Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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corpus callosum volume in aseg.mgz...
by Gonzalo Rojas Costa 16 Mar '11

16 Mar '11

Hi: The CC volume in aseg.mgz is computed using two slices to the left and two sagital slices to the right the midline ?... 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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MCSRCH error
by Juranek, Jenifer 16 Mar '11

16 Mar '11

While processing a normal brain through fsv5.0.0, an unfamiliar message popped up in the screen output (see below). Any ideas what I should do about this message (anything in particular I should check)? Many Thanks, Jenifer IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145193.0 tol 0.000000 final transform: 1.386 -0.067 0.094 -63.518; 0.088 1.120 -0.108 -0.481; -0.131 0.093 0.972 -2.704; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 34 minutes and 38 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details)

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Is there a way to obtain the thickness of every vertex of the whole brain?
by 汪贵宏 16 Mar '11

16 Mar '11

Hi,all: Just as the title says,I wonder if there is a method to obtain the thickness of each vertex in the whole brain,and so,if we can,how do we kown which of the area is the vertex belong to? I am using the freesurfer 5.0. thanks in advance! wang

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Re: [Freesurfer] corpus calosum volume ?...
by Gonzalo Rojas Costa 15 Mar '11

15 Mar '11

Hi Bruce: Thanks you very much for your answer... And, how can I get the volume of the new segmentation of the CC that I got with mri_cc command ?... Sincerely, Gonzalo Rojas Costa El 15-03-2011 21:27, Bruce Fischl escribió: > I mean that if the volume is rotated in any 2d slice it can look as if > only some of the cc is properly labeled, even if the full 3d labeling is > correct > On Tue, 15 Mar 2011, Gonzalo Rojas Costa wrote: > >> Hi Bruce; >> >> I don't understand why you said that in 3D the labeling is usually >> correct... ???... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >> >> El 15-03-2011 15:33, Bruce Fischl escribió: >>> Hi Gonzalo >>> >>> mri_cc computes the optimal rotation. If the patient's head is not >>> straight this can make it look like an inconsistent labeling, but in 3d >>> it usually is correct. >>> >>> Bruce >>> >>> On Tue, 15 Mar 2011, Gonzalo Rojas Costa wrote: >>> >>>> Hi: >>>> >>>> The CC_Posterior, CC_Central, etc, volumes in "aseg.mgz" are the >>>> complete CC volume, or it includes only some sagital slices ?... >>>> >>>> How can I meassure the CC volume for some sagital slices only (5 in >>>> total for example) ?... When I tried using "mri_cc" I got an error >>>> (for example) in the case that the patient is slightly rotated >>>> (freesurfer segments only one section of the CC as CC and the other as >>>> WM)... >>>> >>>> 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 >>>> >>>> >>>> >>> >>> >>> 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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Freesurfer