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30132 discussions

Fwd: gray matter/csf surface reconstruction
by Shani Ben Amitay 30 Oct '11

30 Oct '11

Hi , I have a diffusion weighted dataset and I would like to perform an analysis along the cortical normals. Any advice will be appreciated Thanks, shani On Sun, Oct 23, 2011 at 5:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Shani > > we described in in the recon1 NeuroImage paper (1999) and the PNAS paper, I > think the next year. We don't impose any constrains on the pial surface as > it evolves from the white surface (e.g. "link" terms in the energy > functional), but let the vertices move whereever they want to in order to > find an image intensity that is what we estimate the gray/csf boundary to be > in that region. > > Can you tell us a bit about what you want to do with the normals? We > typically don't use them for sampling of hires data for example, but rather > use mris_expand to generate a series of intermediate surfaces. > > > cheers > Bruce > > > > On Sun, 23 Oct 2011, Shani Ben Amitay wrote: > > Dear freesurfers, >> In order to generate cortical vector normals connecting homologous >> vertices >> of the inner and outer surface, I would like to better understand how the >> gray matter/csf surface is reconstructed and how correspondence between >> inner and outer surfaces is achieved. >> >> Does anyone can explain or give a reference? >> >> Thanks , >> Shani >> >> >> >> >> >> > > 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<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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Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?
by Joshua Lee 30 Oct '11

30 Oct '11

I think I may have found it as a public ami with freesurfer 5.1. Testing it out on Bert right now. Thanks!! - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/10/30 Joshua Lee <jkilee(a)ucdavis.edu> > I think I may have found it as a public ami with freesurfer 5.1. Testing > it out on Bert right now. Thanks!! > - > Joshua Lee > > > > 2011/10/28 Joshua Lee <jkilee(a)ucdavis.edu> > >> Thanks Pedro, that's fantastic! I'm still getting used to the ec2 thing. >> Is there a password Ill need for root access? >> Thanks, >> >> Josh >> - >> Joshua Lee >> Graduate Student >> Center for Mind and Brain & >> Department of Psychology >> University of California, Davis >> 530.747.3805 >> >> >> >> 2011/10/28 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br >> > >> >>> I have one. I'll give you the link >>> >>> -- iOS 5.0 >>> >>> Em 28/10/2011, às 20:52, Joshua Lee <jkilee(a)ucdavis.edu> escreveu: >>> >>> Are there any existing Amazon EC2 AMI registered publicly that can be >>> used? I want to analyze a lot of data fast. >>> >>> Thanks, >>> - >>> Joshua Lee >>> >>> _______________________________________________ >>> 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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sub-cortical group analysis
by xian zhang 29 Oct '11

29 Oct '11

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is very helpful. However, is there any equivalent page detail how to: do group analysis view significant map alpha sim export table ? Appreciate your help.

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Bad vertex in mris_flatten
by Oya, Hiroyuki (UI Health Care) 28 Oct '11

28 Oct '11

Dear sir, Mris_flatten could not be completed due to the fact that only one bad vertex was found in the patch. Is there any quick way to correct the vertex? Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?
by Joshua Lee 28 Oct '11

28 Oct '11

Are there any existing Amazon EC2 AMI registered publicly that can be used? I want to analyze a lot of data fast. Thanks, - Joshua Lee

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TRACULA: how to implement DTI repeat sequence?
by Ansgar Furst 28 Oct '11

28 Oct '11

Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ================================================================== * 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001) set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/ set dcmlist = (Diff001/orig/6-1.dcm) ===================================================================== Oh also, I noticed that in the wiki you have the following settings: ======================================================================= set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt =============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use: "subj,train,difftutorial33.txt" pointing to /usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033 Does that make sense? Thanks so much for your help! Ansgar

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Do cerebellum, pons, and brain stem need to be in input MRI?
by Andreas Schuh 28 Oct '11

28 Oct '11

Hi FreeSurfers, I just processed a dataset using FreeSurfer (the base created from the norm.mgz volumes of a longitudinal study) and noticed that the labels for the cerebellum are causing an incorrect segmentation towards the inferior of the cortex. Further, labels for cerebellum, brain stem and the fourth ventricle can be found outside the brain mask (see attached screenshot). Note that input was not a full head scan, but an already skull stripped brain only image, i.e., also without cerebellum and brain stem. Does FreeSurfer not work with such input data? Must the cerebellum be present? Thanks, Andreas

1 0

Viewing Control Points
by Matt Glasser 27 Oct '11

27 Oct '11

Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt.

2 3

white matter volume in a ROI
by dolphinede＠aol.com 27 Oct '11

27 Oct '11

Dear FreeSurfer experts, i have created a ROI in qdec , where i have found a significant correlation between lgi and age. I mapped this ROI to all subjects. I am interested to compare in this ROI the pial-surface area, the grey matter volume and if possible the white matter volume for this specific region and i am not sure how to do this? Best regards Daniel Klein

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Segmentation error?
by Gergely Orsi 27 Oct '11

27 Oct '11

Dear Freesurfers!! I've encountered two strange segmentation "errors", if they are errors at all. Please see the attached fs.png: You can see that there are excess pial tissues on the superior part of the brain. The pial surface is defined correctly and the excess pial tissue is outside the red line yet it is coloured pink. My question, is : Does this have any impact on the results? The second is related to the hippocampus. Please see the attached fs2.png: The pial surface around the hippocampus looks a bit weird. It actually discards 1/3 of the hippocampus (it is outside the red line). Do you have any suggestions regarding the two problems. I'm using FS 4.5 on several 64bit linux distributions. -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi(a)gmail.com

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