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30132 discussions

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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converting to MNI152 space
by Govindarajan, Koushik Athreya 22 Oct '12

22 Oct '12

Hello group, This may be just a naive question, I tried finding answers in the archives but did not get a straight forward way to do it. So, I need the aseg and aparc files in fsaverage in the MNI152 space (181x217x181) so that it can be compared with data processed elsewhere. Is there an easy way to do this? Thanks Koushik

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Surface recognition. Should I do it by hand?
by o BCC 22 Oct '12

22 Oct '12

Hi, I've just started using Freesurfer, and after running pre-processing steps with recon-all, some of my images have errors recognizing pial and WM surfaces. Specifically, the most frequent problem is that pial and WM surfaces enclose part of the skull (which has not been removed very well). Please find attached two images with examples of what I say. If you cannot see them as an attachment, they're also available at: http://s5.postimage.org/os3auap5z/C801.png http://s5.postimage.org/5oekrp1pj/A202.png It seems like a skull stripping problem; some commands I've implemented to try to fix it are based on re-introducing the coordinates of brain centers by hand: mri_watershed -atlas -c [i j k] T1.mgz brainmask.auto.mgz cp brainmask.auto.mgz brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid [subject_name] or: mri_watershed -atlas -c [i j k] nu.mgz brainmask.auto.mgz mri_normalize -g 1 brainmask.auto.mgz T1.mgz cp T1.mgz brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid [subject_name] (They're, of course, addressed to the right directories.) The first set of commands has worked fine for a minority of all my images. Nonetheless, there are plenty of subjects for whom neither of these scripts have gone well. Should I solve it by manually adjusting pial/WM surfaces? Or... do you have any idea on how to automatically solve it? (New scripts are welcome! :D ) Thanks in advance, Aldo

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TKMedit editing aux. volume - can't remove voxels from volume
by Rosa Lafer-Sousa 22 Oct '12

22 Oct '12

Hi, I'm having a problem with editing an auxiliary volume in TKMedit. I set my brush info such that I am editing the auxillary volume. I configured my brush settings so that button 2 assigns a new value greater than 0 (to "add" voxels) and button 3 assigns a new value of 0 (to "remove" voxels). With these settings I am able to add voxels, but not remove them (that is, I can't reassign a value of 1 to 0). Do you have any advice on fixing this problem? Thanks, Rosa -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlaferso(a)wellesley.edu

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mris_topo_fixer -mgz -warnings -seed 1234
by Anne Uhlmann 22 Oct '12

22 Oct '12

Hi there, I am having trouble with one of my scans where the right hemisphere is not getting included in the analysis from the "Fix Topology rh" point on. This is the error message I get: Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all PWD /lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/MAS112.12.1107.5.2/scripts CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh The orig.mgz looks OKish (it's not great) except for some kind of a scanner artifact in 2 slices of the scan. I tried to fix it with control points and making edits to the white matter, but unfortunately it didn't solve the problem. I am grateful for any suggestions. Thank you and best regards, Anne ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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