Freesurfer March 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
84 discussions

contrast.mat file
by Sasha Wolosin 30 Mar '06

30 Mar '06

What format should my contrast.mat file be for group analysis? e.g. if my contrast vector is [1,-1], should the contrast.mat file be a text file with [1 -1] as the first line? or 1 -1 as the first line? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: Outputting reformatted images in freesurfer
by Salil Soman 30 Mar '06

30 Mar '06

Hi, I have 2 images loaded into freesurfer (1 as an overlay) with the images transformed using a .reg file. Is there a way in freesurfer to output each of the loaded images in the pose they are in after loading the .reg file? (so the pose of each image is the result of whatever transforms are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman sal(a)bwh.harvard.edu

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Talairach question
by Martin Ystad 30 Mar '06

30 Mar '06

Hi, I'm doing a group study and I have a question regarding the Talairach transform. I need to make a new transform for some of my subjects using the brainmask.mgz-volume. For others, the original transform is okay (visually) . Is it a problem to have some transforms based on the brainmask volume, and others made from the nu volume? Should I make new transforms for all subjects, even though some of the original ones are fine? Thanks, Martin Ystad University of Bergen, Norway.

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Questions about new release
by Jeffrey Spielberg 29 Mar '06

29 Mar '06

Hi, I have a couple of questions I was hoping the list might help me with, 1. I am using SuSE Linux version 10 (X86-64) and previously I had been told that the redhat 9 release was the most similar to SuSE 10, but with the release of the CentOS 4 X86_64 release I wondered if this would be best to use. To that end I ran the same subject with both the new CentOS 4 X86_64 release and the new redhat 9 release and came up with different results. For example both the wm.mgz files produced by the two releases have small but noticeable differences. Is this because of rounding error due to the 64 vs 32 bit difference, and if so does anyone know which release would be best to use, that is, is one going to give a better estimate, or are both going to give slightly different, but equally good estimates? If it's not due to rounding error what could be the cause? 2. I want to map automatic segmentation's to fsl feat directories, but fsl uses LAS orientation, while freesurfer uses RAS. Does the feat2anat or aseg/aparc2feat commands take this into account, or should I swap the dimensions of one or the other? If I should swap dimensions, would it be best to simply put my structural scan into freesurfer in LAS format in the first place, or swap things after all the freesurfer analysis has been done? thanks, Jeff

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A question concerning optseq2
by Avram Holmes 29 Mar '06

29 Mar '06

Hi, I have a question concerning the use of optseq2 to optimize my trial presentation. I am designing a task which consists of the presentation of a probe followed by feedback. I am interested in jittering both the ISI (between the probe and feedback) and the ITI (between each trial). Sadly, my knowledge of optseq2 is quite limited and I have thus far been unable to figure out how to accomplish this. I was wondering if there is anyone at the NMR center would might be able to talk me through this. Thank you for your time, Avram Holmes

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recon-all skull-strip correction problem
by Tom Bayer 28 Mar '06

28 Mar '06

After running "recon-all -autorecon1" I saw that brain.mgz was missing some large areas in the cerebellum. I ran "recon-all -skullstrip -wsthreshold 35" and then checked my work with "tkmedit subjid brainmask.auto.mgz -aux T1.mgz" The skullstrip looked very good, so I went on to run autorecon2. brain.mgzwas never updated and the output of autorecon2 was horrendous. I am going to use mri_mask to generate a new brain.mgz using T1.mgz and brainmask.auto.mgz. Is this an appropriate solution to my problem? The document fstutorial/skullstriptutorial, which I used as my guide, indicates tht running recon-all with the -skullstrip flag will generate a new brain.mgz but this did not occur when I used the command. The autorecon help file correctly indicates that recon-all -skullstrip generates brainmask.auto.mgz and brainmask.mgz but lacks explanation of the command's various modes. It appears that the generation of brain.mgz is somehow lost between autorecon1 and autorecon2, at least in my experience. FYI I am using freesurfer stable release 3.0.1 on a pentium 4 running Fedora Core 4 -Tom Bayer

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buckner tutorial data
by Glenn Lawyer 28 Mar '06

28 Mar '06

Hi, We seem to be having a long-standing problem downloading the bucker tutorial data ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz> When we try to download it, the download freezes after about 500 MB and won't resume. We've tried downloading it several times, from different machines/OS/ISPs, both using ftp directly and from within a web browser. Do you have any ideas how to fix this? Perhaps the data could be broken up into 2 or 3 tarballs? Thanks, +glenn -- It is not an aesthetic process; it's a form of magic that interposes itself between us and the hostile universe, a means of seizing power by imposing a form on our terrors as well as on our desires. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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hippocampus surface registration
by chunxiao zhou 28 Mar '06

28 Mar '06

Dear Freesurfers, I am working on a hippocampus surface comparison project. What I want is to register the subject hippocampus surface to a atlas surface and get the displacement vector field. I haven't use Freesurfer yet. But I guess it might work for cortical surface registration.Does it also work for hippocampus surface registration? Would anyone have some information about that? Thank you. Chunxiao University of Illinois at Urbana-Champaign __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Transformation of segmenation
by Shahabuddin Ansari 25 Mar '06

25 Mar '06

Hello Bruce, Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI? Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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how to register subcortical segmentation with the original image
by Shahabuddin Ansari 24 Mar '06

24 Mar '06

Hello, I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking? Any comments? Thanks Shahab --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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Freesurfer March 2006