Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

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

1 0

error finding data on bourget
by qtnguyen＠nmr.mgh.harvard.edu 19 Oct '12

19 Oct '12

Dear Freesurfer experts, I'm trying to run structural reconstruction for two subjects DODASD016 and DODASD017. DODASD016 was scanned last Wed Oct 10 and last week I was able to findsession DODASD016, run dcmdir-info-mgh, and run recon-all using pbsubmit. However, after this was done I was unable to unpack the Bold & DTI Data from Bourget. We believe that the recon-all didn't work and when we tried to re-run: (for DODASD016) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 (and for DODASD017) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 ...I got the error message "ERROR: finding data" Can you help me resolve this issue? Or can you direct me to someone who can help? Thank you! Trang

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local GI calculation Error
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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withe matter of cortical Lables
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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Freesurfer October 2012