, 28 Oct 2016, > Andrews, Derek wrote: > >> Hi Bruce, >> >> As always thank you for your prompt reply. >> >> For the morphological close operation, would you suggest using >> mris_fill >> on the surface ROI I created and then running mri_vol2surf again on >> the >> volume output by mris_fill? >> >> Best, Derek >> >> >> ________________________________________ >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >> London >> >> Telephone: +44 (0)20 7848 5701 >> Email: Derek.Andrews@kcl.ac.uk >> >> >> >> >> >> On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu >> wrote: >> >>> p.s. you could remove many/most of these holes using a >>> morphological >>> close operation >>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>> >>>> Hello Freesurfer Developers and Community, >>>> >>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>> fsaverage >>>> pial surface. >>>> >>>> I have used the following commands >>>> >>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat >>>> ‹init-fsl >>>> ‹12 >>>> ‹t1 >>>> >>>> Then >>>> >>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi >>>> lh >>>> >>>> The ROI appears to be in the right place however is very blotchy. >>>> Have I >>>> missed a step? Or is this correct? >>>> >>>> See bellow a picture of the ROI highlighted in FSL and in >>>> tksurfer >>>> after >>>> mapped using the above. >>>> >>>> Thank you for your support, >>>> >>>> Best, Derek >>>> >>>> [IMAGE] >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> __________________________________________________________________ >>>> _ >>>> __ >>>> __ >>>> __ >>>> ___ >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> >>>> Department of Forensic and Neurodevelopmental Sciences >>>> >>>> Institute of Psychiatry, Psychology & Neuroscience, King's >>>> College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: Derek.Andrews@kcl.ac.uk >>>> >>>> >>>> >>>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2F >>> m >>> ai >>> l. >>> nm >>> >>> >>> >>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7C >>> d >>> er >>> ek >>> .a >>> >>> >>> >>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f >>> 3 >>> 4c >>> 16 >>> b8 >>> >>> >>> >>> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcu >>> o >>> %3 >>> D& >>> re >>> served=0 >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom >>> it >>> is >>> addressed. If you believe this e-mail was sent to you in error and >>> the >>> e-mail >>> contains patient information, please contact the Partners >>> Compliance >>> HelpLine at >>> >>> >>> >>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fw >>> w >>> w. >>> pa >>> rt >>> >>> >>> >>> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk% >>> 7 >>> C6 >>> 5e >>> f7 >>> >>> >>> >>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0& >>> s >>> da >>> ta >>> =% >>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . >>> If >>> the >>> e-mail was sent to you in error >>> but does not contain patient information, please contact the >>> sender >>> and >>> properly >>> dispose of the e-mail. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> >> >> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >> a >> il >> .n >> >> >> mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7C >> d >> er >> ek >> >> >> .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416 >> f >> 34 >> c1 >> >> >> 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9 >> j >> KQ >> %3 >> D&reserved=0 >> >> >> _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma > i > l. > nm > > > r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cde > r > ek > .a > > > ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34 > c > 16 > b8 > > > 3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ% > 3 > D& > re > served=0 > > > The information in this e-mail is intended only for the person to > whom > it > is > addressed. If you believe this e-mail was sent to you in error and > the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > > > https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww > . > pa > rt > > > ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C > 6 > 19 > 83 > > > 9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sd > a > ta > =y > glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the > e-mail > was sent to you in error > but does not contain patient information, please contact the sender > and > properly > dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.p a rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C52 7 f8
01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdat a =H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cdere k .andrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c 1 6b83c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78M k Q4mM%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n m r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek. a ndrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b 8 3c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78MkQ4m M %3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.par t ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C727a e 8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b83c724071654356%7C0&sdata= Z 6ZPFU4U6kIC4pGxlAgx4GDAqIiot74Pj8EgQKOeFRE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7Ca19b19ca9e5141130af508d407fdac90%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=CNW89no5rQuTihVAY8XW7XCTWugQ3FabP29yUsn28h0%3D&re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7Ca19b1 9ca9e5141130af508d407fdac90%7C8370cf1416f34c16b83c724071654356%7C0&sdata=q s3kPvmF1HaaRYygrshVeobomCboo8B16cJW6qLT%2Bio%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Not sure. We are trying to get away from .w files for this reason. Can you use something other than a w file?
On 11/8/16 12:35 PM, Andrews, Derek wrote:
Thank you Doug that worked perfectly.
