Freesurfer

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30132 discussions

Watershed treshold and amygdala volume
by Hendrikx, A.A.E.M. (Anne) 20 Mar '11

20 Mar '11

Dear all, We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following: We are wondering why the amygdala volume changes, after changing the watershed threshold. Besides, if we should nog change the ws-treshold, but manually remove remaining skull, the amygdala volume will not change. We don't understand this. Can anyone explane this to us? And besides, what consequences are there for the accuracy of the calculations? Best wishes, Anne Hendrikx

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Able to load surfaces but not *.mgz files in MATLAB...
by Eggebrecht, Adam 18 Mar '11

18 Mar '11

Hello, I have installed FreeSurfer on a Linux box and everything works great. However, our lab does most all of our processing in MATLAB in a Windows XP-64 platform. Within MATLAB, I am able to import the files existing within the /surf/ folder to work with and visualize the meshes. However, I am unable to load in any of the *.mgz files within the /mri/ folder. I have attempted to use the load_mgh.m and MRIread.m commands. The error returned is the following: The system cannot find the path specified. ERROR: could not open /tmp/tmp5897063.mgh for reading ERROR: loading mri/wm.mgz as MGH The load_mgh.m program is failing between lines 61 and 76. I don't know how your code is compressed, so I can't create a work around for this specific issue. Is this program only useful on a MAC or unix-based system? Is there another way to load in the compressed files into a Windows-based MATLAB? I have searched the relevant help threads, but have not found an answer to this specific problem. Many thanks for your assistance! Cheers, Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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monkey brain problem
by Yang Liu 18 Mar '11

18 Mar '11

Hi surfers, We met a problem when processing a monkey's anatomical brain. We got a very good white matter segmentation (wm.mgz) by manually editing the automatic segmentation. After recon-all, we found that at some regions, the yellow surface won't follow the wm.mgz. It is strange because the wm.mgz at these regions are very well defined and smooth. I would expect that the main surface would follow the wm.mgz tightly and smoothly. You can see the problem from the images I attached. These are coronal and horizontal views of one region. Actually I posted the same type of problem for the other monkey's brain in January. We have solved the problem by filling all the ventricles and improving the smoothness of wm.mgz. However, we tried all methods that we learnt from the previous monkey on the second monkey, but all failed. I am curious about how the main (yellow) surface is generated. Is it purelly reconstructed from wm.mgz, or it also need brainmask.mgz? I also edited the brainmask.mgz by darkening the gray matter surrounding the problematic regions, but it didn't work out either. I think this problem might be quite common for the monkey community, because we met it on both of our monkeys. Thanks, Yang Liu

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2x2x2 design
by Gabriel Go.Es. 18 Mar '11

18 Mar '11

Dear Freesurfer experts, I'm wondering how to set a 2x2x2 anova (diagnosis)x(gender)x(apoe) g1MaleE4 g1MalenoE4 g1FemaleE4 g1FemalenoE4 g2MaleE4 g2MalenoE4 g2FemaleE4 g2FemalenoE4 option 1 [1 1 -1 -1 0 0 0 0] [1 1 0 0 -1 -1 0 0] [1 1 0 0 0 0 -1 -1] /2 option 2 [1 1 1 1 -1 -1 -1 -1] [1 1 -1 -1 1 1 -1 -1] [1 -1 1 -1 1 -1 1 -1] /4 And really have no idea about the interections between factors. Could you tell me for example how to evaluate the diagnosis x gender interaction effect and the interaction among the three factors (diagnosis x gender x apoe). Bests regards, Gabriel

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CUDA installation
by Gonzalo Rojas Costa 17 Mar '11

17 Mar '11

Hi: I tried to install CUDA to use with freesurfer, but I got some errors that I sent to freesurfer list sometime ago... Could you please send how can I install CUDA and freesurfer in a Ubuntu platform ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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hippocampal subfields
by Thomas Wolbers 17 Mar '11

