Freesurfer September 2010

freesurfer@nmr.mgh.harvard.edu

93 participants
127 discussions

recon-all quality control checks on large numbers of subjects
by Avram Holmes 16 Sep '10

16 Sep '10

All, I'm setting up a processing stream for a sizable dataset and I'd like to use .tcl scripts to save out images for some preliminary quality control checks. It was my intention to output images of the the curvature and structural parcelation overlaid on the inflated surface (6 views for each hemi) and the lh/rh.white and aseg.mgz segmentation overlaid on the volume (a midline coronal, sagital, and axial slice). The idea would be that then we could go through and quickly check which subjects may need manual intervention. I wanted to double check that the images I am saving out are consistent with the checks that other folks are doing and I'd love to get some feedback on what else I should look save. Thanks, Avram -- Avram Holmes PhD Postdoctoral fellow Buckner Lab Department of Psychology and Center for Brain Science, Harvard University Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital

3 2

mri_vol2surf resulting in many vertices with NaN's
by Joonkoo Park 16 Sep '10

16 Sep '10

Hi, I am trying to resample two volumetric data onto freesurfer individual subjects. The volume images are NIFTI format from SPM results (spmT_0001.img and con_0001.img). I used the following command to resample spmT map onto the surface: > mri_vol2surf --mov 3t0499/model/ravol/spmT_0001.img --reg 3t0499/register.dat --projfrac 0.5 --interp nearest --hemi lh --o ./lh.spmT_tmp.mgh --surf-fwhm 5 --noreshape > .mri_vol2surf.spmT.txt and this worked fine when I checked lh.spmT_tmp.mgh using tksurfer. Similarly, I tried to resample the con_0001.img image, using the following command: > mri_vol2surf --mov 3t0499/model/ravol/con_0001.img --reg 3t0499/register.dat --projfrac 0.5 --interp nearest --hemi lh --o ./lh.con_tmp.mgh --surf-fwhm 5 --noreshape > .mri_vol2surf.con.txt Now, when I checked the results using tksurfer, majority of the surface vertices are valued zero, and these zero-valued vertices were NaN's when I read the mgh file in matlab. I expect the same resampling procedure to take place for the spmT map and the con map. There should be no difference between the spmT*.img and the con*.img except that the values at each voxel is different. But, why are the two *mgh files look so different? Why do I see NaN's in most of the vertices in the con*.mgh (while it seems spmT*.mgh looks fine)? Joon p.s. FYI, .mri_vol2surf.spmT.txt and mri_vol2surf.con.txt are below: > more .mri_vol2surf.spmT.txt srcvol = 3t0499/model/ravol/spmT_0001.img srcreg = 3t0499/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface ./3t0499/surf/lh.white Done reading source surface Reading thickness ./3t0499/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 10273 Surface smoothing by fwhm = 5 (n=14) Smoothing done, nsteps = 14, tsec = 0.375 Writing to ./lh.spmT_tmp.mgh Dim: 144558 1 1 > more .mri_vol2surf.con.txt srcvol = 3t0499/model/ravol/con_0001.img srcreg = 3t0499/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface ./3t0499/surf/lh.white Done reading source surface Reading thickness ./3t0499/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 10273 Surface smoothing by fwhm = 5 (n=14) Smoothing done, nsteps = 14, tsec = 0.383 Writing to ./lh.con_tmp.mgh Dim: 144558 1 1

2 1

Re: [Freesurfer] mri_convert with Nifti1 files
by Douglas N Greve 16 Sep '10

16 Sep '10

What coordinates is your other tool using and how do you know that they are from the same coordinate system that tkmedit uses? There are many different coorindate systems (tkmedit will show two, volume and scanner). doug roberto.viviani(a)uni-ulm.de wrote: > >> How do you know what coordinates it should be? > Because I can open the Nifti image with something else and use > anatomical landmarks to verify where I am... > > Be it as it may, loading a different mgz image in tkmedit does not > reset the position of the pointer, so I can easily observe the > swapping of coordinates after loading a resliced volume. > >> Also, try looking at >> the scanner coordinates instead of the volume coordinates. > The 'Volume index' label giving coordinates in voxel units? After > reslicement+conversion, these coordinates change, but the raw data are > indeed reordered. > > best, Roberto > > >> >> doug >> >> On 9/16/10 8:27 AM, roberto.viviani(a)uni-ulm.de wrote: >>> Hallo, >>> >>> >>>> HI Roberto, I can't quite tell what the problem is that you are trying >>>> to fix. What is actually going wrong? If it displays correctly in >>>> tkmedit, then the coordinates are probably write. I don't know what >>>> you >>>> mean when you say the the Volume RAS coords are swapped. >>> >>> I mean that when I click on a voxel that is supposed to be at >>> coordinates x, y, z -25 10 -20, say, the Volume RAS label tells me >>> I am at -25, -20, -10. I reslice the image (including the new >>> mapping in the header), reconvert it, then tkmedit displays it just >>> the same as before, but, at the same voxel, the Volume RAS >>> coordinates are 10 -25 -20. >>> >>> Thanks again, >>> Roberto Viviani >>> >>> >>>> >>>> doug >>>> >>>> roberto.viviani(a)uni-ulm.de wrote: >>>>> Dear list, >>>>> >>>>> I am using mri_convert to prepare my pipeline for FreeSurfer, >>>>> and, yes, I have been struggling for a couple of days to get it >>>>> done. >>>>> >>>>> After conversion, I have no problem using tkmedit to display the >>>>> file; however, the Volume RAS coordinates are swapped -- the >>>>> numbers aren't wrong, they are just swapped in place and/or >>>>> inverted, while the image is always displayed fine (left on the >>>>> right, up is up, front is front etc, which shows, I assume, >>>>> that the coordinates are right in the header). >>>>> >>>>> By 'always' I mean that if I reslice the image, and then convert >>>>> it, then mri_convert will always produce an mgz file that will >>>>> be displayed correctly in tkmedit, but will also produce a new >>>>> permutation of the swapping in the Volume RAS coordinates. >>>>> >>>>> Even if a reslice my image in axial slices (it was originally the >>>>> usual sagittal MPRAGE thing from Siemens), I get the wrong >>>>> swapping. Can anyone tell me how to reslice my image to get it >>>>> right? >>>>> >>>>> Thank you in advance, >>>>> Roberto Viviani >>>>> University of Ulm, Germany >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> 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. >>> >>> >>> >>> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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Re: [Freesurfer] mri_convert with Nifti1 files
by Douglas Greve 16 Sep '10