Is it possible then to go back to a .w from a label?
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 16:10, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I think the dev version of mri_label2label supports open/close/dilate/erode operations:
mri_label2label --help USAGE: mri_label2label.bin
--srclabel input label file --erode N erode the label N times before writing --open N open the label N times before writing --close N close the label N times before writing --dilate N dilate the label N times before writing. . .
if your version doesn't have these operations let us know and we can get you an updated one
cheers Bruce
On Fri, 28 Oct 2016, Andrews, Derek wrote:
> Hi Bruce, > > As always thank you for your prompt reply. > > For the morphological close operation, would you suggest using > mris_fill > on the surface ROI I created and then running mri_vol2surf again on > the > volume output by mris_fill? > > Best, Derek > > > ________________________________________ > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopment > Department of Forensic and Neurodevelopmental Sciences > Institute of Psychiatry, Psychology & Neuroscience, King's College > London > > Telephone: +44 (0)20 7848 5701 > Email: Derek.Andrews@kcl.ac.uk > > > > > > On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu > wrote: > >> p.s. you could remove many/most of these holes using a >> morphological >> close operation >> On Fri, 28 Oct 2016, Andrews, Derek wrote: >> >>> Hello Freesurfer Developers and Community, >>> >>> I am looking to map a ROI.nii based on the MNI152 template to the >>> fsaverage >>> pial surface. >>> >>> I have used the following commands >>> >>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat >>> ‹init-fsl >>> ‹12 >>> ‹t1 >>> >>> Then >>> >>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi >>> lh >>> >>> The ROI appears to be in the right place however is very blotchy. >>> Have I >>> missed a step? Or is this correct? >>> >>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>> after >>> mapped using the above. >>> >>> Thank you for your support, >>> >>> Best, Derek >>> >>> [IMAGE] >>> >>> >>> >>> >>> >>> >>> >>> ___________________________________________________________________ >>> __ >>> __ >>> __ >>> ___ >>> >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>> London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews@kcl.ac.uk >>> >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> >> >> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >> ai >> l. >> nm >> >> >> >> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd >> er >> ek >> .a >> >> >> >> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f3 >> 4c >> 16 >> b8 >> >> >> >> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo >> %3 >> D& >> re >> served=0 >> >> >> The information in this e-mail is intended only for the person to >> whom >> it >> is >> addressed. If you believe this e-mail was sent to you in error and >> the >> e-mail >> contains patient information, please contact the Partners >> Compliance >> HelpLine at >> >> >> >> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww >> w. >> pa >> rt >> >> >> >> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7 >> C6 >> 5e >> f7 >> >> >> >> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&s >> da >> ta >> =% >> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If >> the >> e-mail was sent to you in error >> but does not contain patient information, please contact the sender >> and >> properly >> dispose of the e-mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > > > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma > il > .n > > > mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd > er > ek > > > .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f > 34 > c1 > > > 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9j > KQ > %3 > D&reserved=0 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai l. nm
r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder ek .a
ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c 16 b8
3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 D& re served=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C6 19 83
9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sda ta =y glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C527 f8
01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdata =H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .andrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c1 6b83c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78Mk Q4mM%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78MkQ4mM %3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C727ae 8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=Z 6ZPFU4U6kIC4pGxlAgx4GDAqIiot74Pj8EgQKOeFRE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hou could do it easily enough in matlab with read_label.m and write_wfile.m, but as Doug says, w files are a goofy format that we never use anymore.
On Tue, 8 Nov 2016, Douglas Greve wrote:
Not sure. We are trying to get away from .w files for this reason. Can you use something other than a w file?
On 11/8/16 12:35 PM, Andrews, Derek wrote:
Thank you Doug that worked perfectly.
Is it possible then to go back to a .w from a label?
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 16:10, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label
On 11/8/16 9:41 AM, Andrews, Derek wrote:
Hi Bruce and Freesurfer developers,
Thank you. Any suggestions on converting a binary .w file to a label would be very helpful.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 08/11/2016 14:04, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Derek
I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label.
cheers Bruce
On Tue, 8 Nov 2016, Andrews, Derek wrote:
Hi Bruce,
Apologies for contacting you directly but I’m not sure if my message is getting through to the list.
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag.
Any help you could provide would be appreciated.
