Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Ridiculous story about Freesurfer
by Andrew Dumas 18 Jun '12

18 Jun '12

Did anyone else happen to see this ridiculous story on Gizmodo today? http://gizmodo.com/5919149/your-brain-scan-looks-different-on-mac-and-pc It cites the recent article "The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements" as its only source, and then goes on to completely misinterpret it. This sentence (if I had to pick one) is particularly troubling to me: "The finding is completely crazy, and casts doubt over the way many scans—such as CT and MRI—are analyzed in routine practice." Crazy, right? Enjoy... Andrew

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mri_cnr
by Kushal Kapse 18 Jun '12

18 Jun '12

hi fellas, i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf.... the command gives following info as help: -bash-3.2$ mri_cnr usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ... -s <slope fname> <dist in> <dist out> <step in> <step out> i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname......it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command..... i checked on freesurfer mail archive, but no info since 2009 about any update on this command..... may someone please give an info if anyone ever used this command thanks kk

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memory allocation error with mris_register for one subject
by Arno Klein 18 Jun '12

18 Jun '12

hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno

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Cannot access "Apply" button in Configure Overlay Display dialog
by Vadim Axel 18 Jun '12

18 Jun '12

Dear developers/users, This is completely ridiculous known issue on a low resolution monitor :( Presumably, it was solved here: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer, but the file is inaccessible via ftp. Any other workaround? All I need is to change Min statistic threshold and hit apply button. Probably, something via command line? Unfortunately, there are no hot-keys and it is impossible to reach with a tab because the non-visible dialog elements presumable do not exist (tab goes to the top of the dialog after the last visible dialog element). I am using Ubuntu virtual box FS 5.1. Thanks a lot, Vadim

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.license file
by Monica Giraldo 18 Jun '12

18 Jun '12

Hello, I created a file with this data, but when I'm going to save it as .license doesnt let me because a message appears and says that files starting with . are of the system and that i have to choose another name. What can I do? Thanks. Mónica Giraldo Chica PhD. Candidate Biomedicine Sherman Health Science Research Centre www.monicagiraldochica.com

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Flipped and non-flipped data
by Schur, Remmelt R. 18 Jun '12

18 Jun '12

Dear Freesurfers, Grey matter volumes of the same structure seem to be measured differently depending on if FreeSurfer establishes it as in the left or in the right hemisphere. For example, if I take a look at the caudal anterior cingulate in the right hemisphere and I flip the image (creating a mirror image of the same hemisphere, which will then be treated by FreeSurfer as a left hemisphere), the same structure has a totally different grey matter volume (see attachment, on the right the original and on the left the flipped version). Does anybody know what's the logic behind this and what's the best way to avoid FreeSurfer creating asymmetry between left and right hemisphere (maybe averaging flipped and non-flipped data?) Thanks! Kind regards, Remmelt Schür IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Use of separate manual segmentation for hippocampus formation
by Dhinakaran Chinappen 17 Jun '12

17 Jun '12

Hi Freesurfer Experts and Advisors, Would it be possible to use different manually segmented images (of the hippocampus formation only) as a-priori maps and then use Freesurfer to automatically segment the hippocampus formation only, based on the furnished manually segmented images? This would be relevant if the hippcampus formation needed to be automatically segmented for subjects over an age range, whereby those different manually segmented images would also be over an age range. Thanks, Dhinakaran.

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Rejoindre mon réseau sur LinkedIn
by Luisa Leo via LinkedIn 17 Jun '12

17 Jun '12

LinkedIn ------------ Luisa Leo a indiqué que vous êtes un(e) ami(e) ------------------------------------------ Vorrei aggiungerti alla mia rete professionale. - Luisa Leo Accepter l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h3jz1ttz-53/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h3jz1ttz-53/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Luisa Leo ? Le réseau de Luisa Leo développera votre propre réseau : Si vous acceptez l'invitation de Luisa Leo, vous pourrez voir qui vous connaissez dans son réseau et demander à Luisa Leo de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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mri_register memory error
by Shantanu Ghosh 15 Jun '12

15 Jun '12

Hi Freesurfer experts, I am receiving an error message while processing registration to fsaverage using mri_register. Please tell me why it is happening and how to get this going. Here is the terminal output: glia:shantanu[219] mri_register /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/AC058/mri/brainmask.mgz /autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz AC058.reg.mgz reading 1 input volumes... logging results to AC058.reg.log reading input volume '/autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/AC058/mri/brainmask.mgz'... reading GCA '/autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz'... gcaAllocMax: node dims 15 15 15 gcaAllocMax: prior dims 15 15 15 gcaAllocMax: max_labels 0 GCAread(/autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz): could not allocate -136441340 labels @ (0,0,0) Cannot allocate memory Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

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Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]
by Priti Srinivasan 15 Jun '12

15 Jun '12

Hi XJ, I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out? When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that. Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question. Hope that helps, Priti > > ---------------------------- Original Message ---------------------------- > Subject: Re: [Freesurfer] TRACULA dpath problem > From: "XJ Kang" <xkang(a)ucdavis.edu> > Date: Fri, June 15, 2012 2:22 pm > To: "Priti Srinivasan" <rspriti(a)nmr.mgh.harvard.edu> > -------------------------------------------------------------------------- > > Hi Priti, > > Attached are the tracula conf file and log files from two subjects. > > I ran the two subjects. The results are almost the same. Here are what I > found so far: > > 1. There are NaN values in the 4D image. I created it from 3D images > using "fslmerge -a", and the 3G images have no NaNs. > 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably > this is the origin of all the problems? > > Do you want me to send the email to you or to the mailing list? Probably > many people are not interested in my email if I post on the whole list. > > Thank you. > > XJ > > On 6/15/2012 11:02 AM, Priti Srinivasan wrote: >> Can you send us your configuration file (mytracula.conf) and log file >> (it >> should be under scripts/trac-all.log). I can take a look. >> >> Priti >> >>> Hi, >>> >>> I am trying to run the last step of TRACULA. I used the command line: >>> >>> % trac-all -path -c mytracula.conf >>> >>> Here is all the info I got on the screen: >>> >>> INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio >>> INFO: Diffusion root is /home/xkang/DTI/ >>> Actual FREESURFER_HOME /home/local/freesurfer-v510 >>> trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log >>> /home/xkang/DTI//S0006/scripts/trac-all.log -cmd >>> /home/xkang/DTI//S0006/scripts/trac-all.cmd >>> #------------------------------------- >>> /usr/local/freesurfer/bin/trac-paths >>> #------------------------------------- >>> #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 >>> #------------------------------------- >>> trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012 >>> >>> >>> >>> I didn't see "dpath" under the subject's directory. Seems nothing has >>> been done. I already ran the "trac-all -prep" and "trac-all -bedp". I >>> have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can >>> any body help where the problems are? >>> >>> I use DTI images in NIFTI format and the resolution is 2x2x2, which is >>> not the same as that of the FreeSurfer orig.mgz. Probably this is fine. >>> >>> Thanks. >>> >>> XJ Kang >>> _______________________________________________ >>> 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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