Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

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Extract a color table from an annotation
by Anisha Keshavan 23 Oct '12

23 Oct '12

How do I extract a color table from an annotation? Thanks, Anisha

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Running gcut fails to create brainmask.gcuts.mgz
by Vincent 23 Oct '12

23 Oct '12

I'm attempting to remove some dura which is affecting my surfaces, but upon completion of running gcut I can see no differences in my images, nor can I use tkmedit to view my T1 with brainmask.gcuts.mgz, because it says it "couldn't import the segmentation volume". I looked for brainmask.gcuts.mgz but using ls recursively and grepping for it, but I can't find it anywhere. What explanations might there be for this? Thank you in advance. ::vincent

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Dealing with MS lesions
by Julio Alberto González Torre 23 Oct '12

23 Oct '12

Hi. My question is about dealing with multiple sclerosis lesions in white matter. I have previously worked with this sample in SPM8, and I have a binary mask for each subject with the white matter lesions marked. Instead of painting manually each lesion with the freesurfer interface, could I provide to the freesurfer the T1 images with the lesions painted with another program? (exactly, with the IMcalc of SPM, to set lesion values of each T1 image to a standard WM value according to the binary mask). Is this procedure correct? What value should I provide to this lesions? Thanks.

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MEMPRAGE
by Gina Caetano 23 Oct '12

23 Oct '12

Dear FreeSurfers, I am processing MEMPRAGE images: 1) I use the RMS (of the echoes) output from the scanner 2) the echoes were converted to mgz format [memprage_echo1(to4).mgz], conformed to 256³ , 1mm isotropic, and no further processing. 3) I ran the mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh, and got new files as output (?h.white_addedname, ?h.pial_addedname etc) However, I expected to have more of the dura discarded from the ?h.pial boundaries as what I am getting May I be missing something in the processing of this type of images? How can I improve the output? Thank you in advance, Gina

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trac-all -prep error during inter-subject registration with mri_cvs_register
by Verena Gramse 23 Oct '12

23 Oct '12

________________________________ From: Verena Gramse Sent: Monday, October 22, 2012 8:19 PM To: freesurfer(a)nmr.mgh.harvard Subject: trac-all -prep error during inter-subject registration with mri_cvs_register Dear Tracula Team, I have been running into problems during Inter-subject registration at the mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But norm.mgz exists at the specified location and it can be opened with freeview without problems. Did I oversee anything? Thanks in advance! Verena Find attached my dmrirc and the error.log

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relationship between cortical volume, cortical area and cortical thickness
by L. Koenders 23 Oct '12

23 Oct '12

Dear Freesurfer people, We posted this question before, but maybe you missed it. We have a question regarding the relationship between cortical volume, cortical area and cortical thickness measurements derived from the parcellation stat-file. We were under the impression that the volume is equal to the area*thickness. However, this is not the case. Can you tell us how these three measurements relate to each other? Thanks for your help! Kind regards, Marise Machielsen & Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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AAL labels
by MCLAREN, Donald 23 Oct '12

23 Oct '12

Has anyone created an AAL label file for Freesurfer? I've done some ROI analysis using AAL regions and want to display regional values on the freesurfer surface. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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mri_ca_register_cuda error
by Chris Adamson 22 Oct '12

22 Oct '12

I downloaded the mri_ca_register_cuda binary from the ftp site ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86… I'm not sure whether this is an unstable version or not but when I use it the subsequent inversion step does not work: I'm happy to send the m3z file if you wish to debug it. mri_ca_register -invert-and-save transforms/talairach.m3z MatrixAsciiReadFrom: could not scanf parms Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Segmentation fault (core dumped) -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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coordinate transform
by octavian lie 22 Oct '12

22 Oct '12

Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file (see attached) in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie.

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rerunning FS data with FS 5.1.0
by Judit Haász 22 Oct '12

22 Oct '12

Dear FreeSurfer developers, We are planning to rerun previously processed data (3 waves) with the newest FS version from scratch. We have some questions before starting the pipeline. 1) to keep white matter edits is it enough to copy tmp/control.dat file or we need to copy the complete FS tree to subj folders? 2) when is version 5.2 coming out? (should we wait?) Thank you Regards Judit Haasz

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Freesurfer October 2012