Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

Getmatlab
by Lena Palaniyappan 02 Jan '11

02 Jan '11

I have MATLABR2010b, on a Mac 10.6.4, using freesurfer 5.0 I am not able to getmatlab when I invoke freesurfer Can someone help? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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.

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merging average cortical thickness data
by tina roostaei 02 Jan '11

02 Jan '11

Dear all, I have access to a dataset of freesurfer segmentation products (i.e. cortical volume, surface area, cortical thickness average and standard deviation) for a number of patients. I wanted to merge the data of some segmented parts (e.g. to compute a general cortical thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data). I wanted to know if it is right to compute the average cortical thickness using the following formula: Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + (part 2 cortical thickness*part 2 surface area) + …]/ (part 1 surface area + part 2 surface area + …) BTW, I also checked whether the cortical volume equals ‘surface area*average cortical thickness’, to see if I could use the following formula instead: Average cortical thickness= (part 1 cortical volume + part 2 cortical volume + …)/ (part 1 surface area + part 2 surface area + …) But it simply proved wrong. Any suggestion is greatly appreciated. Thanks in advance. Tina

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QA on wmparc.mgz
by Jeff Sadino 02 Jan '11

02 Jan '11

Hello, I am trying to verify the wmparc.mgz segmentations. I have identified outlier regions statistically, but then when I load up the wmparc.mgz file to QA visually, I find it is very difficult to QA the white matter regions. The problem is that because there is no contrast in the white matter, it is difficult to decide where one region ends and another one begins. I would like to ask if anybody has any suggestions as to a better way to visually verify the wmparc.mgz file. Thank you, Jeff

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Subtracting thickness maps
by Lena Palaniyappan 02 Jan '11

02 Jan '11

I have two groups - in each of the groups I have studied the relationship between a variable of interest and thickness. I want to show a subtraction between the two thickness correlation maps to highlight the regions with differing relationships with the variable in the two groups. In other words, I want to generate a single image on an average surface, that shows the regional differences between the correlated thickness maps. Is this feasible? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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.

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Alignment of non whole-brain functional slabs
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am working towards multi-modal integration of BOLD data. For some of my data, the entire brain was not recorded (in this case, I have 12 slices covering the superior half of the brain). I have been working to align this data using bbregister and have had very inconsistent results: in 1 subject it worked great; in another 6, the alignment failed (resulting in an alignment that is sometimes close, and sometimes way off). I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I have used this method successfully with a number of other sessions so far (with functional slabs that do cover the entire brain) with outstanding results. Is this troublesome for bbregister, or is there potentially something I'm doing incorrectly? Thanks in advance! If I'm repeating well-worn topics, I apologize, I couldn't find anything following a search through the archives. Joakim

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trgicoorder flag in mri_surf2surf
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am interested in doing sub-sampling of functional data for some new analyses. Just about the only reference I can find to sub-sampling of data in FreeSurfer is in mri_surf2surf, which has an optional flag trgicoorder. The comment for this flag is: "This specifies the size of the icosahedron according to the formula #vertices=10*4^n+2. In general, it is best to use the largest size available." It would seem that I might be able to use this flag in order to sub-sample surface data by using a smaller n (it seems as if the default for fsaverage is 7 according to the specified formula). Is this correct? Are there any particular guidelines to n? Other surfaces have a variety of vertices, so it seems that n does not have to be an integer? If I computer a surface of functional data for a given subject with a specific 'n' and resulting nVertices, should I also calculate an according anatomical surface with the same number of vertices for display and analysis? Thanks! Joakim

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matlab loading problem (mkcontrast, selxavg3-sess)
by Katherine Sledge Moore 02 Jan '11

02 Jan '11

I am having trouble with the interface between freesurfer and matlab. When I run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the script does not finish.) When I force it to quit, I get the error "-display: Command not found." In both mkcontrast and selxavg3-sess, the command to call matlab is something along the lines of "matlab -display iconic". Any thoughts as to why the "-display iconic" part is not being interpreted? Katherine Sledge Moore Postdoctoral Associate Visual Cognitive Neuroscience Laboratory Yale University http://camplab.psych.yale.edu/ http://pantheon.yale.edu/~khs8

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the usage of mri_surf2vol program
by qizhu wu 02 Jan '11

02 Jan '11

Dear all, Continue with my previous question in "To use the file thickness.mgh outside Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to convert mgh files into image format, such as NIFTI. But I failed due to wrong setting on several arguments: 1, '--volreg': I do not understand what file it requires. It's declared in --help that "Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume". But I am only dealing with the structural volumes, and has this file been created in any step during the previous processing? Or could anyone tell me clearly how to set this argument? 2, --surfval: if only pthname rather than single file is allowed as input here? 3, --template: couldI use mni305.cor.mgz, or just left these optional arguments empty? thanks in advance. Qizhu Wu

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Covariates in Qdec
by Gallen, Courtney (NIH/NIDA) [F] 30 Dec '10

30 Dec '10

Hi, I'm running an analysis in Qdec in which I'd like to control for 3 variables (1 discrete (sex), 2 continuous (age and IQ)). In the output after I run the model: I only see a reference to an effect of my factor of interest controlling for sex (i.e., there is no contrast that also explicitly says controlling for sex, age, and IQ). Is this implied? Or are age and IQ not controlled for here? Is there a way to specify that I'd like to look for an effect controlling for all 3 variables? Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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Re: [Freesurfer] inter vertex distance
by YUMI MAEDA 29 Dec '10

29 Dec '10

Yes, I will ask him more information. yumi > did Rudolpha's answer work for you? > On Wed, 29 Dec 2010, YUMI MAEDA wrote: > >> Bruce, >> I meant the distance of 2 nodes along the surface. >> >> YUMI >> >> >>> do you mean on along the surface or in the volume? >>> On Mon, 27 Dec 2010, YUMI >>> MAEDA wrote: >>> >>>> HI, >>>> >>>> I am wondering if there is a way to calculate inter vertex distance on >>>> fsaverage surface with freesurfer. thanks for your help. >>>> >>>> YUMI >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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Freesurfer December 2010