Re: [Freesurfer] Changing roi label display color in tkmedit

[Victoria Williams]

Hi Lena,

Have you tried loading your labels as a segmentation volume? As long as 
each of your labels has a different voxel value, you can load that label 
volume as a segmentation, and then make a corresponding color look up 
table making each label whatever color you want (as long as you can 
figure out what the RGB values are for that color - there are conversion 
tables if you search on the internet).

-Tori


On Wed, 19 May 2010, Krish Subramaniam wrote:

> Hi Lena
>
> Do you have a Mac? In that case, I can send you an experimental build
> of freeview if your OS is 10.5.x ( Leopard ). It doesn't work on
> 10.6.x ( Snow Leopard ) which we are working on.
>
> Best
> Krish
>
> On May 19, 2010, at 3:37 PM, Bruce Fischl wrote:
>
>> it should be in our current distribution
>>
>> On Wed, 19 May 2010, Lena Palaniyappan wrote:
>>
>>> I don't seem to get freeview on commandline - where can I download
>>> this?
>>>
>>> Thanks
>>> LKP
>>>
>>>
>>> On 19/05/2010 17:47, "Bruce Fischl" 
>>> wrote:
>>>
 Hi Lena,

 I'm not sure you can do this in tkmedit. You might try freeview
 instead.

 cheers
 Bruce
 On
 Wed, 19 May 2010, Lena Palaniyappan wrote:

> I want to show a group of 5 labels  ach with a different color in
> tkmedit
> (Orig.mgz) display  can I manipulate the colors of these lables
> I am able
> to do this in tksurfer: not tkmedit. Am I missing something?
>
> Cheers
> Lena
> ___
> Lena Palaniyappan
> PhD Student & Honorary StR | Division of Psychiatry ( University of
> Nottingham)
> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
>
>
> This message has been checked for viruses but the contents of an
> attachment
> may still contain software viruses which could damage your
> computer system:
> you are advised to perform your own checks. Email communications
> with the
> University of Nottingham may be monitored as permitted by UK
> legislation.


 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
 http://www.partners.org/complianceline . 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.
>>>
>>> ___
>>> Lena Palaniyappan
>>> Clinical Lecturer & Honorary StR | Division of Psychiatry
>>> ( University of
>>> Nottingham)
>>> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
>>>
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Reporting coordinates from Group analysis

[Rajagopalan, Venkateswaran]

Dear All,

I checked the archives but couldn't get a complete answer. I performed group 
analysis of cortical thickness using mri_glmfit. I am wondering how to report 
the coordinates of regions where cortical thickness is significantly different, 
i used FDR for multiple comparisons in tksurfer. So how to get these 
coordinates after FDR where is this file stored.

Thanks

venkat

===

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2009).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy.  Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] Reporting coordinates from Group analysis

[Douglas N Greve]

If you click on a point, it should tell you in the control window what 
the talairach coordinates are

doug

Rajagopalan, Venkateswaran wrote:
>
> Dear All,
>
> I checked the archives but couldn't get a complete answer. I performed 
> group analysis of cortical thickness using mri_glmfit. I am wondering 
> how to report the coordinates of regions where cortical thickness is 
> significantly different, i used FDR for multiple comparisons in 
> tksurfer. So how to get these coordinates after FDR where is this file 
> stored.
>
> Thanks
>
> venkat
>
> ===
>
> P Please consider the environment before printing this e-mail
>
>
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2009).  
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>   
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] Reporting coordinates from Group analysis

[Rajagopalan, Venkateswaran]

Thanks Doug, but for instance in my result the inferiorparietal region is 
significantly different in some areas but not in the entire region, so in this 
case it will difficult because i have to move the cursor to regions where it is 
significant and other vertex where it is not significant  this means that i 
will have two or more coordinates to report  a single region, i am wondering is 
there a way to identify in this map which cluster is significant and report its 
center coordinate.
 
Thanks in advance
 
venkat 



From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Thu 5/20/2010 1:33 PM
To: Rajagopalan, Venkateswaran
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Reporting coordinates from Group analysis



If you click on a point, it should tell you in the control window what
the talairach coordinates are

doug

Rajagopalan, Venkateswaran wrote:
>
> Dear All,
>
> I checked the archives but couldn't get a complete answer. I performed
> group analysis of cortical thickness using mri_glmfit. I am wondering
> how to report the coordinates of regions where cortical thickness is
> significantly different, i used FDR for multiple comparisons in
> tksurfer. So how to get these coordinates after FDR where is this file
> stored.
>
> Thanks
>
> venkat
>
> ===
>
> P Please consider the environment before printing this e-mail
>
>
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2009). 
> Visit us online at http://www.clevelandclinic.org 
>   for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>  
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html





===

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2009).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy.  Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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] Creating annotation file for lobar regions...

