[Freesurfer] NIFTI q-factor in NIFTI header
Dear FS experts Please can you confirm that the NIFTI q-factor in the NIFTI header has to be negative (e.g. -1) in order to have correct right and left orientation. When the NIFTI q-factor is positive in my T1-w. and DTI images, then the left and the right hemisphere seem to be flipped. Thanks in advance Regards Jürgen Hänggi Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] tksurfer - rotate surface with mouse
Is it possible to rotate the surface model in tksurfer with the mouse instead of the rotation buttons on the GUI. (i.e. grab the surface model with the mouse and spin it) Jon Wieser jonwie...@netzero.com "When the going gets tough, switch to power tools." - Red Green NetZero now offers 4G mobile broadband. Sign up now. http://www.netzero.net/?refcd=NZINTISP0512T4GOUT1 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] tksurfer - rotate surface with mouse
Hi Jon glad to see you are now able to post :>. No, I don't think you can do this in tksurfer due to its age and slow redraw rate. Freeview can do it though. cheers Bruce On Fri, 11 Jan 2013, jonwie...@netzero.net wrote: > > Is it possible to rotate the surface model in tksurfer > with the mouse instead of the rotation buttons on the GUI. (i.e. grab the > surface model > with the mouse and spin it) > > Jon Wieser > jonwie...@netzero.com > > "When the going gets tough, switch to power tools." - Red Green > > > NetZero now offers 4G mobile broadband. Sign up now. > http://www.netzero.net/?refcd=NZINTISP0512T4GOUT1 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] NIFTI q-factor in NIFTI header
Hi Juergen, how are you judging whether a volume is flipped or not? The freesurfer tools should display properly regardless of the qfactor as long as the qform matrix is correct. doug On 01/11/2013 08:40 AM, Jürgen Hänggi wrote: > NIFTI q-factor Dear FS experts Please can you confirm that the NIFTI q-factor in the NIFTI header has to be negative (e.g. -1) in order to have correct right and left orientation. When the NIFTI q-factor is positive in my T1-w. and DTI images, then the left and the right hemisphere seem to be flipped. Thanks in advance Regards Jürgen Hänggi -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Fw: Re: tksurfer - rotate surface with mouse
> I tried running freeview and it aborted
>
> psy-cerebrum-r1:data brainlab$ freeview -f rh.orig
>
> bus error
> we are using a Mac Pro 2.26GHz 8 cores mac Os X 10.6.8 RAM : 12 GB
> with X11 and Xquartz
> tkmedit works fine
>
> here's the problem report from our machine
>
> Process: freeview.bin [21698]
> Path:
> /usr/local/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin
> Identifier: freeview.bin
> Version: 'latest trunk' ('latest trunk')
> Code Type: X86 (Native)
> Parent Process: bash [555]
>
> Date/Time: 2013-01-11 09:16:52.146 -0600
> OS Version: Mac OS X 10.6.8 (10K549)
> Report Version: 6
>
> Interval Since Last Report: 2980979 sec
> Crashes Since Last Report: 6
> Per-App Crashes Since Last Report: 4
> Anonymous UUID: 314FF2FE-43B0-4221-BF9A-F4428211ADA0
>
> Exception Type: EXC_BAD_ACCESS (SIGBUS)
> Exception Codes: KERN_PROTECTION_FAILURE at 0x
> Crashed Thread: 0 Dispatch queue: com.apple.main-thread
>
> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
> 0 ??? 00 0 + 0
> 1 libvtkRendering.5.2.dylib 0x02b3d1a9
> vtkCarbonRenderWindow::CreateAWindow() + 281
> 2 libvtkRendering.5.2.dylib 0x02b3bfa4
> vtkCarbonRenderWindow::WindowInitialize() + 52
> 3 libvtkRendering.5.2.dylib 0x02b3a435
> vtkCarbonRenderWindow::Start() + 21
> 4 libvtkRendering.5.2.dylib 0x02aa11db
> vtkRenderWindow::DoStereoRender() + 27
