Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Coordinate Question
by Ishan Patel 08 Oct '15

08 Oct '15

Hello, When I create a label file, it looks something like this: #!ascii label , from subject ECoG7_Output vox2ras=TkReg coords=white 111 1062 -19.007 -81.861 3.862 0.0000000000 3917 -29.743 -75.417 2.343 0.0000000000 6599 -37.731 -70.574 6.918 0.0000000000 9428 -44.497 -65.013 8.765 0.0000000000 Is there any way I can convert from the above coordinate system to Talariach normalized? Thanks!

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wm.mgz ventricle white matter problem
by Anastasia Klimovich-Smith 08 Oct '15

08 Oct '15

Dear freesurfer experts, I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). Sometimes the ventricles are not fully filled and the white matter is localized within the remaining gaps. After manually filling the gaps in the wm.mgz (following the wiki - Fixing Common Geometric Inaccuracies in White Matter Surfaces) and rerunning (-autorecon2-wm) I still have the wm surface following the ventricle holes, even though I can see they are filled on wm.mgz. I used freesurfer v.5.1.0 before and didn't have these issues. How would you recommend fixing this? Thanks a lot, Ana

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Cortical Parcellation Atlas Question
by Yun Wang 08 Oct '15

08 Oct '15

Hi All, I am currently doing resting state fMRI functional connectivity across the cortical. Is it appropriate that I use Freesurfer cortical Parcellation altas such as Desikan-Killany Atlas to extract time series? Thanks! Yun

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tilted head
by Thục Trinh 08 Oct '15

08 Oct '15

Hi Freesurfer Experts, We are on the process of troubleshooting on all of our subjects and come across with the problem that we have not faced before. Here it is: We have several subjects that their heads were not in a perfectly straight line captured by using MRI. Does that affect to the segmentation of a recon, and more importantly somehow carry out some statistical values for further analysis (volume, cortical thickness)? As you can see, Axial view shows the head being tilted to the right. Sagital_lh and Sagital_rh images show how the white matter and gray matter segmentation are being bounded on the same slice 130 but in different hemisphere. Do we need to do something about it? If yes, how are we going to fix it? We are greatly appreciated to your patience and hopefully to get your response as soon as possible. Trinh

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VirtualBox Block
by Maya De Belder 08 Oct '15

08 Oct '15

Hi, I’m stuck with the following problem: I can’t start up the VirtualBox for Freesurfer5.3 because of a memory problem. I put 12GB of patient data on the disk en ran two subjects successfully through Freesurfer. However, I closed the VirtualBox and don’t seem to be able to restart it. My question is: - Is there a way to get around this? Is there a possibility to increase de memory size? - How much data is constructed by Freesurferprocesses when you run an MPRAGE through the processes? - Assume I don’t mind re-running those two subjects and will completely re-install the Virtualbox: is there a possibility to increase the disk size? - The data I have for 1 single patient will always be +- 500 MB, my study contains over 100 subjects. Is there a way to run the analysis in Virtualbox that way, or is an alternative suggested? Thanks in advance for the feedback, Maya De Belder PhD Student Ghent University Department of Experimental Psychology Henri Dunantlaan 2 B-9000 Ghent, Belgium +32 9 264 64 03

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error in qdec
by chenhf_uestc 08 Oct '15

08 Oct '15

Dear Freesurfer experts, I used qdec for group comparison, but there is error (acctached error.png). I check all the files but do not find where is the erros. Could anyone give me some suggestions? Best, Feng

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mri_glmfit dev
by Dídac Vidal 07 Oct '15

07 Oct '15

Hi Freesurfers! I am using development version of mri_glmfit (as I want to take advantadge of --frame-mask option). As control analysis I performed an identical (simple) analysis both in mri_glmfit and its dev version. Suprisingly, while F.nii.gz were identical for the given contrast sig.nii.gz map differed betweem both versions. If possible (and If I am not doing anything wrong), I'd like to know the reason why they differ and also which one I should stick with. Thank you in advance -- Dídac Vidal Piñeiro

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extract time series from surface vertices
by Yun Wang 07 Oct '15

07 Oct '15

Hi All, If I use mri_vol2surf to sample the functional volume onto surface, how can I extract the time series from surface vertices corresponding to certain ROI or Label which were created by freesurfer. Thanks! Yun

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Query about the calculation of surface area
by chenhf_uestc 07 Oct '15

07 Oct '15

Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki. Best, Feng

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Individual regions of CorticalParcellation_Yeo2011
by Yi-Chia Erica Kung 07 Oct '15

07 Oct '15

Dear Prof. Yeo, I would like to extract the brain regions of the functional canonical network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have provided the split regions of 7&17 Network in previous discussion string. (https://www.mail-archive.com/freesurfer %40nmr.mgh.harvard.edu/msg41288.html ) However, the dropbox download link you offered has expired. Would you mind uploading it again? Thank you very much. Erica

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