Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

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.andr...@kcl.ac.uk





On 08/11/2016 16:10, "Douglas Greve"  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.andr...@kcl.ac.uk





On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl" 
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  Ndilate 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.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl" 
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 

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

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.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 16:10, "Douglas Greve"  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.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 15:53, "Bruce Fischl" 
> 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  Ndilate 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.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2016 14:54, "Bruce Fischl" 
>>> wrote:
>>>
 p.s. you could remove many/most of these holes using a
 morphological
 close operation

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

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.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 17:35, "Andrews, Derek"  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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 08/11/2016 16:10, "Douglas Greve"  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.andr...@kcl.ac.uk





 On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 15:53, "Bruce Fischl" 
>> 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  Ndilate 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
 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 08/11/2016 17:35, "Andrews, Derek"  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.andr...@kcl.ac.uk
>
>
>
>
>
>On 08/11/2016 16:10, "Douglas Greve"  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.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 15:53, "Bruce Fischl" 
>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  Ndilate 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 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 08/11/2016 16:10, "Douglas Greve"  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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk





 On 28/10/2016 15:53, "Bruce Fischl" 
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  Ndilate 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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl" 
>> 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 

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

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.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 14:54, "Bruce Fischl" 
> 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 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 08/11/2016 14:04, "Bruce Fischl"  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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk





 On 28/10/2016 14:54, "Bruce Fischl" 
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.andr...@kcl.ac.uk
>>
>>
>>
>> 

Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

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.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk



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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





> On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk
>> 
>> 
>> 
>> 
>> 
>>> On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@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=01%7C01%7Cderek
>>> .a
>>> 
>>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16
>>> b8
>>> 
>>> 3c724071654356%7C0=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=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e
>>> f7
>>> 
>>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0
>>> =%
>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=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
>> 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@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=01%7C01%7Cderek
>>>.a
>>> 
>>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16
>>>b8
>>> 
>>>3c724071654356%7C0=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=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e
>>>f7
>>> 
>>>af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0
>>>=%
>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=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=01%7C01%7Cderek

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

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.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 15:59, "dgw"  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
>>  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  Ndilate 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.andr...@kcl.ac.uk





 On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk
>>
>>
>>
>> ___
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>
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> k.a
>
>
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> 6b8
>
>
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> 
> served=0
>
>
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> ef7
>
>
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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl"  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  Ndilate 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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk



 ___
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>>>b8
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>>>re
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>>>
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>>>it
>>> is
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>>> e-mail
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>>> HelpLine at
>>> 
>>>https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa
>>>rt
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>>>ners.org%2Fcomplianceline=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e
>>>f7
>>> 
>>>af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0
>>>=%
>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=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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>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n
>>mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek
>>.andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c1
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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 28/10/2016 15:59, "dgw"  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
> 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  Ndilate 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.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk
>
>
>
> ___

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>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> 

Re: [Freesurfer] mapping ROI to surface space

[dgw]

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
 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  Ndilate 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.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk



 ___
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>>>
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>>>
>>> 3c724071654356%7C0=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D
>>> 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=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65ef7
>>>
>>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0=%
>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=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
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>>
>>
>
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> 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
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Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

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  Ndilate 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.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk



___

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

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.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl"  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.andr...@kcl.ac.uk
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Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

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.andr...@kcl.ac.uk 



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Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

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.andr...@kcl.ac.uk 



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