17 Mar '11

Hi there, I was wondering whether there is any chance the automated segmentation of hippocampal subfields might be incorporated in the next Freesurfer update... Cheers, Thomas Wolbers -- --------------------------------------------------------- Dr. rer. nat. Thomas Wolbers Senior Lecturer Centre for Cognitive and Neural Systems& Centre for Cognitive Ageing and Cognitive Epidemiology The University of Edinburgh 1 George Square Edinburgh EH8 9JZ - email: twolbers(a)ed.ac.uk url: www.sal.mvm.ed.ac.uk ---------------------------------------------------------- On 09/03/2011 13:58, Thomas Wolbers wrote: > Dear Koen, > > I found your email from early 2009 regarding segmentation of > hippocampal subfields - may I ask whether there is any chance that > this feature will be implemented in Freesurfer any time soon? > > Best, > Thomas Wolbers > > We have recently developed a method for automatically segmenting the > hippocampal subfields from ultra-high resolution MRI data. The > software code > is not yet in FreeSurfer, but will be in the future. It produces > volumetric > segmentations, rather than surface representations, though. > > - Koen > >> >> Can freesurfer flatten (and only display) a (or several) segmented >> subcortical area(s), e.g. hippocampal region? If yes, can the fine >> structures in such a region (such as CA1,2,3, DG, etc.) be labeled? >> >> >> >> Thanks, >> >> Mingwu > > The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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recon-all
by leonardo kay 17 Mar '11

17 Mar '11

Hi I have been trying to import my data and create a subject directory using the following command: recon-all -i <path-to-first-structural> -s <subjid> replacing <path-to-first-structural> with the path where my T1 structural nifti is allocated, and -s <subjid> with the name of the subject (susu), which is supposed to be the name of the directory too. But after running this command i receive this message: *recon-all /home/virtualuser/apps/freesurfer/subjects susu ERROR: Flag /home/virtualuser/apps/freesurfer/subjects unrecognized. /home/virtualuser/apps/freesurfer/subjects susu Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s exited with ERRORS at Thu Mar 17 14:49:33 EDT 2011*. Can anyone help me determining the problem. Thanks in advance Leo

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mri_normalize
by Juranek, Jenifer 17 Mar '11

17 Mar '11

I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions have intensity values >110; cortical GM regions have intensity values 70-106; csf intensity values are around 60. The output file (T1.mgz) is all black (no different when changing intensity/contrast display options). I tried a "kinder gentler" normalization to write out a T1_gentler.mgz file, but got the same result (all black output image). I see that the # of peaks is not >1 (MRIsplineNormalize)...but not sure how to intervene at this stage. Any ideas? Many Thanks, Jenifer [jjuranek@localhost subjects]$ mri_normalize -gentle ATIS_0009_B_cw256/mri/nu.mgz ATIS_0009_B_cw256/mri/T1_gentle.mgz performing kinder gentler normalization... reading from ATIS_0009_B_cw256/mri/nu.mgz... normalizing image... talairach transform 1.081 -0.071 0.112 -2.139; 0.079 1.020 0.075 -20.692; -0.117 -0.062 1.133 -11.092; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 1 ERROR: number of peaks must be > 1 for spline 1d normalization failed - trying no1d... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to ATIS_0009_B_cw256/mri/T1_gentle.mgz 3D bias adjustment took 0 minutes and 42 seconds.

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scatterplot saving problem with qdec 1.4
by johanna feiler 17 Mar '11

17 Mar '11

Dear FreeSurfer experts, I'm using qdec 1.4 and I want to save the scatterplot with the "save GDF plot as postscript" button. It pretends saving a file but in fact it doesn't. Instead, in the terminal window following error message appears: wrong # args: should be "FsgdfPlot_SaveToPostscript iID ifnPS" Any ideas about how to solve that problem? Beside that, is there any possibility to stream out the beta weights for a simple group comparison? Thanks a lot for your answers and kind regards, Johanna Feiler ___________________________________________________________ Empfehlen Sie WEB.DE DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 100,- Euro! https://freundschaftswerbung.web.de

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Re: [Freesurfer] mri_mask problem
by Gabriel Go.Es. 17 Mar '11

