Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Invitation to connect on LinkedIn
by Luke Tseng 06 May '10

06 May '10

LinkedIn ------------Luke Tseng souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Luke Accepter l'invitation de Luke Tseng http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… Voir l'invitation de Luke Tseng http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… ------------------------------------------ Quel est l' intérêt de faire partie du réseau de Luke Tseng ? Le réseau de Luke Tseng développera votre propre réseau : Si vous acceptez l'invitation de Luke Tseng, vous pourrez voir qui vous connaissez dans son réseau et demander à Luke Tseng de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. ------ (c) 2010, LinkedIn Corporation

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Re: [Freesurfer] Technical Doubts
by Nick Schmansky 06 May '10

06 May '10

hi, no, matlab is not used in the default (structural) processing stream. it is only used by the FS-FAST toolset included with freesurfer, which is used for processing fmri data. so you dont need to mention Matlab. n. On Thu, 2010-05-06 at 14:00 -0500, Dr. Luis Guillermo Almeida Montes wrote: > Dear Nick: > > I need to clarify some technical aspects about statistical calculations in FreeSurfer Software.I understood that I require MATLAB software only when I work with fMRI -is this correct?-, but as you know, I have been working only with structural MRI and their results (e.g. areas). So, I need to clarify If I need MATLAB software to realize the work for structural MRI or the installation program of FreeSurfer has the necessary utilities for these. Maybe I misundestood that FreeSurfer runs in MATLAB software to realize my work. > > I hope you can explain me the real need of MATLAB software for FreeSurfer because I need to give some of these technical details in the articles I will publish about my current work. I have been working in MacOSX Snow Leopard. > > Best Regards. > Dr. Luis G. Almeida > > >

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Group comparison
by Rajagopalan, Venkateswaran 06 May '10

06 May '10

Dear All, I am sorry to post this message again. Since i am not able to find from the tutorial and archives what i need i am posting it. I want to compare cortical thickness values in each region from aparc.stats file between control and patients. I am wondering whether it is possible to compare all the regions given in aparc.stats file and give a map showing which of these regions are significantly between the two groups (like VBM the final p map will give you regions which are significantly different). Do i need to create a separate contrast matrix for each and every regions (for eg one contrast for lh.cuneus,one for lh.temporalpole etc) or like in VBM studies you give a single contrast matrix and design matrix since you are testing the same hypothesis in different regions of the cortex. I also would like to know whether i have to do multiple comparisions when i am testing for same hypothesis in different regions or not needed. In the tutorials i find mostly regression between thickness and demographic parameters so any suggestion or guidance to where i can find tutorial or materials related to my above questions. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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GLM analysis on individual surface
by YUMI MAEDA 05 May '10

05 May '10

HI, I am trying to do GLM analysis on individual surface data. I found the online documentation about group feat on surface but I could not find how to do first-level feat on surface. Thank you for any information. YUMI

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Basal forebrain
by Kelly Silva 05 May '10

05 May '10

Hello! Is there any way to know the basal forebrain structure with the Freesurfer (aseg.stats)? Thanks in advance, Kelly

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Qdec Error Question
by blazey＠artsci.wustl.edu 05 May '10

05 May '10

Hi All, I am trying to use Qdec to analyze a dataset, and am getting the following error: ERROR: All stat files should have the same segmentations If one or more stats file have different segs from others, use --common-segs or --all-segs flag depending on the need. The problem is that I haven't been able to find any documentation about using these flags. It would be great is someone could either show me where the documentation is, or give me a brief explanation as to how to use these flags. Thanks in advance for any help. - Tyler Blazey

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passing a WM lesion mask to recon-all
by Mehul Sampat 04 May '10

04 May '10

Hi Folks, We have some subjects with very large white matter (WM) lesion loads. We noticed that the pial and main are pial surfaces are not affected by WM lesions. However, they seem to be affection by the juxta-cortical WM lesions (which have dark intensity) In the past, my colleagues have manually outlined the lesions and created a binary lesion masks. I was wondering if : 1. I can pass this white matter lesion mask as input to recon-all as an input variable ? essentially the idea is to find a way to make recon-all to consider these as white matter (i am only interested in the cortical thickness measurements and not the WM volume so i think it is okay to do so ) 2. if this is not possible, can i use this white matter lesion mask to edit wm.mgz ? in this option, i could find the locations of the non-zero pixels of the lesion mask and then set the corresponding locations in wm.mgz to 110. Does this sound like a bad idea ? or would you suggest a different way to do this ? thanks Mehul

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contrast correction
by Ilana Hairston 04 May '10

04 May '10

Hi there, We have been doing contrast correction using mri_nu_correct.mni (e.g., mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2). My question is, after subsequent corrections (control points, white matter) do we need to specify nu2.mgz as the target file for secondary recon steps in the command line (e.g., recon-all -autorecon2-cp -autorecon3 -s FS090620ll -i FS090620ll/mri/orig/nu2.mgz -force) thanks ilana

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Combined stats from labels?
by Dankner, Nathan (NIH/NIMH) [F] 04 May '10

04 May '10

Hi all, I have a set of 32 labels that I am attempting to pull average thickness from. I would prefer not to run 32 different asegstats2table commands, so I was wondering if there was any way to consolidate the thickness stats from these labels into one file so I can pull them all out simultaneously. Thanks for your help! Nathan

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missing stats files -posting again
by Rajagopalan, Venkateswaran 04 May '10

04 May '10

Dear All, I am new to freesurfer, in some of our patients stats files lh and rh.curv.stats are missing at the end of recon-all -all. recon-all finished without error in these patients so i am wondering what is the mistake i am doing and where will need these lh and rh.curv stats files. Thanks in advance venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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