Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

conversion
by Lindsay Nagamatsu 12 Aug '09

12 Aug '09

Hi, The output files that I get from our scanner are .par and .rec files, but I am now using fsl and freesurfer to analyze my data. How can I convert my files into a Nifti format to be used by fsl and freesurfer? Is there a way that freesurfer can do this? Thank you, Lindsay -- Lindsay Nagamatsu, BA MA Candidate Department of Psychology University of British Columbia 2136 West Mall Vancouver, B.C. Canada, V6T 1Z4 Tel: (604) 822-3120 Fax: (604) 822-6923

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Re: [Freesurfer] Clusterwise correction
by Dankner, Nathan (NIH/NIMH) [F] 12 Aug '09

12 Aug '09

Another question: I've noticed that when loading the cluster .annot file, tksurfer also loads the desikan parcellation color table. How can I load the clusters by themselves? And also, I know that loading the cluster overlay allows you to see which clusters are significant by looking at their level of transparency, but is there a way to load ONLY the clusters that are significant? Thanks again, Nathan On 8/12/09 3:49 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: The QDEC script runs mri_glmfit-sim, which automatically finds and uses the FWHM, so you should not have to do anything. Recently (about a month ago), I found a bug in some of the simulation software, so you should upgrade to the latest FS version. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Doug, > > Sorry, I'm still a bit unclear on how/when I need to pass along the fwhm. I have been generating my scripts for the cluster correction through the qdec GUI. Where along the line do I need to pass it the fwhm? Do I need to go into the script itself and add it somewhere? > > > On 8/12/09 2:02 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > > > If you are running an MC simulation (not perm) directly from mri_glmfit > (and not mri_glmfit-sim) then you must pass it a fwhm or the results > will be wrong. The smoothing level is measured by QDEC (mri_glmfit) as > part of the analysis. You can't run the simulation from QDEC, so > specifying the smoothing level for the simulation from QDEC is not an issue. > > doug > > > Dankner, Nathan (NIH/NIMH) [F] wrote: > >> Doug, >> >> Thanks for the info. One quick follow-up question: Let's say for example the smoothing before I run the simulation is 2.75. When you say I need to match the smoothing, do I achieve that by adding 2.75mm of smoothness to the data before running the cluster simulation? In the qdec GUI it only allows you to smooth in increments of 5. Is there a command line flag that would allow me to choose my own level? >> >> >> On 8/11/09 5:48 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >> >> 1) The smoother the data, the more likely a cluster will be found by >> chance. When the data are created, they start with some smoothness >> level. When you smooth them you add more. So you need to match the total >> level of smoothing when you do the simulations, otherwise your clusters >> will be way too significant. mri_glmfit creates a fwhm.dat file with an >> estimate of the total smoothness. >> >> 2) Just if they are nearest neighbors. There is no option to tinker with >> this. >> >> 3) Vertices in the maps created by the simulation are thresholded at the >> level you pass. This is what defines the cluster. >> >> doug >> >> Dankner, Nathan (NIH/NIMH) [F] wrote: >> >> >>> Hello all, >>> >>> I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great so I am just trying to get some background. First of all, how does smoothing the data prior to running the simulation affect the results? I've run corrections on the same data smoothed with a 10mm FWHM, and also on completely unsmoothed data, and the cluster results were different. Secondly, what determines whether vertices are neighbors or not? Is there an option to tinker with this or is it predetermined? Lastly, how do the p values of individual vertices factor into the simulation? Are they taken into account when the determination of the max cluster size under the null hypothesis is performed? Thanks in advance, >>> >>> Nate >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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installation help
by Lindsay Nagamatsu 12 Aug '09

12 Aug '09

Hi, I am trying to install freesurfer on my computer (mac 10.5). When I put the .license file into the installation directory, my computer gives the error that all files beginning with "." are reserved for the computer, and won't let me save the file. Is there any way around this? Thank you, Lindsay -- Lindsay Nagamatsu, BA MA Candidate Department of Psychology University of British Columbia 2136 West Mall Vancouver, B.C. Canada, V6T 1Z4 Tel: (604) 822-3120 Fax: (604) 822-6923 -- Lindsay Nagamatsu, BA MA Candidate Department of Psychology University of British Columbia 2136 West Mall Vancouver, B.C. Canada, V6T 1Z4 Tel: (604) 822-3120 Fax: (604) 822-6923

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Non-human primate surface template
by MCLAREN, Donald 12 Aug '09

12 Aug '09

Dear all, Does anyone have or is perhaps working on a surface template for the rhesus macaque brain? -- Best Regards, Donald McLaren ===================== Support the Alzheimer's Association Memory Walk 2009 ~~~ Join the Wisconsin Alzheimer's Disease Research Center team or make a donation. http://madison.kintera.org/2009/donaldmclaren ================= D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Office: (608) 265-9672 Lab: (608) 256-1901 ext 12914 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (608) 265-9672 or email.

