Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

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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Bad pial surface - continued
by Ed Gronenschild 10 May '10

10 May '10

Hi, I've mailed this once before and tried to solve a persistent problem. Reviewing the results of recon-all I noticed that the derived pial surface chopped away an unacceptable amount of gm voxels. First of all I tried to manually edit some wm voxels, however with no success. Then I tried another solution by combining the FSL-FAST wm segmentation with wm.mgz because I noticed that FSL_FAST produced better results. Although the results did improve, still the pial surface was incorrect. The last option I tried was another set of parameters for nu_correct. Because it concerns 3T scans I used --proto-iters1000 and --distance 50 (see paper of Zheng et al, NeuroImage 48, 73-83 (2009)) and previous e-mails on this subject ("nu-correct parameters", 27 April 2010). Also with these settings the pial surface chopped away too many voxels. I'm desperate, the manuals provide no options on how to fix such problems. The pial surface can be corrected by only REMOVING voxels that are included erroneously but there is no way to extent the pial surface by ADDING voxels. Ed

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Talairach failure
by Antoine Leflon 10 May '10

10 May '10

My files are dicoms and have no extension in the end of their name (IM_0465 for example) . Is it possible to change the format ? thanks , Antoine ________________________________________________________________________________ Talairach is about orientation. What is the format of your file? If it is .hdr and.img, it will fail. On 4 May 2010 11:43, Antoine Leflon <antoine1.leflon(a)etudiant.univ-lille1.fr> wrote: Hi all , I've used data from another Doctor , freesurfer told me the FOV was 330 so I put the flag -cw256 in the command recon-all but the Talairach just failed ... I got this error message . Can someone explain please ? ________________________________________________________________________________ #@# Talairach Failure Detection Tue May 4 12:31:55 IST 2010 /home/cami/freesurfer/subjects/a1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Tue May 4 12:31:55 IST 2010 ________________________________________________________________________________ thanks , Antoine _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Freesurfer May 2010