16 Sep '10

How do you know what coordinates it should be? Also, try looking at the scanner coordinates instead of the volume coordinates. doug On 9/16/10 8:27 AM, roberto.viviani(a)uni-ulm.de wrote: > Hallo, > > >> HI Roberto, I can't quite tell what the problem is that you are trying >> to fix. What is actually going wrong? If it displays correctly in >> tkmedit, then the coordinates are probably write. I don't know what you >> mean when you say the the Volume RAS coords are swapped. > > I mean that when I click on a voxel that is supposed to be at > coordinates x, y, z -25 10 -20, say, the Volume RAS label tells me I > am at -25, -20, -10. I reslice the image (including the new mapping > in the header), reconvert it, then tkmedit displays it just the same > as before, but, at the same voxel, the Volume RAS coordinates are 10 > -25 -20. > > Thanks again, > Roberto Viviani > > >> >> doug >> >> roberto.viviani(a)uni-ulm.de wrote: >>> Dear list, >>> >>> I am using mri_convert to prepare my pipeline for FreeSurfer, and, >>> yes, I have been struggling for a couple of days to get it done. >>> >>> After conversion, I have no problem using tkmedit to display the >>> file; however, the Volume RAS coordinates are swapped -- the >>> numbers aren't wrong, they are just swapped in place and/or >>> inverted, while the image is always displayed fine (left on the >>> right, up is up, front is front etc, which shows, I assume, that >>> the coordinates are right in the header). >>> >>> By 'always' I mean that if I reslice the image, and then convert >>> it, then mri_convert will always produce an mgz file that will be >>> displayed correctly in tkmedit, but will also produce a new >>> permutation of the swapping in the Volume RAS coordinates. >>> >>> Even if a reslice my image in axial slices (it was originally the >>> usual sagittal MPRAGE thing from Siemens), I get the wrong >>> swapping. Can anyone tell me how to reslice my image to get it >>> right? >>> >>> Thank you in advance, >>> Roberto Viviani >>> University of Ulm, Germany >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. > > > >

