Freesurfer May 2004

freesurfer@nmr.mgh.harvard.edu

14 participants
13 discussions

non-primate brains
by Geoffrey Aguirre 29 Jun '04

29 Jun '04

Free surfers -- I am collecting data from dogs. Any advice regarding passing this data through the system? I have a couple of specific questions: 1) Should I acquire data with voxel sizes smaller than 1mm, given that the brain is much smaller? How would I tell free-surfer to operate with this higher resolution data? 2) So far, automated skull stripping has been a failure, even with definition of a "seed point" in the white matter. The routine strips away the brain around the seed point, leaving a large chunk of scalp and muscle with a bit of cortex attached. Any thoughts on how to get this going? Thanks in advance for any help, Geoff -- Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

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relationship between white and pial surfaces
by Satrajit Ghosh 31 May '04

31 May '04

Is there an easily quantifiable relationship between the white and pial surfaces? Such as: pial_vertex = white_vertex + vertex_thickness*vertex_normal; I understand that vertex_normals could be computed in different ways (Eg, Desbrun et al 2000). If so, could we find out which computation scheme is used (a reference would be sufficient)? Thanks, Satra -- Satrajit S. Ghosh Department of Cognitive and Neural Systems, Boston University (I): http://www.cns.bu.edu/~satra

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Freesurfer & tkmedit
by X.Chitnis＠iop.kcl.ac.uk 28 May '04

28 May '04

Hi, I'm a new user of Freesurfer and am having a problem viewing files. I installed the software on a PC running Mandrake Linux 10.0. Everything seemed fine. Mandrake comes with Tcl/Tk 8.4 rather than 8.3 which freesurfer looks for, so I made links back to (for example) libtcl8.3.so When I try to view the files through the "volume" button, the button changes to puple and says "quit volume" but no window appears, and after ~20 seconds it just goes back to "volume". No error message is generated in the log - it just says "Command Finished". Having searched the mailing list, I tried it from the command line with: /home/spbcxac/freesurfer/bin/Linux/tkmedit.static test T1 It pauses for a few seconds, as if it is trying to display something, but then goes back to the prompt without a window appearing. Again no error message is generated. I would be very grateful for any suggestions as to what I'm doing wrong! Best wishes Xavier Chitnis Institute of Psychiatry, London

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RAS to mm
by Rutvik Desai 27 May '04

27 May '04

Hello, I have FreeSurfer surface models created from Talairached AFNI (+tlrc) briks. I am interested in computing distances between nodes on these (orig or smoothwm) surfaces in mm units. The +tlrc briks are 161mm (R-L) X 191mm (A-P) X 151mm (I-S). with 1X1X1 mm^3 voxels. talairach.xfm or any such files or transformations were not used. As I understand, FreeSurfer would resample this brik into a 256 X 256 X 256 RAS coordinate space. There are the coordinates you see when you look at say a ?h.smoothwm.asc file. To interpret these coordinates in terms of mm, one could multiply the X coordinate by 161/256, Y by 191/25, and Z by 151/256. The distance between two nodes computed with these modified coordinates should be in mm. Is this correct or am I missing something? thanks, Rutvik

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cache_volume_range
by orphoebe＠polyu.edu.hk 27 May '04

27 May '04

Hi Bruce and Yasunari, Thanks for your suggestions. The setenv LANG C works for 'Out of memory' error. However, after I get through the mritotal, it comes with another error of 'Not implemented yet in cache_volume range...' as follows. I see that somebody asks this question before but I can't find the solution. Any suggestions? Thanks, Phoebe. ******************************* mri_add_xform_to_header /mnt/usb1/uch_language/inflated/040415_ckh/mri/transforms/talairach.xfm /mnt/usb1/uch_language/inflated/040415_ckh/mri/orig /mnt/usb1/uch_language/inflated/040415_ckh/mri/orig Thu May 27 15:56:30 GMT+8 2004 --------------------------------------------- Nu Intensity Correction Thu May 27 15:56:30 GMT+8 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, te=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [phoebe@marvin:/mnt/usb1/uch_language/inflated/040415_ckh/mri/] [2004-05-27 15:56:40] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_6196/ nu/nu0.mnc nu/nu1.imp Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() ---- Original message ---- >Date: Wed, 26 May 2004 14:45:07 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Out of memory error >To: orphoebe(a)polyu.edu.hk >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi Phoebe, > >I think this is a problem with the MNI tools that they know about. Someone >posted a solution here, which I think involved setting the LANG env >variable. Check out the MNI website. > >Bruce > >On Thu, >27 May 2004 orphoebe(a)polyu.edu.hk wrote: > >> Hi, >> >> I recently collected a 1-mm anatomical scan and tried to >> inflate it using the recon-all script. However, I got an >> error message 'Out of memory!' everytime at mritotal. I tried >> to increase the output size when I converted the dcm images to >> COR format, but it didn't work either. Do you have any >> suggestions? >> >> Thanks, >> Phoebe. >> >> --- >> Phoebe Suk-tak Chan, Ph.D. >> Assistant Professor >> Hong Kong Polytechnic University >> Department of Optometry and Radiography >> Hunghom, Kowloon >> Hong Kong SAR >> Tel: (852) 2766 6095 >> Fax: (852) 2764 6051 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Out of memory error
by orphoebe＠polyu.edu.hk 26 May '04

