Freesurfer

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19 participants
30088 discussions

bbregister
by Christopher Bell 19 Mar '12

19 Mar '12

I have run a bunch of cases through bbregister and overall it worked great! 315 out of about 325 cases the alignments were very good, but on 10 subjects it did very poorly. I can not so far find anything unusual about this data. Per earlier posts, I have tried the different initilization options with no luck. I also tried an fsl_rigid_register 6 DOF to create a starting .dat ,but that was way off too, maybe because it uses similar initilization information? I also saw the post to use --init-reg-out to save the init transform but I am not sure what to make of the output. This is aligning data that has been through the 1000FC pre-processing. This converts our RAS scans to RPI, and also de-obliques using AFNI. Would you suspect either of these steps as confusing bbregister? We are using dcm2nii (mricron) for dicom to nifti conversion.

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FreeSurfer Course in Amsterdam!
by Allison Stevens Player 19 Mar '12

19 Mar '12

Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.freesurfercourseamsterdam.nl/ Questions about the Amsterdam course should go to Veronica Popescu (info(a)freesurfercourseamsterdam.nl) Hope to see you there, Allison

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TRACULA: isn't the posterior distribution a probability?
by Juke Cha 18 Mar '12

18 Mar '12

Dear Dr. Yendiki and TRACULA experts, I was wondering what the unit of posterior distributions of reconstructed paths? By looking at the intensities, it ranges from 0 to ~150. I thought this is supposed to be a probability, but it's not? If it's in arbitrary unit, should I z-score them in order to show PD maps across subjects? Thanks for your help in advance. -- Juke Cha, M.S. Ph.D Candidate, Program in Neuroscience Laboratory for Computational Neurodiagnostics (LCN)<http://www.lcneuro.org/> Dept of Biomedical Engineering Stony Brook University School of Medicine email: cha(a)lcneuro.org office: 631-632-1992 fax: 631-632-3222

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Version differences of freesurfer for cortical thickness analysis
by Martin Lan 16 Mar '12

16 Mar '12

Hello, I am planning to do an analysis of cortical thickness, comparing a group of brain samples from patients to those of healthy control subjects. The laboratory that I am working in has freesurfer 4.5.0 loaded on our hardware. With our system, it would be labor intensive to load an updated version of freesurfer. My question is whether there would be significant disadvantages to using the 4.5.0 version for this function over the 5.1.0. Particularly, should we anticipate criticisms of reviewers of future manuscripts because of the use of the older version? Thank you in advance for your help, Martin

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LGI cluster correction
by Robustelli, Briana (NIH/NIMH) [F] 16 Mar '12

16 Mar '12

Dear Freesurfer Team, My group has been working with an lGI dataset for a while now and we were able to successfully complete a Monte Carlo cluster correction in FreeSurfer 4.5. It took a very long time but we did not receive any error messages. Now when we try to perform cluster corrections in 5.1, we receive this message, (Error: fwhm out-of-range (<1 or >30)!). So we wanted to check that the results we received from the cluster correction run in 4.5 are sound and to see if there is any solution to the 5.1 error. Thanks! Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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glut fatal error in tkmedit.bin visual with necessary capabilities not found
by Alex Liu 16 Mar '12

16 Mar '12

Hello all, I'm relatively new to freesurfer so this may be a simple fix. I was using freesurfer the other day and I came across the following message: GLUT: fatal error in tkmedit.bin visual with necessary capabilities not found. I'm using a mac laptop and I'm not sure if this is just an issue with computer settings. Any info on this matter would be greatly appreciated. Thank you. -- Alex

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License Installation problem
by Talvadkar, Kunal Girish 15 Mar '12

15 Mar '12

Hi, I tried installing the free surfer license,but was not able to do so,if anyone could help me with a detailed approach to this,I would be most grateful.I am saying detailed cause i am not familiar with some computing procedures. Thanks, Kunal

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Re: [Freesurfer] strangely low lhCorticalWhiteMatterVol estimate
by Michael Harms 15 Mar '12

