Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

Suggestions for ways to present brain images of FreeSurfer results in a manuscript?
by Max Gunther 29 Aug '10

29 Aug '10

Hi all, I am relatively new to FreeSurfer and I am wondering if people have suggestions for how to display images of brains in my sample that will be meaningful to reviewers and readers? Right now the most meaningful results are depicted using scatter plots and regression lines, etc. but I would definitely like to put some actual images of the sample's brain's in the paper. It is about 90 brains with old patient with significant atrophy. I am just not familiar enough with the FreeSufer options to know what kinds of tools A) are available and B) would be appropriate for communicating the effect of a clinical variable on brain atrophy. Many thanks for your time and suggestions! Sincerely, Max Gunther Max Gunther, PhD Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org

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iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 28 Aug '10

28 Aug '10

Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version ate welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4

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PALS-B12-based ROIs in fsaverage in v5.0.0
by Nick Schmansky 27 Aug '10

27 Aug '10

there is one new feature in the new v5.0.0 which was missing from the early release notes, but that which some people might have an interest. the Van Essen Lab created some ROIs on their PALS-B12 atlas, and then mapped them to the freesurfer fsaverage subject. some basic info is here: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 it will take a bit of freesurfer expertise on your part to make use of these, as you would need to: 1) identify which labels (ROIs) are of interest to you (by viewing the .annot file on fsaverage) 2) use mri_annotation2label to extract the labels 3) use mri_label2label to map from fsaverage to your subject 3) optionally use mri_anatomical_stats to get stats about those labels n.

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freesurfer 5.0 in ubuntu 10.04
by Guang Zeng 27 Aug '10

27 Aug '10

Hi, there, I just downloaded and installed freesurfer 5.0 under Ubunto 10. The version I am downlaoded is freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz I ran a subject, but it failed at the first step, the error message I got is: talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux guangzeng-desktop 2.6.32-24-generic-pae #41-Ubuntu SMP Thu Aug 19 02:43:57 UTC 2010 i686 GNU/Linux I checked the talairach_avi.log, and I found this: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted So, how can I fix this problem? Thanks a lot! Guang

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Partial voluming - mri_segstats --pv
by Wu, Paula (NIH/NIMH) [F] 27 Aug '10

27 Aug '10

Hi, I'd like to learn more about how the mri_segstats -pv calculation is done. Could someone send me the source code for this algorithm? Thanks! Paula Wu Summer Intramural Research Training Assistant Laboratory of Brain and Cognition, Section on Functional Imaging Methods, NIMH/NIH/DHHS Building 10, Room 1D80 10 Center Dr MSC 1148 Bethesda MD 20892-1148 wup2(a)mail.nih.gov

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Re: [Freesurfer] MRI Files Doubts
by Nick Schmansky 26 Aug '10

26 Aug '10

the reason, as i understand it, is that the analyze format does not store orientation information. this means there is no way to tell left from right, which can lead to problems in both atlas alignment, and during multimodal (fmri) registration. n. On Thu, 2010-08-26 at 13:32 -0500, Dr. Luis Guillermo Almeida Montes wrote: > Dear Nick: > > Some colleagues asked me some doubts about pre-processing in > FreeSurfer for MRI files. I remember you told me once that MRI files > in analyze format would be inappropiate to pre-process in FreeSurfer > suite. They work with this analyze format since their DICOM files can > ´t be processed because their files are compressed.Can you give > technicals details about the reasons about why analyze files cannot be > used in FreeSurfer for pre-processing? > > Thank you. > > > Best Regards. > Dr. Luis G. Almeida >

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do I have to reprocess my subjects if I install new version of Freesurfer?
by Kevin Head 26 Aug '10

26 Aug '10

Do I have to reprocess my data if I install the new (v5.0.0) version of Freesurfer? If I don't, and process more subjects in the study with v5.0.0 will that be problematic?

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initial G-W contrast is negative
by Hansen, Kathleen (NIH/NIMH) [F] 26 Aug '10

26 Aug '10

Hello, The following command has produced a very wrong registration and a warning: bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat **** WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 **** The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas? Thank you, Kathleen

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scp issue??
by Gennan Chen 26 Aug '10

26 Aug '10

Hi! All, I download and install freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 on my macbook pro yesterday. After that, scp command from terminal is not working anymore. Below is an example: gnchen@mbp:tmp]$ scp -i ~/.ssh/id_dsa.pub sdg.zip macpro:~/tmp -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 -------- It shows freesurfer's version and did not copy file at all. I have no idea why scp command will have something to do with freesurfer. Does anyone know anything about this?? Gen

1 1

ftp server down??
by Gennan Chen 25 Aug '10

25 Aug '10

Hi! I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. Is it down? Gen

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Freesurfer August 2010