26 May '04

Hi, I recently collected a 1-mm anatomical scan and tried to inflate it using the recon-all script. However, I got an error message 'Out of memory!' everytime at mritotal. I tried to increase the output size when I converted the dcm images to COR format, but it didn't work either. Do you have any suggestions? Thanks, Phoebe. --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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New Segmentation
by Keyma Prince 22 May '04

22 May '04

I'm trying to draw a label onto the T1 brain by using the "New Segmentation" tool in TkMedit. When you select a color table shouldn't an additional window appear with the different label options within it? -keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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FW: job announcement (fwd)
by Bruce Fischl 14 May '04

14 May '04

For anyone who is interested Bruce While the FreeSurfer mailing list is provided as a public resource for academic researchers, we wanted to inform you of an opening at CorTechs Labs, Inc. Computational Imaging Scientist/Engineer - Neurosciences A full-time Computational Imaging Scientist/Engineering position to develop software for the quantification and measurement of structural 3-D MR images at CorTechs, Labs, Inc. is currently available. This is an opportunity to work with leading neuroscience researchers and scientists in an exciting medical device software company focused on developing imaging diagnostics for central nervous system diseases. Advanced theoretical abilities, creative problem solving and well-developed computational skills are required. Qualifications Experienced with Linux development environments, including with HPC's (high performance computation environments), such as clustering and optimized math libraries Advanced programming abilities with C and C++ Advanced development experience with Matlab(tm) Expert in Pattern Classification, such as Bayesian classifier design, neural network, SVM (Support Vector Machine), and signal processing Strong written and verbal communication skills Prior computational experience with neuro-MRI is required Deep experience with FreeSurfer(c) or other comparable software is a plus, as is any sequence development on any of the MR vendor platforms Duties and Responsibilities Develop software and algorithms for segmentation and quantification of neuro-MRI data Help optimize MR image acquisition protocols for quantitative analysis Generate and implement advanced computational software based upon specifications Interact and communicate effectively within the scientific engineering group Plan, schedule and execute assignments within projected timelines Education A Ph.D. in Computer Science, Imaging Processing, or related field is required, as is U.S. Citizenship or Permanent Resident status. CorTechs provides a competitive salary, health and dental benefits, as well as membership in a local health club. To apply, please email your resume to info(a)cortechs.net <mailto:info@cortechs.net> . No phone calls please. For additional information about Cortechs, please see our web site at www.cortechs.net <http://www.cortechs.net/> CorTechs Labs, Inc. is an equal opportunity employer.

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surface normal
by darren.weber＠radiology.ucsf.edu 09 May '04

09 May '04

Is the freesurfer surface tesselation consistent with the "right-hand" rule? That is, if we have a triangle of three vertex points (P1, P2 & P3), we can find 2 edges, E1 = P3 - P2 E2 = P2 - P1 and we can find the normal to this triangle surface by taking the cross product of the edge vectors N = E1 x E2 and the unit normal from this, of course. The question is, then, wether N is directed outside of the surface. Note that E1 x E2 = -1 * ( E2 x E1 ) That is, the order of the cross product is important. Also, now note that the order of the points (P1, P2 & P3) in the triangle is important. Without a consistent convention for their order, we cannot know whether the surface normal is directed inside or outside the closed brain surface. Best, Darren --------------------------------------------- This message was sent using Endymion MailMan. http://www.endymion.com/products/mailman/

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R L flipping
by Mark A. Pinsk 09 May '04

09 May '04

Hello, we are desperately in search of a way to flip our freesurfered data. There was a post a while back referring to mris_reverse but it doesn't seem to be included in the current distribution. any help would be greatly appreciated ! thanks mark _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

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Freesurfer May 2004