17 Mar '11

Hello Nick I'm wondering if you're able to verify my data today, I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked, I'm guessing you'll need my data, to see if there is something wrong on it, but I think is gonna be hard to send it to through the e-mail. Bests, Gabriel. > Subject: RE: [Freesurfer] mri_mask problem > From: nicks(a)nmr.mgh.harvard.edu > To: gabriellbk(a)hotmail.com > Date: Thu, 10 Mar 2011 21:38:50 -0500 > > i'd have to try to replicate this myself, although it will have to wait > till monday (i'm with the freesurfer group three days a week). > > i wonder if you can use the brain.mgz as your mask instead of > brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their > actually not there (zeroed). > > n. > > On Thu, 2011-03-10 at 08:42 +0000, Gabriel Go.Es. wrote: > > Hello Nick, > > good mornig for you, when you read this, Now I have tryed the flag in > > the mri_mask command but it seems too similar to what was doing > > before, it says that will transfer 1 voxel edits to dst vol, but there > > many more voxels edited, I have also tryed mri_vol2vol in the > > brainmask.mgz intead of brain.mgz but the result is exactly the same > > (the output from mri_vol2vol has the voxel 'deletions', but the > > mri_mask ignore them. Now i have no idea how to solve this, do you? > > > > Bests, > > Gabriel > > > > > > > > > > > > > > > > > Subject: RE: [Freesurfer] mri_mask problem > > > From: nicks(a)nmr.mgh.harvard.edu > > > To: gabriellbk(a)hotmail.com > > > Date: Wed, 9 Mar 2011 18:00:37 -0500 > > > > > > we've improved some of the help text for the next version (5.1), > > which > > > is the only reason i noticed it this time. > > > > > > > > > On Wed, 2011-03-09 at 22:58 +0000, Gabriel Go.Es. wrote: > > > > > > > > Than you Nick, > > > > > > > > Actually that was exactly what i did, delete some voxels from the > > > > brainmask, I will try adding the flag and let you know, I dind't > > saw > > > > that this option exist in the mri_mask. > > > > > > > > thank you again, > > > > Gabriel > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Subject: Re: [Freesurfer] mri_mask problem > > > > > From: nicks(a)nmr.mgh.harvard.edu > > > > > To: gabriellbk(a)hotmail.com > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > Date: Wed, 9 Mar 2011 17:52:34 -0500 > > > > > > > > > > hi, not sure what you are trying to do, as the commands below > > seem > > > > to do > > > > > what i expect them to do, which is to create a masked > > > > (skull-stripped) > > > > > version of rawavg.mgz. what do you mean by 'manual segmentation > > > > > changes'?, and what exactly is going wrong? > > > > > > > > > > if you deleted voxels in brainmask.mgz, then perhaps you need to > > add > > > > the > > > > > flag -keep_mask_deletion_edits to mri_mask to transfer those > > voxels > > > > > ('deleted' voxels actually have a special value to indicate > > > > deleted). > > > > > > > > > > n. > > > > > > > > > > > > > > > > > > > > On Wed, 2011-03-09 at 22:28 +0000, Gabriel Go.Es. wrote: > > > > > > > > > > > > Hello everybody, > > > > > > Sorry for the insistance, but I need to solve this... > > > > > > > > > > > > I'm making some manual segmentation changes in the > > brainmask.mgz > > > > and > > > > > > using mri_vol2vol and mri_mask commands to apply these changes > > to > > > > the > > > > > > rawavg.mgz, the output from the mri_vol2vol looks perfectly > > > > normal,and > > > > > > retains all changed made by me, but when I use the mri_mask > > > > command > > > > > > over the rawavg.mgz no segmentation seems to be donne in the > > final > > > > > > output file. > > > > > > > > > > > > > > > > > > Does any one has an idea of what could be wrong? > > > > > > > > > > > > > > > > > > the commands after manual corrections are: > > > > > > > > > > > > > > > > > > mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out > > brain2raw.mgz > > > > > > --regheader > > > > > > mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Thanks in advanced, > > > > > > Gabriel > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > 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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