15 Mar '12

Hi Doug, As a post-mortem to this thread, in the process of going to "tweak" the wm.mgz as you suggested, I noticed that there were actually some substantial errors in the surfaces in the calcarine, presumably due to topology correction gone astray. So, whether or not that precipitated the problem with the filling operation of mris_wm_volume, it was something that needed wm editing, and once that was done, the ensuing lhCorticalWhiteMatterVol was again normal. cheers, -MH > On Thu, 2012-03-01 at 13:29 -0500, Douglas N Greve wrote: > It must be that the shell is not quite getting closed. Didn't Gheorghe > use a ray tracing algorithm for this? > > Bruce Fischl wrote: > > hmmmmm, I don't understand why the filling is failing then. I can't > > remember who's code this is. I think it started life as Andre's > > (shocking!), but maybe Krish or Martin has taken it over since then? > > > > On Thu, 1 Mar 2012, Douglas N Greve wrote: > > > >> > >> mris_euler_number surf/lh.white > >> euler # = v-e+f = 2g-2: 166103 - 498303 + 332202 = 2 --> 0 holes > >> F =2V-4: 332202 = 332206-4 (0) > >> 2E=3F: 996606 = 996606 (0) > >> total defect index = 0 > >> > >> mris_euler_number surf/rh.white > >> euler # = v-e+f = 2g-2: 167114 - 501336 + 334224 = 2 --> 0 holes > >> F =2V-4: 334224 = 334228-4 (0) > >> 2E=3F: 1002672 = 1002672 (0) > >> total defect index = 0 > >> > >> > >> Bruce Fischl wrote: > >>> what is the euler number for the white surface for this subject > >>> (mris_euler_number)? > >>> On Thu, 1 Mar 2012, Douglas N Greve wrote: > >>> > >>>> Hi Mike, I *think* I've found the problem with this subject. The way > >>>> that the volume inside the white surface is computed is to create a > >>>> high-res volume (.25mm iso), then create a shell based on the > >>>> intersection of the faces with the volume. The outside of the shell is > >>>> "flooded", the result is inverted to give a map of voxels inside the > >>>> white surface. This includes subcortical voxels, so the voxels > >>>> known to > >>>> be in the WM from the aseg are added. The .25mm voxels that are > >>>> labeled > >>>> as cortical gray matter are also included since these represent > >>>> partial > >>>> volume that are really WM. So far so good. I think the problem is that > >>>> the shell for this subject has a hole in it, so the flood leaks into > >>>> most the interior. When inverted, there are very few voxels left > >>>> and so > >>>> the WM volume is way too low. It might take a while to find a solution > >>>> to this, so I just wanted to give you a heads up. One possible > >>>> work-around is to make an edit that causes the surface to change. > >>>> It is > >>>> probably the case that even a small change causes the hole to fill and > >>>> everything works out. > >>>> > >>>> doug > >>>> > >>>> Michael Harms wrote: > >>>>> Hello, > >>>>> > >>>>> Anyone have a chance to look at this? Should we just forget about > >>>>> trying to get an accurate lhCorticalWhiteMatterVol value for this > >>>>> subject? > >>>>> > >>>>> thanks, > >>>>> -MH > >>>>> > >>>>> On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote: > >>>>> > >>>>>> Hi guys, > >>>>>> > >>>>>> We have a subject processed with FS v5.1 in which > >>>>>> lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781 > >>>>>> mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume > >>>>>> lh.white' > >>>>>> returns 287261 and running mri_segstats without the --excl-ctxgmwm > >>>>>> option returns a Left-Cerebral-White-Matter volume of 245169. > >>>>>> 'mris_euler_number' indicates no problems with lh.white. > >>>>>> > >>>>>> Running 'mris_wm_volume' on its own generates the same value of > >>>>>> 33781. > >>>>>> I also tried running 'mris_wm_volume' with the -v option to see > >>>>>> if any > >>>>>> interesting messages popped up, but got the message "unknown > >>>>>> option -v". > >>>>>> > >>>>>> Any idea what is going wrong here? So you can see for yourself, > >>>>>> I went > >>>>>> ahead and uploaded the subject's processed data to your FTP server > >>>>>> (110107_L206.tgz) > >>>>>> > >>>>>> thanks, > >>>>>> -MH > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. >

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Q: Tkmedit
by Yiyu Chou 15 Mar '12

15 Mar '12

Dear FS users,

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HELP needed to improving quality while processing CHILDREN'S DATA
by Karla Zúñiga 15 Mar '12

15 Mar '12

Hello Freesurfers, I am new using freesurfer and I would like to know if any of you have some ideas (tools, tips, ...) on how to improve the quality of my results while processing structural T1 data from children aged 5 to 7 years old. Syncerly, Karla -- Karla Monzalvo Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Tél : 33 (0)1 69 08 90 66 Fax : 33 (0)1 69 08 79 73 karla.monzalvo(a)cea.fr http://www.unicog.org/

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