> 5 libvtkRendering.5.2.dylib 0x02aa13a9
> vtkRenderWindow::DoFDRender() + 153
> 6 libvtkRendering.5.2.dylib 0x02aa1832
> vtkRenderWindow::DoAARender() + 98
> 7 libvtkRendering.5.2.dylib 0x02a9fc54 vtkRenderWindow::Render() +
> 644
> 8 freeview.bin 0x0011d547
> wxVTKRenderWindowInteractor::OnPaint(wxPaintEvent&) + 151
> 9 freeview.bin 0x00407b53
> wxAppConsole::HandleEvent(wxEvtHandler*, void (wxEvtHandler::*)(wxEvent&),
> wxEvent&) const + 65
> 10 freeview.bin 0x00452f30
> wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const&,
> wxEvtHandler*, wxEvent&) + 212
> 11 freeview.bin 0x004532d4
> wxEventHashTable::HandleEvent(wxEvent&, wxEvtHandler*) + 204
> 12 freeview.bin 0x00453f5e
> wxEvtHandler::ProcessEvent(wxEvent&) + 240
> 13 freeview.bin 0x003525e3 wxWindow::MacDoRedraw(void*,
> long) + 975
> 14 freeview.bin 0x00353985
> wxMacWindowControlEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*,
> void*) + 815
> 15 freeview.bin 0x00354135
> wxMacWindowEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) +
> 181
> 16 com.apple.HIToolbox 0x9527ac0f
> DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) +
> 1567
> 17 com.apple.HIToolbox 0x95279ed6
> SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*,
> HandlerCallRec*) + 411
> 18 com.apple.HIToolbox 0x95279d35
> SendEventToEventTargetWithOptions + 58
> 19 com.apple.HIToolbox 0x952a1e85 HIView::SendDraw(short,
> OpaqueGrafPtr*, __HIShape const*, CGContext*) + 475
> 20 com.apple.HIToolbox 0x952a17d9
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 713
> 21 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 22 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 23 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 24 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 25 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 26 com.apple.HIToolbox 0x952a1a4c
> HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*,
> CGContext*, unsigned char, float) + 1340
> 27 com.apple.HIToolbox 0x952a07ff
> HIView::DrawComposited(short, OpaqueGrafPtr*, __HIShape const*, unsigned
> long, HIView*, CGContext*) + 873
> 28 com.apple.HIToolbox 0x952a0445 HIView::Draw(short,
> OpaqueGrafPtr*, unsigned long) + 83
> 29 com.apple.HIToolbox 0x952a0395 HIView::Render(unsigned
> long, CGContext*) + 45
> 30 com.apple.HIToolbox 0x9529fcdd
> WindowData::Pre
Re: [Freesurfer] NIFTI q-factor in NIFTI header
Hi Douglas Thanks for your answer. Our problem is actually not directly related to FS. We converted Philips .par/.rec files with two different converters, one of which was recently updated for a new platform and scanner software release, and realized that they produce different q-form matrices. The FS outputs of the differently converted data were therefore also different. I will use a vitamin A capsule as a marker to determine the hemisphere. Cheers Jürgen On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: > Hi Juergen, how are you judging whether a volume is flipped or not? The > freesurfer tools should display properly regardless of the qfactor as > long as the qform matrix is correct. > doug > > > On 01/11/2013 08:40 AM, Jürgen Hänggi wrote: >> NIFTI q-factor > > Dear FS experts > > Please can you confirm that the NIFTI q-factor in the NIFTI header has to be > negative (e.g. -1) in order to have correct right and left orientation. > > When the NIFTI q-factor is positive in my T1-w. and DTI images, then the > left and the right hemisphere seem to be flipped. > > Thanks in advance > Regards > Jürgen Hänggi Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@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.
