Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

RE: [Freesurfer] intensity normalization failure
by Fornito, Alexander 15 Sep '05

15 Sep '05

Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes? Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu; Tracy Wang Subject: RE: [Freesurfer] intensity normalization failure You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help doug On Wed, 14 Sep 2005, Bruce Fischl wrote: > should be easy enough to do in matlab. Just load the wm volume, then find all > the T1 voxels that are nonzero in it. > > Bruce > On Thu, 15 Sep 2005, Fornito, Alexander wrote: > >> Is it possible to obtain and intensity histogram of the wm voxels, or >> descriptive stats (eg., Mean, SD) as a quick check? >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Thursday, September 15, 2005 3:33 AM >> To: Tracy Wang >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] intensity normalization failure >> >> if it succeeds then the intensity in the wm should be exactly 110 over >> much of the brain, and 90<wm<120 pretty much everywhere >> >> Bruce >> >> On Wed, 14 Sep >> 2005, Tracy Wang wrote: >> >>> Hi >>> >>> What is a typical example of when the intensity normalization process >> fails? >>> Does the over-all image seem brighter? What is a good indicator of >> success >>> or failure? >>> >>> Thanks, >>> Tracy >>> >>> >>> Tracy Wang >>> Research Assistant >>> Cognitive Neuroscience Laboratory >>> >>> Washington University >>> Department of Psychology, Campus Box 1125 >>> One Brookings Drive >>> St. Louis MO 63130-4899 >>> 314-935-5019 >>> twang(a)artsci.wustl.edu >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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

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average curvatures
by Sheeva Azma 15 Sep '05

15 Sep '05

Hello, I am trying to superimpose an average curvature on the inflated brain surface of another subject. I know that you can use mris_average_curvature to create an average curvature of some specified brains, but I would like to use an average curvature that is not an average of the subjects' curvatures; instead, I'd like it to be an average of curvatures from a general atlas. How do I create, based on this average, the lh.avg_curv and rh.avg_curv files in a subject's surf/ directory? Thanks, Sheeva Azma

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tkregister2
by Sasha Wolosin 15 Sep '05

15 Sep '05

Dear all, I am having trouble running tkregister2. I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [root@bwy-1-113mm subjects]$ Any help is greatly appreciated. Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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RE: [Freesurfer] intensity normalization failure
by Fornito, Alexander 14 Sep '05

14 Sep '05

Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90<wm<120 pretty much everywhere Bruce On Wed, 14 Sep 2005, Tracy Wang wrote: > Hi > > What is a typical example of when the intensity normalization process fails? > Does the over-all image seem brighter? What is a good indicator of success > or failure? > > Thanks, > Tracy > > > Tracy Wang > Research Assistant > Cognitive Neuroscience Laboratory > > Washington University > Department of Psychology, Campus Box 1125 > One Brookings Drive > St. Louis MO 63130-4899 > 314-935-5019 > twang(a)artsci.wustl.edu > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] intensity normalization failure
by Bagnato, Francesca (NIH/NINDS) 14 Sep '05

14 Sep '05

Just a cuoriosity: which kind of volumes are you using? I had lots of troubles with 3T SPGRs and saw the center of the images just brighter. francesca _____ From: Tracy Wang [mailto:twang@artsci.wustl.edu] Sent: Wed 9/14/2005 1:23 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] intensity normalization failure Hi What is a typical example of when the intensity normalization process fails? Does the over-all image seem brighter? What is a good indicator of success or failure? Thanks, Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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intensity normalization failure
by Tracy Wang 14 Sep '05

14 Sep '05

Hi What is a typical example of when the intensity normalization process fails? Does the over-all image seem brighter? What is a good indicator of success or failure? Thanks, Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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Problems with nifti file format
by Hans Johnson 14 Sep '05

