Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Volumes of four major cortical lobes
by caoaize 03 Mar '10

03 Mar '10

Hi, Bruce, We want calculate the four major cortical lobe volumes, i.e. frontal, parietal, temporal, and occipital, to see the relationship between them and some ROIs. I did fully run recon-all, but not clear which file should be used and what cortical areas should be included in these four lobes seperatively. May you please give me some instruction? Thanks. Aize _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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autorecon with one image
by ayumi＠haskins.yale.edu 02 Mar '10

02 Mar '10

Hi, I am analyzing structural data (analyze format). How can I run autorecon with one image? A similar question was already asked on 14 Jun 2008, but I couldnt find how to run it. Thanks, Amy

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Application of Default Surface Based Registration to Surfaces Other than the Sphere
by Matt Glasser 02 Mar '10

02 Mar '10

Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am wanting to have registered white matter surfaces that I can map data from the volume to the surface to and then average across subjects. Thanks, Matt.

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thickness of frontal lobe
by Liukarl 02 Mar '10

02 Mar '10

Hello, I looked at the results from stage 3 and found out it has 1100 regions (we might not use qdec since we have many other variables to control). But it is beyond manageable levels. What we want might two things: The first one might be a general measure of thickness (or volume) of each lobe (frontal, parietal,…) or which one from these 1100 regions? And we are particularly interested in the prefrontal lobe and behavior. Is there any finer measure of frontal lobe (thickness/volume, dorsal frontal/ventral frontal)? Thanks a lot Karl _________________________________________________________________ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TL&swm=1

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Standard Desikan map and/or qdec blurb?
by Dankner, Nathan (NIH/NIMH) [F] 02 Mar '10

02 Mar '10

Hi all, I'm about to start writing up a paper, and was curious as to whether there is a standard figure displaying the Desikan parcellations that is floating around out there, and also whether or not there is a standard blurb describing QDEC's GLM analyses. Thanks! Nathan

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cortex bad segmentation...
by Gonzalo Rojas Costa 02 Mar '10

02 Mar '10

Hi: In a patient, I got a bad cortex segmentation... I try to adjust the skull stripping, but I couldn't got a better stripping... How can I correct that segmentation ?... Sincerely, Gonzalo Rojas Costa

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Loading new data into Freesurfer
by Janani Dhinakaran 02 Mar '10

02 Mar '10

Hello to everyone! Hope the new month is bringing better weather to all of you. I am trying to load new data. I cd-d to the location of the files (.hdr and .img). Now I am trying to convert the data. It doesn't recognise the information. I've manually created the files JS, MRI, and Orig within to allocate an appropriate path for it. Here is a copy of what I did. Please let me knwo what I need to do. Thank you! s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA$ cd 1_1 s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS mri_convert: can't determine type of output volume s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/001.mgz mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/001.mgz file not found or unknown file type for file /Desktop/Newdata/RAW_DATA/1_1 s0964091@CRIC-0012:~/Desktop/Newdata/RAW_DATA/1_1$ mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/mri/orig/001.mgz mri_convert /Desktop/Newdata/RAW_DATA/1_1 /Desktop/Newdata/JS/mri/orig/001.mgz file not found or unknown file type for file /Desktop/Newdata/RAW_DATA/1_1 -- I am the Sun, I know no darkness.

2 3

signal loss in the orbitofrontal cortex
by Cindy Eckart 02 Mar '10

02 Mar '10

Dear FreeSurfers, in the FreeSurfer cortical parcellation procedure, a volume measure is calculated for the lateral orbitofrontal cortex and in my study population I indeed do find a significant group difference in the volumes of this region. However, there certainly is signal loss of the MR signal in the orbitofrontal region... However, I am not quite sure how much of the lateral orbitofrontal cortex is concerned by this phanomenon. Thus, my question: Is there any data how reliable the volume measurement of the FreeSurfer cortical parcellation might be in the lateral orbitofrontal cortex? Is there a way to check how much of this parcel is concered from signal loss in my own data? And do you have any experience how reasonable it may be to interpret a group difference in this region? Thank you very much in advance! Cindy ___________________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

2 1

software versions
by Roser Sala 02 Mar '10

02 Mar '10

Hello freesurfers, we have several data processed (with recon-all) using FreeSurfer v.4.3.1, but we are thinking in moving to v.4.5. Do we have to re-run recon-all again for all the subjects, or can we just run the new features implemented in the new version (If so, is there any 'easy way' to do it?) Thanks in advance, - Roser -

1 0

continue longitudinal processing...
by Gonzalo Rojas Costa 02 Mar '10

02 Mar '10

Hi: I was processing a longitudinal processing using a command line like: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all but it couldn't finished because the power cut produced by a 8.8 magnitude earthquake here in Chile... How can I continue the processing without starting again from the beginning ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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