Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

RE: [Freesurfer] good news and bad news
by Bruce Fischl 22 Nov '05

22 Nov '05

sorry, I didn't mean to say it is half broken. I meant that we haven't had time to go through the set of regression and system tests that we want to in order to make sure that everything works as well as we can make it. We've been going through that process and finding little things that we can improve, and have decided to make the improvements and retest rather than release things. Mostly the current dev version works extremely well. sorry for the confusion. Bruce On Sat, 22 Oct 2005, Fornito, Alexander wrote: > Hi Bruce, Just wanted to clarify: When you say the dev releases are "half > broken" does that mean there may be some minor niggles but results > generated should be (on the whole) trustworthy, or does it mean that we > should definitely avoid doing a complete study (eg., from surface > generation through to morphometric or fMR analysis) using a dev version? > Thanks, Alex > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl > Sent: Sat 22/10/2005 2:57 AM > To: freesurfer(a)surfer.nmr.mgh.harvard.edu > Subject: [Freesurfer] good news and bad news > > Hi All, > > I'll start with the good: > > thanks to Anders Dale (UCSD), Howard Pinsky (CorTechs) and Christian > Euseman (MGH), we have finally signed an open source agreement for > FreeSurfer. We will be posting a "read-only" tarball on the website in the > next couple of weeks, and anyone is free to download it and look at it. We > will *not* be supporting a make/configure type env for people to download > and build, as we simply aren't ready to do so. We plan to implement such a > procedure, but it will be a while. Instead of waiting until that was ready, > I thought people would like to have access to the source to at least see > what things are doing, and be able to see file formats and such. > > Now the bad news. I know we've been promising a new release, but it is > being delayed for another month or two. Partially this is due to the > opensourcing, which has taken our time and resources, but it is also > because we *really* don't want to release something that is half broken. > There are also a number of features that we want to get into the release, > and not have updates to it right away. We have continued to post current > versions on the website as prereleases, but *please* be aware that we can't > guarantee that these versions will be compatible with the one we ultimately > release. I think they will be, but can't say for sure. Our hope is that > datasets processed with the prerelease versions can be rerun automatically > with recon-all --rerun or something like that, but again, no guarantees. > > cheers, > Bruce > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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MAC OS X Tiger version
by peggy christidis 22 Nov '05

22 Nov '05

Does the MAC OS X Tiger developmental release of FreeSurfer have the MNI tools? I ask this because I installed this version and created a surface (via the GUI for demonstrative purposes), but I get that "cannot find talairach.xfm file" comment in the logs and no talairach coordinates for my surface. Thanks, Peggy

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request
by hengameh haghighat 22 Nov '05

22 Nov '05

Dear Professor Bruce Fischle Thank you for your reply . I would like to use Freesurfer for segmenting the hippocampus . I am a MSC student and the dead time of my thesis is very close. Please explain me in detail how can I use the software for segmenting . Thanks in advance for your helping. Best Regard -- Tehran University of Medical Sciences (www.tums.ac.ir)

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Postdoc Position in Berlin, Germany
by Hauke Heekeren 22 Nov '05

22 Nov '05

The independent junior research group "Neurocognition of Decision-Making" at the Max-Planck-Institute for Human Development in Berlin, Germany invites applications for a postdoctoral position ("Wissenschaftlicher Mitarbeiter"). We are a young, interdisciplinary team investigating mechanisms of decision-making in the human brain. We employ a combination of psychophysical methods, computational modeling, functional and structural neuroimaging (MRI, MEG, EEG, simultaneous EEG-fMRI), and we are using both the MPI's as well as the Berlin NeuroImaging Center's infrastructure. A successful applicant will need to have a PhD in a field related to cognitive neuroscience (e.g. informatics, neuroscience, engineering, physics, medicine, psychology). Applicants should have a background in computational (cognitive) neuroscience and/or neuroimaging (experience with MEG, EEG, fMRI or other brain imaging techniques) and experience in experimental design, computer programming and statistical methods. The position is for three years, available immediately and has the option of extension. Salary will be according to "EG 13 TVöD", formerly BAT Ib/IIa. For further information, please email Hauke Heekeren at heekeren(a)mpib-berlin.mpg.de. http://www.heekerenlab.org/ http://www.mpib-berlin.mpg.de/en/forschung/snwg/

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mri_convert problem?
by Daniel Goldman 21 Nov '05

21 Nov '05

I've been getting this error message whenever I try to convert to .mgz format: ---------------------------------------- mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz reading from /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img... INFO: analyzeRead(): min = 0, max = 1000 TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.027317, -0.986145, 0.163619) j_ras = (0.0506652, -0.164836, -0.985019) k_ras = (-0.998342, 0.018618, -0.054466) writing to /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... gzip: stdout: Operation not permitted Broken pipe ------------------------------------------- Is this a problem with mri_convert or am I doing something wrong that's preventing mri_convert from working properly? Thanks, - Daniel

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Normalization problem
by Martin Ystad 21 Nov '05

21 Nov '05

I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control points. This works if I add enough points across the brain ( over 200), and I get a better normalization result after running "recon-all -normalization -usecontrolpoints" and another skull-stripping on the new T1-volume. To test whether or not this produces a good segmentaition of white matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with the segmentation result, I move on to the surface processing stage, and run the -autorecon2 -script. The problem is that after running the -autorecon2, the normalization is completely wrong again, looking more like the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway.

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warning
by Sasha Wolosin 21 Nov '05

21 Nov '05

Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. 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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Freesurfer mailing list and google
by Satrajit Ghosh 21 Nov '05

21 Nov '05

Dear freesurfer users, By adding the following phrase to google's search box, you can search the freesurfer mailing list archives. site:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ I have found this extremely useful. Satra

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Normalization problem
by Martin Ystad 20 Nov '05

20 Nov '05

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problems with process volume
by hengameh haghighat 18 Nov '05

18 Nov '05

Hello I have three problems with FreeSurfer software. 1- I don't know how to segment the hippocampus with FreeSurfer software. For this reason i segmentated the hippocampus with another software (MRIcro) and then gave these slides to FreeSurfer software for measuring volume of hippocampus. The obtained volume was greater than the normal volume. For this reason I made a phantom with the specific volume of 27.142 cm3 to obtained correction factor. 2- In the guide's FreeSurfer it is said when watershed algorithm is corrupted , change the preflooding height to 30% in the setting section of RmSkull tab in expert preference , however I didn't get any result. 3- when an analyze file including one slide or all of the taken slides are given to the FreeSurfer software the watershed algorithm is corrupted and the volume is not calculated . 4- How much is the difference between the volume of the subject brain with FreeSurfer software (Albert) and the obtained volume in FreeSurfer software? how have you obtained it's correction factor? I would be thankful if you help me in this matter. I look forward to hearing for you soon Sincerely Yours -- Tehran University of Medical Sciences (www.tums.ac.ir)

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