14 Sep '05

Developers: I am trying to convert a nifti formated image to the mgz format using mri_convert, but there is an error stating that the time units are unknown. Since there are only 3 dimension, the time dimension should not matter. mri_convert -it nii -ic 128 128 128 -oc 128 128 128 -iid 1.0 0.0 0.0 new_all.nii new.mgz mri_convert -it nii -ic 128 128 128 -oc 128 128 128 -iid 1.0 0.0 0.0 new_all.nii new.mgz reading from new_all.nii... niiRead(): unknown time units in /Users/hjmjohnson/src/regressiontest/SGI/MR/B2-downsampled/TEST/20_ACPC/harr is/new_all.nii Any help would be greatly appreciated. Thanks, Hans PS: Here is a dump of the nifti header that I am trying to use: ~/src/deleteme/utils/nifti_tool -disp_hdr -infile new_all.nii header file 'new_all.nii', num_fields = 43 all fields: name offset nvals values ------------------- ------ ----- ------ sizeof_hdr 0 1 348 data_type 4 10 db_name 14 18 extents 32 1 0 session_error 36 1 0 regular 38 1 r dim_info 39 1 0 dim 40 8 3 100 100 124 1 1 1 1 intent_p1 56 1 0.0 intent_p2 60 1 0.0 intent_p3 64 1 0.0 intent_code 68 1 0 datatype 70 1 2 bitpix 72 1 8 slice_start 74 1 0 pixdim 76 8 0.0 2.0 2.0 1.6 1.0 1.0 1.0 1.0 vox_offset 108 1 352.0 scl_slope 112 1 1.0 scl_inter 116 1 0.0 slice_end 120 1 0 slice_code 122 1 0 xyzt_units 123 1 2 cal_max 124 1 0.0 cal_min 128 1 0.0 slice_duration 132 1 0.0 toffset 136 1 0.0 glmax 140 1 0 glmin 144 1 0 descrip 148 80 aux_file 228 24 qform_code 252 1 0 sform_code 254 1 2 quatern_b 256 1 0.0 quatern_c 260 1 0.0 quatern_d 264 1 0.0 qoffset_x 268 1 0.0 qoffset_y 272 1 0.0 qoffset_z 276 1 0.0 srow_x 280 4 -2.0 0.0 0.0 0.0 srow_y 296 4 0.0 0.0 -2.0 0.0 srow_z 312 4 0.0 1.6 0.0 0.0 intent_name 328 16 magic 344 4 n+1

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RE: [Freesurfer] large radius
by Fornito, Alexander 13 Sep '05

13 Sep '05

Hi Bruce and Florent, Your comments re: isoptropic voxels raised a question for me. How is mgz different to cor format? Does mri_convert not interpolate to 1mm3 for mgz? The imaging parameters are: IR prep time, 500 ms; TE minimum, 2.8 ms; TR 13.9 ms; bandwidth, 15.63 kHz; 1 NEX; 20° flip angle; 2 mm contiguous slices; FOV 24 cm; up to 128 volumes for full brain coverage; 512 (frequency, SI) by 256 (phase) matrix, zipped to 512 in phase direction with extended dynamic range. -----Original Message----- From: florent segonne [mailto:fsegonne@csail.mit.edu] Sent: Wed 14/09/2005 6:29 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] large radius Hi Alex, I think that mri_watershed is 'incorrectly' assuming 1*1*1mmm isotropic voxels. We'll update the code so that it won't stop there. Florent ------------------------------------- Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne ------------------------------------- On Tue, 13 Sep 2005, Bruce Fischl wrote: > Hi Alex, > > the 2mm slice thickness could be trouble. Usually we don't recommend trying > to recon cortical models with any dimension greater than 1.5mm. Why do > anisotropic? Can you describe the rest of the acquisition parameters? > > Bruce > > > On Tue, 13 Sep 2005, Fornito, Alexander wrote: > >> HI, >> I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I >> seem to be able to convert them to .mgz ok, but when I run mri_watershed I >> get an error saying "main radius too high" (output below). Any ideas as to >> what's happening? >> Thanks, >> Alex >> >> >> mri_watershed 1001670.mgz 1001670_brain.mgz >> >> >> ************************************************************ >> The input file is 1001670.mgz >> The output file is 1001670_brain.mgz >> If this is incorrect, please exit quickly the program (Ctl-C) >> >> >> *************************WATERSHED************************** >> preflooding height equal to 25 percent >> Sorting... >> first estimation of the COG coord: x=253 y=50 z=235 r=135 >> first estimation of the main basin volume: 10415397 voxels >> Error >> main radius too high >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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freesurfer transformation matrix
by Bakkour, Akram 13 Sep '05

13 Sep '05

Dear all, I am an undergraduate student working in Dr. David Ress' lab at Brown University making a comparison of different brain segmentation applications among them freesurfer. However, I ran into much difficulty conducting a proper quantitative comparison of outputs. Indeed, I noticed that the data was shifted and possibly rotated in freesurfer. In order to superimpose the output by the different applications I must put all data back in its original coordinate system. I was wondering if there is a way of obtaining the transformation matrix used by freesufer. Thank you very much for your help. My very best regards, Akram.

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large radius
by Fornito, Alexander 13 Sep '05

13 Sep '05

HI, I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I seem to be able to convert them to .mgz ok, but when I run mri_watershed I get an error saying "main radius too high" (output below). Any ideas as to what's happening? Thanks, Alex mri_watershed 1001670.mgz 1001670_brain.mgz ************************************************************ The input file is 1001670.mgz The output file is 1001670_brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=253 y=50 z=235 r=135 first estimation of the main basin volume: 10415397 voxels Error main radius too high

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Freesurfer