Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Label two volume conversion
by Martin Kavec 13 May '10

13 May '10

Hi, using tksurfer, I have created labels corresponding to significantly thinner cortex between two groups of my subjects. After that I converted the labels to volumes (mri_label2vol), which I would like to use for further analysis. However, the volumes cover only the interface between gray and white matter, while I would need the entire cortex. Is there any way to achieve this? Thanks in advance, Martin

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Re: [Freesurfer] Number of Voxels different between wmparc.mgz and wmparc.stats
by Sita Kakunoori 12 May '10

12 May '10

Hi Christopher, the values in wmparc.stats are computed with partial volume correction. Sita. On Wed, 12 May 2010, Christopher Coello wrote: > Hello, > > > > After segmenting using recon-all all, I want to look at how much voxels > there is in each segmented structure. > > I did the following procedure : I opened the wmparc.mgz volume with 3DSlicer > as a label volume and computed the LabelStatistics. > > For the label 1005 (ctx-lh-cuneus), the count value is 3133. But in the > wmparc.stats, the numVox in front of the label 1005 is 2729. This difference > exists for many of the segmented structures. > > To double check, I also opened the wmparc.mgz with Matlab to count the > number of voxels labeled 1005 in the volume, and I do find 3133. > > Am I comparing 2 different values ? Or is there a bug in the writing of the > wmparc.stats ? > > > > Best regards, > > > > Christopher Coello, > > Postdoctoral Research Fellow > > Center for Diagnostic Imaging, > > Akershus University Hospital, > > Sykehusveien 25, 1478 Lørenskøg > > tel : +4745154516 > > e-mail : christopher.coello(a)medisin.uio.no > > > >

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talairach
by Tina Jeon 12 May '10

12 May '10

Hello freesurfer team, I am trying to run tkregister2 and I come up with this error message : No glx extension! register: ### tkoInitWindow(name) failed Any idea on what this could be from? Previously this command had worked. Thanks, Tina Jeon

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MRS mask
by Lena Palaniyappan 12 May '10

12 May '10

Hi Bruce and team I have a ROI mask in analyze (img_hdr) format obtained from MR spectroscopic group analysis using a different registration (talairach based). I want to use this ROI as a label to extract thickness measures on a group of subjects. How can I do this? If I use mri_vol2surf will I be not projecting contrasts from a differently registered image set onto reconstructed freesurfer anatomical? 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 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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Number of Voxels different between wmparc.mgz and wmparc.stats
by Christopher Coello 12 May '10

12 May '10

Hello, After segmenting using recon-all all, I want to look at how much voxels there is in each segmented structure. I did the following procedure : I opened the wmparc.mgz volume with 3DSlicer as a label volume and computed the LabelStatistics. For the label 1005 (ctx-lh-cuneus), the count value is 3133. But in the wmparc.stats, the numVox in front of the label 1005 is 2729. This difference exists for many of the segmented structures. To double check, I also opened the wmparc.mgz with Matlab to count the number of voxels labeled 1005 in the volume, and I do find 3133. Am I comparing 2 different values ? Or is there a bug in the writing of the wmparc.stats ? Best regards, Christopher Coello, Postdoctoral Research Fellow Center for Diagnostic Imaging, Akershus University Hospital, Sykehusveien 25, 1478 Lørenskøg tel : +4745154516 e-mail : christopher.coello(a)medisin.uio.no

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Buried sulci problem and freesurfer
by Lena Palaniyappan 12 May '10

12 May '10

I recently came across Chloe Hutton¹s buried (or closed sulci) problem discussed here Hutton, C., De Vita, E., Ashburner, J., Deichmann, R., & Turner, R. (2008). Voxel-based cortical thickness measurements in MRI. NeuroImage, 40(4), 1701-1710. doi:10.1016/j.neuroimage.2008.01.027 How well does freesurfer handle this issue I am using freesurfer to compute gyrification values: this is a major issue any help will be appreciated 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 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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Tadeu Takao Almodovar Kubo has invited you to Dropbox
by Dropbox 11 May '10

11 May '10

We're excited to let you know that Tadeu Takao Almodovar Kubo has invited you to Dropbox! Tadeu Takao Almodovar Kubo has been using Dropbox to sync and share files online and across computers, and thought you might want it too. Visit http://www.dropbox.com/link/20.dR8lfOqJiy/NjE3MTczNDAyNw to get started. - The Dropbox Team ____________________________________________________ To stop receiving invites from Dropbox, please go to http://www.dropbox.com/bl/0bbe861e473f/freesurfer%40nmr.mgh.harvard.edu

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Contrast Problem
by Andrés Camarena 11 May '10

11 May '10

I am having an issue where the sig.nii file created after running mkanalysis and slxavg sets the value in a high contrast region to zero. Any idea what could be the problem. I've attached an image of the problem. -- Department of Aeronautics and Astronautics Massachusetts Institute of Technology Class of 2010

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after mri_glmfit whats next
by Samantha Clark 11 May '10

11 May '10

Hi Doug, I did the first level analysis for my DTI data per the tutorial mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir Not sure how to proceed from here to view the regions that are statistically signifiant. Can you help? Thanks Samantha

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QDEC discrete covariate question
by Dominic Brendon Dwyer 11 May '10

11 May '10

Hi all, We're using QDEC DODS to compare the average thickness maps of patients V. controls using sex and age as covariates. The results are identical for "Does the average thickness differ between patientsVscontrols with sex and age as covariates" and "Does the average thickness differ between sex with patientsVscontrols and age as covariates". This doesn't seem to make sense (with my limited statistical knowledge) because the criterion variable has changed. Also it is not the case that the groups contain only one sex. Could anyone shed light on this? Also, we tried to check the contrasts but weren't able to find the categories for each of the columns in the vector. Where can this be found? Thanks very much in advance, Dominic Melbourne Neuropsychiatry Centre

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