Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

bad reconstructions; why?
by Catherine Bois 23 Nov '12

23 Nov '12

Hello, I have a question re reconstructing brains (ie after doing the edits and running them again to ensure the edits went through). Before the reconstruction, the whole brain was there, however afterwards, large chunks of the brain is missing. Im worried whether this is something to do with the edits i have done; ie can control points/white matter edits actually make parts of the brain "go missing"? Or is it more likely that somewhere along the process the watershed parameters changed/gone wrong? Has anybody else experienced this problem? Thank you so much for your help Regards Cathy

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optic radiation ROI
by Ritobrato Datta 22 Nov '12

22 Nov '12

Hi All, Is there an Optic Radiation ROI in freesurfer or some other program ? Please let me know. Thank you Ri

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wm vol mismatch
by Gabriel Gonzalez Escamilla 22 Nov '12

22 Nov '12

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Tool for incorporating T2-SPACE data in pial surface recons?
by Winter, Warren 22 Nov '12

22 Nov '12

Hi all, Back in January and October Bruce mentioned that he had under development some scripts designed to utilize T2-SPACE images for better pial surface reconstruction in the presence of dura -- I was just wondering if any of that is ready for trial? Thanks! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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intrinsic curvature
by irene.mat＠libero.it 22 Nov '12

22 Nov '12

Hi FS Developers,I would like to know if the measures of intrinsic curvature of FS are quite reliable; I would like to launch a project with this parameter, but I've never used this.Which is your experience? Thanks,IreneResident in Neurology, Italy

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Re: [Freesurfer] tksurfer crashes
by Johan Carlin 22 Nov '12

22 Nov '12

On the off chance that you are using a Mac - I had a similar issue with X11 and tksurfer becoming unresponsive at the tkoInitWindow stage. I think this is because a recent OS X update broke X11. This update (from X11 2.5.4 to 2.6.5) fixed the problem for me: http://support.apple.com/kb/DL1605 Cheers, Johan Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a solution to this problem in the mailing list. Any suggestions are welcome! Ruthger Righart Hi Michelle, hmmm, no idea. Do you want to upload the the subject and we'll see if we can replicate the problem? Do you have enough memory on that machine? Bruce On Mon, 19 Mar 2012, Michelle Umali wrote: Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07) _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Johan Carlin, PhD Research Associate MRC Cognition & Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF UK johan.carlin(a)mrc-cbu.cam.ac.uk +44 (0)1223 355294 ext 278

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selection of a restricted structure, easy question ?
by charles laidi 21 Nov '12

21 Nov '12

Dear Freesurfers, I already have some experiment in segmentation : I just used FSL to perform cerebellar segmentation. I wanted to know if it's possible to run segmentation on a restricted structure (i.e cerebellum) instead of performing segmentation on the whole brain. It ll be easier for me and eventually faster since I have a lot of MRI. I know it's possible in FSL so my question is : can I do the same in freesurfer ? Thanks a lot, Charles (Paris)

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the positions of white/pial surfaces and the brain.mgz
by Longchuan Li 21 Nov '12

21 Nov '12

Hi, FreeSurfer experts I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For example, when I used "mris_fill" to write white and pial surfaces into volume files, they do not have same sto_xyz and qto_xyz values as these in the brain.mgz. This is not the case for human data. So my questions are: (1) how could I find a transformation matrix between the two, so that when I am using surface-based tractography in the future, the program can find the correspondence between the points on the surfaces and those in the volumetric diffusion MRI data? (2) How in the future, can I avoid such misregistrations in generating non-human primate surface files in FreeSurfer? Thank you very much in advance! Longchuan

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recon-all crashes at nu_estimate_np_and_em
by Negar Memarian 21 Nov '12

21 Nov '12

Hi, The recon-all command crashes at the nu_estimate_np_and_em step with this error message: nu_estimate_np_and_em: crashed while running spline_smooth (termination status = 6) nu_correct: crashed while running nu_estimate_np_and_em (termination status = 65280) ERROR: nu_correct The recon-all.log file is attached. I want to use this for a subject whose images were imported from DICOM to mgz using recon-all -i Thank you, Negar

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problem with c_ras in converted AFNI .BRIK
by Tom Holroyd (NIH/NIMH) [E] 21 Nov '12

21 Nov '12

If I do "3dcopy ortho+orig ortho.nii" then 3dinfo shows that the two datasets share the same coordinate system, however when I use mri_info, the results differ. For example, 3dinfo, both .BRIK and .nii: Geometry String: "MATRIX(0,0,-1,127,1,0,0,-127,0,-1,0,180):256,256,256" R-to-L extent: -128.000 [R] -to- 127.000 [L] -step- 1.000 mm [256 voxels] A-to-P extent: -127.000 [A] -to- 128.000 [P] -step- 1.000 mm [256 voxels] I-to-S extent: -75.000 {I] -to- 180.000 [S] -step- 1.000 mm [256 voxels]* mri_info ortho+orig says: voxel to ras transform: 0.0000 0.0000 1.0000 -128.5000 -1.0000 0.0000 0.0000 127.5000 0.0000 -1.0000 0.0000 75.5000 0.0000 0.0000 0.0000 1.0000 while mri_info ortho.nii produces (this is correct): voxel to ras transform: -0.0000 -0.0000 1.0000 -127.0000 -1.0000 -0.0000 -0.0000 127.0000 0.0000 -1.0000 0.0000 180.0000 0.0000 0.0000 0.0000 1.0000 in particular, the center of the volume appears to be translated. So if you run FreeSurfer on the .nii file, the surface is shifted relative to what you get when you run FreeSurfer on the .BRIK file, even though the original input was the same. Also mri_info seems to have shifted things to half-integer coordinates, while the .nii version doesn't. I'm not really sure about the half-integer thing, but it's a separate issue. I think the problem is a bug in utils/afni.c, where it calculates c_ras. I've attached a patch. The problem is that FreeSurfer wants ras coordinates, which are LPI coordinates in AFNI notation, and we're staring in dataset coordinates (here ASL). First the transform matrix is computed (correctly). Then c_ras is calculated using the AFNI DELTA and ORIGIN header fields. I'm really not sure what the old code was doing, the terms seem to be associated the wrong way. The new code correctly multiplies the ORIGIN times the DELTAs to get all negative numbers in dataset coordinates (that is, the origin). This is then added to the center, also in dataset coordinates, and then this is multiplied by the rest of the transform matrix, which is a vox2ras matrix, yielding c_ras that agrees with the result from the .nii file. Except for that half-integer thing, which boils down to the afni.c code doing (w-1)/2 and the .nii file code doing w/2. Perhaps the AFNI code shouldn't subtract 1 either ? {the relevant lines are also part of the patch, but I left in the (w-1)/2} Unfortunately it seems there is no easy way to compute the correct c_ras if you started with a .BRIK, unless you have the original .BRIK. In that case 3dcopy it to a .nii file and mri_info that. Err, I haven't actually tested the patch ... I'm fairly certain it's the .nii file results that are correct, and not the other way around. It would be nice to confirm that this happens with other datasets besides the one I tried. It's easy to check if you have an AFNI dataset sitting around. Thanks, Tom -- The white knight is talking backwards.

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Freesurfer November 2012