Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

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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RE: [Freesurfer] subcortical segmentation
by Fornito, Alexander 12 Sep '05

12 Sep '05

Fair enough. If recon-all is run without the subcortical segmentation, do manual edits to the wm volumes (eg., filling in ventricles, basal ganglia, etc) need to be performed? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 9/13/2005 6:59 AM To: Fornito, Alexander Cc: Bosky Ravindranath; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] subcortical segmentation Hi Alex, that was a prerelease version. The subcortical stuff seems fine, but we have fixed a couple of small bugs in other things, so we are going to recommend that people rerun things with the new official release that we are hoping to be done with soon (note that rerunning won't involve any manual interactions). Bruce On Tue, 13 Sep 2005, Fornito, Alexander wrote: > I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tue 9/13/2005 5:45 AM > To: Bosky Ravindranath > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] subcortical segmentation > > > > not quite, sorry. We *really* don't want to release a version with major > problems, so we've been going through everything repeatedly trying to catch > everything. We're getting there. > > Bruce > > > On Mon, 12 Sep 2005, Bosky Ravindranath wrote: > > > To Bruce Fischl and List, > > I just wanted to know if the subcortical segmentation feature has been > > released. > > Thanks, > > Bosky > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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RE: [Freesurfer] subcortical segmentation
by Tracy Wang 12 Sep '05

12 Sep '05

Hi Bruce, When you say "manual interactions" are you referring to the manual troubleshooting of the talairach transform, skull stripping and intensity normalization? Thanks, Tracy > Hi Alex, > > that was a prerelease version. The subcortical stuff seems fine, but we > have fixed a couple of small bugs in other things, so we are going to > recommend that people rerun things with the new official release that we > are hoping to be done with soon (note that rerunning won't involve any > manual interactions). > > Bruce > > On Tue, 13 Sep 2005, Fornito, Alexander wrote: > > > I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912- full.tar.gz didthe subcortical segmentation. I've run it on a couplde of brains so far and it seems to beok. Are there still some bugs with it? > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Tue 9/13/2005 5:45 AM > > To: Bosky Ravindranath > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] subcortical segmentation > > > > > > > > not quite, sorry. We *really* don't want to release a version with major > > problems, so we've been going through everything repeatedly trying to catch > > everything. We're getting there. > > > > Bruce > > > > > > On Mon, 12 Sep 2005, Bosky Ravindranath wrote: > > > > > To Bruce Fischl and List, > > > I just wanted to know if the subcortical segmentation feature has been > > > released. > > > Thanks, > > > Bosky > > > > > _______________________________________________ > > 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 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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RE: [Freesurfer] subcortical segmentation
by Fornito, Alexander 12 Sep '05

12 Sep '05

I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: > To Bruce Fischl and List, > I just wanted to know if the subcortical segmentation feature has been > released. > Thanks, > Bosky > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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subcortical segmentation
by Bosky Ravindranath 12 Sep '05

12 Sep '05

To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky

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Editing pial surface
by Lars Tjelta Westlye 12 Sep '05

12 Sep '05

Dear all, I am trying to edit the pial surface by editing/deleting voxels in the brain volume within the pial surface ('labeled' as a part of cortex), but clearly are parts of dura when manually inspected. When I rerun the last automatic procedures (fix, make_final, morph), and check the pial surface, nothing has appeared to have changed. The voxels I deleted are gone, though the pial surface still looks the same. How can I fix this without having to regenerate/reconstruct all my subjects? (I have approx. 100). Any tip? I am by the way using the Freesurfer version from june (?) 2005, and due to time restrictions I am not considering changing to the latest version for this project. Thanks a lot! Best wishes, Lars Tjelta Westlye University of Oslo

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Freesurfer