Best, Derek
Derek Sayre Andrews, MSc PhD Candidate
The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London
Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
> Hi Derek > > I think the dev version of mri_label2label supports > open/close/dilate/erode > operations: > > mri_label2label --help > USAGE: mri_label2label.bin > > --srclabel input label file > > --erode N erode the label N times before writing > --open N open the label N times before writing > --close N close the label N times before writing > --dilate N dilate the label N times before writing > . > . > . > > if your version doesn't have these operations let us know and we can > get > you an updated one > > cheers > Bruce > > > > On Fri, 28 Oct 2016, > Andrews, Derek wrote: > >> Hi Bruce, >> >> As always thank you for your prompt reply. >> >> For the morphological close operation, would you suggest using >> mris_fill >> on the surface ROI I created and then running mri_vol2surf again on >> the >> volume output by mris_fill? >> >> Best, Derek >> >> >> ________________________________________ >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >> London >> >> Telephone: +44 (0)20 7848 5701 >> Email: Derek.Andrews@kcl.ac.uk >> >> >> >> >> >> On 28/10/2016 14:54, "Bruce Fischl" fischl@nmr.mgh.harvard.edu >> wrote: >> >>> p.s. you could remove many/most of these holes using a >>> morphological >>> close operation >>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>> >>>> Hello Freesurfer Developers and Community, >>>> >>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>> fsaverage >>>> pial surface. >>>> >>>> I have used the following commands >>>> >>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat >>>> ‹init-fsl >>>> ‹12 >>>> ‹t1 >>>> >>>> Then >>>> >>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi >>>> lh >>>> >>>> The ROI appears to be in the right place however is very blotchy. >>>> Have I >>>> missed a step? Or is this correct? >>>> >>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>> after >>>> mapped using the above. >>>> >>>> Thank you for your support, >>>> >>>> Best, Derek >>>> >>>> [IMAGE] >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ___________________________________________________________________ >>>> __ >>>> __ >>>> __ >>>> ___ >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> >>>> Department of Forensic and Neurodevelopmental Sciences >>>> >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: Derek.Andrews@kcl.ac.uk >>>> >>>> >>>> >>>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >>> ai >>> l. >>> nm >>> >>> >>> >>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd >>> er >>> ek >>> .a >>> >>> >>> >>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f3 >>> 4c >>> 16 >>> b8 >>> >>> >>> >>> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo >>> %3 >>> D& >>> re >>> served=0 >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom >>> it >>> is >>> addressed. If you believe this e-mail was sent to you in error and >>> the >>> e-mail >>> contains patient information, please contact the Partners >>> Compliance >>> HelpLine at >>> >>> >>> >>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fww >>> w. >>> pa >>> rt >>> >>> >>> >>> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7 >>> C6 >>> 5e >>> f7 >>> >>> >>> >>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&s >>> da >>> ta >>> =% >>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If >>> the >>> e-mail was sent to you in error >>> but does not contain patient information, please contact the sender >>> and >>> properly >>> dispose of the e-mail. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> >> >> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma >> il >> .n >> >> >> mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd >> er >> ek >> >> >> .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f >> 34 >> c1 >> >> >> 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9j >> KQ >> %3 >> D&reserved=0 >> >> >> _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai > l. > nm > > > r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder > ek > .a > > > ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c > 16 > b8 > > > 3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 > D& > re > served=0 > > > The information in this e-mail is intended only for the person to > whom > it > is > addressed. If you believe this e-mail was sent to you in error and > the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > > > https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. > pa > rt > > > ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C6 > 19 > 83 > > > 9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sda > ta > =y > glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the > e-mail > was sent to you in error > but does not contain patient information, please contact the sender > and > properly > dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa rt
ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C527 f8
01e5db94c2db77508d407e02538%7C8370cf1416f34c16b83c724071654356%7C0&sdata =H fsqNPsj5Qo43gUM6QZcE0DQ%2F9BJC3ggGF1dY6pRRvk%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek .andrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c1 6b83c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78Mk Q4mM%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a ndrews%40kcl.ac.uk%7C727ae8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=O1%2B%2F72eSNhO9uJtgUBh%2Bl88Nh2gvw7jsLZk78MkQ4mM %3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C727ae 8120ed04c2847d108d407f1bac8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=Z 6ZPFU4U6kIC4pGxlAgx4GDAqIiot74Pj8EgQKOeFRE%3D&reserved=0 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
-
Andrews, Derek -
Bruce Fischl -
Douglas Greve