[Rudolph Pienaar]

Hi all --

Is there a simple way to create an annotation for 
frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot 
files in a FS 'label' dir? Ideally speaking, I'd like to have a 
?h.lobar.annot with corresponding lobar.annot.ctab.

Apologies if this question has come up before... a quick google didn't 
reveal anything.

Many thanks
-=R

-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] how to QC hippocampal measurement

[Guang Zeng]

Hello, Bruce,

Thanks a lot! Currently, I am using Slicer 2.6. 
Is the QA tool in VTKFreeSurfer Module the tool you mean to make flythrough 
movies?

Thanks!
Guang

> Date: Thu, 4 Feb 2010 14:20:42 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] how to QC hippocampal measurement
> 
> Hi Guang,
> 
> there are some tools in slicer for making flythrough movies you could use 
> to make a quick check.
> 
> cheers,
> Bruce
> 
> On Thu, 4 Feb 2010, Guang Zeng 
> wrote:
> 
> >
> > Hi, there,
> >
> > I have used FreeSurfer to measure the hippocampal size of 200 ADNI 
> > subjects, and now I'd like to QC the hippocampal measurement.
> > Anyone can give me some suggestion to do this, instead of loading they 
> > one-by-one ?
> >
> > Thanks!
> > Guang
> >
> > _
> > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.
> > http://clk.atdmt.com/GBL/go/201469229/direct/01/
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
_
The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with 
Hotmail. 
http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] how to QC hippocampal measurement

[Bruce Fischl]

I don't know - you should ask the slicer folks.
Bruce
On Thu, 20 May 2010, Guang 
Zeng wrote:

>
> Hello, Bruce,
>
> Thanks a lot! Currently, I am using Slicer 2.6.
> Is the QA tool in VTKFreeSurfer Module the tool you mean to make flythrough 
> movies?
>
> Thanks!
> Guang
>
>> Date: Thu, 4 Feb 2010 14:20:42 -0500
>> From: fis...@nmr.mgh.harvard.edu
>> To: freesurfer...@hotmail.com
>> CC: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] how to QC hippocampal measurement
>>
>> Hi Guang,
>>
>> there are some tools in slicer for making flythrough movies you could use
>> to make a quick check.
>>
>> cheers,
>> Bruce
>>
>> On Thu, 4 Feb 2010, Guang Zeng
>> wrote:
>>
>>>
>>> Hi, there,
>>>
>>> I have used FreeSurfer to measure the hippocampal size of 200 ADNI 
>>> subjects, and now I'd like to QC the hippocampal measurement.
>>> Anyone can give me some suggestion to do this, instead of loading they 
>>> one-by-one ?
>>>
>>> Thanks!
>>> Guang
>>>
>>> _
>>> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.
>>> http://clk.atdmt.com/GBL/go/201469229/direct/01/
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _
> The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with 
> Hotmail.
> http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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] transform ribbon to FSL-diffusion space

[Theodor R?ber]

Dear Freesurfers,

I am trying to transform a Freesurfer-generated white
matter mask (ribbon) to FSL diffusion space in order to
use it as a stop-mask in fibertracking. I have tried to
coregister and reslice it to the normalized dti_FA with
SPM and I also tried to transform it with FSL-FLIRT and
FSL-FNIRT as described on 
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html.
Unfortunately, neither approach yielded satisfying
results. What steps would you recommend to turn the
Freesurfer output into a FSL-FDT compatible white matter
mask?

Thank you very much in advance. Your help will be greatly
appreciated.

Best,

Theodor
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] transform ribbon to FSL-diffusion space

[Douglas N Greve]

Try using bbregister to register the freesurfer anatomical to the low b 
in the native diffusion space, then use mri_vol2vol or mri_label2vol to 
map the ribbon to the native diffusion space.

doug

Theodor R?ber wrote:
> Dear Freesurfers,
>
> I am trying to transform a Freesurfer-generated white
> matter mask (ribbon) to FSL diffusion space in order to
> use it as a stop-mask in fibertracking. I have tried to
> coregister and reslice it to the normalized dti_FA with
> SPM and I also tried to transform it with FSL-FLIRT and
> FSL-FNIRT as described on 
> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html.
> Unfortunately, neither approach yielded satisfying
> results. What steps would you recommend to turn the
> Freesurfer output into a FSL-FDT compatible white matter
> mask?
>
> Thank you very much in advance. Your help will be greatly
> appreciated.
>
> Best,
>
> Theodor
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
http://www.partners.org/complianceline . 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.