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
[cid:20AF047A-6501-433B-9BE0-F5410F5ED296]
________________________________
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
Hi Andrew
that is to be expected. It's because the cortex is blurred in the MNI template, and so a ROI there is likely to cut across a gyrus or sulcus, missing either the fundus or the crown (both of which seem to be happening in your ROI)
cheers Bruce 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
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
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%7C8370cf1416f34c16b8 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D&re served=0
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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%7C8370cf1416f34c16b8 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.part ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65ef7 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.
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another thing to check is that you are using a binary ROI file. The Volume based image looked like it had a range of values.
hth d
On Fri, Oct 28, 2016 at 10:53 AM, 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
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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.
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The ROI volume is not binary however I binarized it after mapping to the surface space. Should I have binarized the ROI prior to running mri_vol2surf?
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 15:59, "dgw" dgwakeman@gmail.com wrote:
another thing to check is that you are using a binary ROI file. The Volume based image looked like it had a range of values.
hth d
On Fri, Oct 28, 2016 at 10:53 AM, 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
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ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c1 6b8
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af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sdat a=% 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.
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not necessary. mri_vol2surf by default uses nearest neighbor interpolation
On 10/28/16 11:17 AM, Andrews, Derek wrote:
The ROI volume is not binary however I binarized it after mapping to the surface space. Should I have binarized the ROI prior to running mri_vol2surf?
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 15:59, "dgw" dgwakeman@gmail.com wrote:
another thing to check is that you are using a binary ROI file. The Volume based image looked like it had a range of values.
hth d
On Fri, Oct 28, 2016 at 10:53 AM, 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
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Hi Bruce,
It doesn’t look like I have those operations. If you could provide me with a copy of the dev version of the function I would very much appreciate it.
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
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Hello Freesurfer Developers,
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.
Thank you.
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
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Hello Freesurfer Developers,
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.
Thank you.
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
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freesurfer@nmr.mgh.harvard.edu
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dgw -
Douglas Greve