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30088 discussions

Tksurfer + Histogram
by Saurabh Thakur 11 Mar '14

11 Mar '14

Hello Freesurfer Expert, Can anyone help me with histogram plotting of different surfaces in tksurfer. I looking to calculate the thickness of cortex. Thanks in advance, Saurabh Thakur,

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Cortical thickness measuring algo
by Saurabh Thakur 11 Mar '14

11 Mar '14

Hello Freesurfer, Laplacian based method for measuring Cortical thickness Can u anyone help me to understand how freesurfer has implemented this algo and where to find this algo for better understanding. Thanks, Saurabh Thakur,

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applying Yeo atlas to individual brains
by Jeff Eriksen 10 Mar '14

10 Mar '14

Our lab has a need to apply the Yeo atlas to individual brains. As I understand it, Yeo atlas is only currently available for the FSAverage brain. Any plans to incorporate Yeo on to the default FS segmentation, or have it available as an option? -Jeff Eriksen

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Re: [Freesurfer] applying Yeo atlas to individual brains
by Gregory Kirk 10 Mar '14

10 Mar '14

problem with surf2surf is it deals with scalar fields ( data ) so don't think that will do it. problem with label2label is that it deals with a single label which has a diferent structure than anot. so a way to do it 1. mri_annotation2label ... to convert the yeo anotation file to individual labels 2. mri_label2label ... to map each label from the fsaverage space to the individual subject space 3. then the function that takes the labels on the individual subject space and makes a .annot of it in indiv. subject space. you will need to supply a colormap table to, don't remember the name ( google freesurfer make annotation file, or something like that) seems like a lot of work but just make a little script and you only need to figure it out once. if any problems i could dig in my notes, i did not find one function to map a .annot in 1one space to a .annot in another. gref On 03/10/14, Thomas Yeo wrote: > Hi Jeff, > > I am a little unsure myself since I usually work with data mapped to > fsaverage space. I think you might want to use mri_surf2surf, since > there's a "--sval-annot" option. It's hard for me to check now because > I am away at a conference. > > Can someone chime in if mri_surf2surf is wrong? > > Thanks, > Thomas > > > > > > On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen <eriksenj(a)ohsu.edu> wrote: > > What I need are the ?h.Yeo.annot files for the individual subjects, similar to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will mri_label2labe give me that directly? > > > > Thanks, > > -Jeff > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu](javascript:main.compose() > > Sent: Monday, March 10, 2014 9:50 AM > > To: Jeff Eriksen > > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > > Subject: Re: [Freesurfer] applying Yeo atlas to individual brains > > > > Hi Jeff > > > > you should be able to use mri_label2label to map the Yeo atlas from fsaverage to any subject. > > > > cheers > > Bruce > > On Mon, 10 Mar 2014, Jeff Eriksen wrote: > > > >> > >> Our lab has a need to apply the Yeo atlas to individual brains. As I > >> understand it, Yeo atlas is only currently available for the FSAverage > >> brain. Any plans to incorporate Yeo on to the default FS segmentation, > >> or have it available as an option? > >> > >> > >> > >> -Jeff Eriksen > >> > >> > >> > >> > >> > > > > > > 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 mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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vtk conversion
by LAOUCHEDI MAKHLOUF 10 Mar '14

10 Mar '14

Hi all i am developping an application for neuronavigation, and i want to use freesurfer cortical parcellation and sub-cortical segmentation, is there any freesurfer command to convert surface files to vtk files ? Thanks

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primary auditory cortex ROI
by Ritobrato Datta 10 Mar '14

10 Mar '14

Hi All, My email may have fallen through the cracks over the weekend so I am sending it again. I need to demarcate primary auditory cortex in a group of subjects anatomically and I came across the following papers - https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_a… https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf Is there a script that I can use on my 3T MPRAGE images to get primary auditory cortex ROI ? That will be very helpful. Best, Ri

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version 5.3 bug fix
by Gregory Kirk 10 Mar '14

10 Mar '14

In the release notes for 5.3 i find Stable release version 5.3.0 is a bug fix release to correct the problem with pial and white surface creation affecting thickness and area measures. Is this only related to netative thickness values, which i have never found. I have 150 subjects * 3 timepoints that i ran on a cluster with condor linux and freesurfer version 5.1 i myself inspected time point 1 and did analysis and did not find any unusual problems. i am preparing to do a longitudinal analysis of all 3 timepoints and wondering if i should reprocess and reinspect everything, considering the bug fix and improvements for longitudinal stream. thanks greg

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Looking for cortical thickness procedure
by Saurabh Thakur 10 Mar '14

10 Mar '14

Hello freesurfer Expert, Steps for measuring cortical thickness are in tkmedit : 1. Intensity normalisation, 2. Registration to Talairach space, 3. Skull stripping, 4. Segmentation of white matter, 5. *Tesselation of the WM boundary, * 6. *Smoothing of the tesselated surface and automatic topology correction* Can u help me to step no 5 and 6. How to do this steps. Thanks, Saurabh Thakur,

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fix this error in segmentation
by charujing123 09 Mar '14

09 Mar '14

Hi all, How to fix this problem in segmentation, which can be got in the attachment? Thanks.All the best. Rujing Zha 2014-03-08 charujing123

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cannot sign white matter area by control point and white matter edit
by charujing123 08 Mar '14

08 Mar '14

Hi all. In troubleshooting, I want to sign some area as white matter by control point and wm edit. However neither of them can work. Thanks. the picture can be got in the attachment. All the best. Rujing Zha 2014-03-04 charujing123

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