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mri_surf2surf --cortex
by DRC SPM 12 Aug '09

12 Aug '09

Dear FreeSurfers, Please can you explain how mri_surf2surf's --cortex option for smoothing is implemented? I assumed it would be along the following lines: - mask the data to zero-out the medial wall - smooth this masked data - smooth the mask itself - divide the smoothed data by the smoothed mask - (perhaps) re-mask the data But I've tried doing that long-hand (i.e. calling mri_surf2surf without the --cortex flag for each smoothing, and using l load_mgh and save_mgh in MATLAB for the rest), and it doesn't seem to quite match the results of the --cortex flag. Now I'm guessing that it instead might do something like the following. For each connected-neighbour iteration of the smoothing, only include the neighbour in the average if it is inside the cortex (not medial wall). However, I can't easily/lazily reimplement this to check, so could someone reveal the truth? ;-) Many thanks, Ged

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new release v4.5.0
by Nick Schmansky 12 Aug '09

12 Aug '09

A new freesurfer release is now available, v4.5.0: http://surfer.nmr.mgh.harvard.edu/fswiki/Download The release notes page describes the bug fixes and new features: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Mainly this release is intended to make available necessary improvements to the longitudinal analysis stream. Freesurfer team

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the space for sphere registration
by Zhong Jidan 12 Aug '09

12 Aug '09

Hi, In Freesurfer, we use recon-all to create the white, pial, inflated, spherical surface of each subject. And the sphere registration is done between the subject and the sphere template. I want to know that, what space are the spheres in? Do you do any translation and rotation for the sphere created to make them in the same space as the template? Or do you just leave them in their own space and do registration? -- Regards, Jidan

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talairach.xfm p=0.0000 error, brainmask.mgz not created
by Prantik Kundu 11 Aug '09

11 Aug '09

Hello In default FS usage, all of the MPRAGE's from this particular study that I'm analyzing are dying with the error shown below. MPRAGE's from other studies appear to be processed just fine. The MPRAGEs from the experiment that FS is failing on are generally of higher quality than those where FS is succeeding. The failure seems to be happening even before brainmask.mgz is being created. When I turn off the automated tlrc checking, then brainmask.mgz is created but of very poor quality. This is reproducible on Linux 32 and 64 bit as well as OSX. Please help. -Prantik FROM recon-all.log : __________________________________________________________________ Mon Aug 10 14:05:54 EDT 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 10 14:05:55 EDT 2009 /home/kundup/FS_SUBJECTS/BrVi.S06/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux cadmium 2.6.28-14-generic #47-Ubuntu SMP Sat Jul 25 01:19:55 UTC 2009 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Aug 10 14:05:55 EDT 2009

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MS lesions
by Jose Soares 11 Aug '09

11 Aug '09

Hi, what kind of information can I get with FreeSUrfer about MS lesions? Number of lesions? Lesion volume? Thanks, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Less smoothing in version 4.1 than 4.0?
by DRC SPM 11 Aug '09

11 Aug '09

Dear FreeSurfers, My apologies if this is mentioned in the release notes, but I couldn't find it with a quick search. I'm using the following command to smooth some data: mri_surf2surf --hemi rh --s average --sval in.mgh --fwhm 20 --tval out.mgh Under FreeSurfer version 4.0.3, part of the output is: Reading in average area average/surf/rh.white.avg.area.mgh Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 379 iterations of nearest-neighbor smoothing Whereas under FreeSurfer version 4.1.0, I see: Reading in average area average/surf/rh.white.avg.area.mgh INFO: fwhm2niters: Fixing group surface area Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 290 iterations of nearest-neighbor smoothing It seems that there is less actual smoothing occurring for the same requested FWHM (unless the altered surface area estimate cancels out somewhere else?), is that correct? Since the 20mm itself was fairly arbitrarily chosen in my lab, I'm wondering whether it would make sense to increase this to get the same number of iterations (on the same data) with the newer version, so that results are smoothed by the same amount. Is there a way of adjusting the FWHM to undo the effect of the above fwhm2niters fix? Thanks, Ged P.S. I realise that 4.1.0 is not exactly "new" itself... I'd also be interested to know whether this has changed again in more recent versions. Thanks!

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