Freesurfer

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30089 discussions

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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global and hemispherical average GI
by Ambrosino di Bruttopilo-2, S. 22 Oct '12

22 Oct '12

Dear FreeSurfer experts, I am using FS 5.1 to measure local Gyrification index (lGI). I would need to know if and how is possible to calculate the average GI for each hemisphere and for the total cortex...given the local values, is there any formula to compute the hemisperical and global GI? Thanks for any help Sara ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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relationship between cortical volume, cortical area and cortical thickness
by L. Koenders 22 Oct '12

22 Oct '12

Dear Freesurfer people, 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? Kind regards, Marise Machielsen & Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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Re: [Freesurfer] local GI calculation Error
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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