1 0

how to fix the this problem when I open freeview.
by Rahyeong Juh 16 Sep '10

16 Sep '10

Hi Experts, I am extremely new to Freesurfer and I have a basic question that I didn't "freeview" I have a big problem when I open "freeview" , "bus error" like under .. Can you help me fix the this problem? Best regards Rahyeong Juh ======================================== Process: freeview.bin [691] Path: /Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin Identifier: freeview.bin Version: 'latest trunk' ('latest trunk') Code Type: X86 (Native) Parent Process: tcsh [596] Date/Time: 2010-09-11 16:47:28.575 +0900 OS Version: Mac OS X 10.6.4 (10F569) Report Version: 6 Interval Since Last Report: 3749 sec Crashes Since Last Report: 12 Per-App Crashes Since Last Report: 11 Anonymous UUID: 17FFC01A-48E3-4002-A7A6-D7F30E7CCFD5 Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 ??? 0000000000 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 0x97c7af2f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1567 17 com.apple.HIToolbox 0x97c7a1f6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411 18 com.apple.HIToolbox 0x97c7a055 SendEventToEventTargetWithOptions + 58 19 com.apple.HIToolbox 0x97ca20c5 HIView::SendDraw(short, OpaqueGrafPtr*, __HIShape const*, CGContext*) + 475 20 com.apple.HIToolbox 0x97ca1a19 HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 713 21 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 22 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 23 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 24 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 25 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 26 com.apple.HIToolbox 0x97ca1c8c HIView::RecursiveDrawComposited(__HIShape const*, unsigned long, HIView*, CGContext*, unsigned char, float) + 1340 27 com.apple.HIToolbox 0x97ca0a3f HIView::DrawComposited(short, OpaqueGrafPtr*, __HIShape const*, unsigned long, HIView*, CGContext*) + 873 28 com.apple.HIToolbox 0x97ca0685 HIView::Draw(short, OpaqueGrafPtr*, unsigned long) + 83 29 com.apple.HIToolbox 0x97ca05d5 HIView::Render(unsigned long, CGContext*) + 45 30 com.apple.HIToolbox 0x97c9ff1d WindowData::PrepareForVisibility() + 145 31 com.apple.HIToolbox 0x97c9f4d8 _ShowHideWindows + 291 32 com.apple.HIToolbox 0x97d021fb ShowWindow + 79 33 freeview.bin 0x00346f86 wxTopLevelWindowMac::Show(bool) + 280 34 freeview.bin 0x00072060 MainApp::CreateMainWindow() + 96 35 freeview.bin 0x000727b5 MainApp::InitializeGUI() + 581 36 freeview.bin 0x0007301a MainApp::OnInit() + 1898 37 freeview.bin 0x00076abf wxAppConsole::CallOnInit() + 15 38 freeview.bin 0x0042b70c wxEntry(int&, char**) + 110 39 freeview.bin 0x00071f87 main + 23 40 freeview.bin 0x00003406 start + 54 Thread 1: Dispatch queue: com.apple.libdispatch-manager 0 libSystem.B.dylib 0x9382d942 kevent + 10 1 libSystem.B.dylib 0x9382e05c _dispatch_mgr_invoke + 215 2 libSystem.B.dylib 0x9382d519 _dispatch_queue_invoke + 163 3 libSystem.B.dylib 0x9382d2be _dispatch_worker_thread2 + 240 4 libSystem.B.dylib 0x9382cd41 _pthread_wqthread + 390 5 libSystem.B.dylib 0x9382cb86 start_wqthread + 30 Thread 2: 0 libSystem.B.dylib 0x9382c9d2 __workq_kernreturn + 10 1 libSystem.B.dylib 0x9382cf68 _pthread_wqthread + 941 2 libSystem.B.dylib 0x9382cb86 start_wqthread + 30 Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00f101a0 ebx: 0x02b187eb ecx: 0x00000000 edx: 0x00efbd68 edi: 0x02b536f8 esi: 0x098ccc50 ebp: 0xbfffcda8 esp: 0xbfffcd7c ss: 0x0000001f efl: 0x00010206 eip: 0x00000000 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00000000 Binary Images: 0x1000 - 0x622ff7 +freeview.bin 'latest trunk' ('latest trunk') <D46BB610-8C7E-9068-6317-4581178C2A87> /Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin 0xe83000 - 0xee0ffb +libGLU.1.dylib 1.3.0 (compatibility 1.3.0) <E6C003F1-0CF9-C1C1-E8EE-A24A8D2A7568> /usr/X11/lib/libGLU.1.dylib 0xef4000 - 0xf0eff7 +libGL.1.dylib 1.2.0 (compatibility 1.2.0) <DC1F80B1-08E9-7BD4-53B3-E93EF1D44E2A> /usr/X11/lib/libGL.1.dylib 0xf25000 - 0xf34fe7 +libXmu.6.dylib 9.0.0 (compatibility 9.0.0) <146AD83F-6740-CFA7-6106-87DE2C305911> /usr/X11/lib/libXmu.6.dylib 0xf3d000 - 0xf78ff7 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(???) <3441F338-2218-6D36-3F95-3A16FBF6713D> /usr/lib/libSystem.B.dylib Model: MacBookPro5,2, BootROM MBP52.008E.B05, 2 processors, Intel Core 2 Duo, 3.06 GHz, 4 GB, SMC 1.42f4 Graphics: NVIDIA GeForce 9600M GT, NVIDIA GeForce 9600M GT, PCIe, 512 MB Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.91.27) Bluetooth: Version 2.3.7f1, 2 service, 19 devices, 1 incoming serial ports Network Service: Ethernet Adaptor (en2), Ethernet, en2 Network Service: Ethernet Adaptor (en3), Ethernet, en3 Network Service: AirPort, AirPort, en1 Serial ATA Device: ST9500420ASG, 465.76 GB Serial ATA Device: HL-DT-ST DVDRW GS21N, 403.3 MB USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x24400000 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0236, 0x04600000 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x04500000 USB Device: Microsoft® 2.4GHz Transceiver v5.0, 0x045e (Microsoft Corporation), 0x074f, 0x04100000 USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x06100000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8217, 0x06110000 -------------------------------------------------- From: <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, September 15, 2010 11:37 PM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 79, Issue 25 > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. substract clusters (Gabriel Go.Es.) > 2. mri_convert with Nifti1 files (roberto.viviani(a)uni-ulm.de) > 3. Re: substract clusters (Bruce Fischl) > 4. Re: substract clusters (Douglas Greve) > 5. how to fix the this problem when I open freeview. (Rahyeong Juh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 15 Sep 2010 10:49:02 +0000 > From: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> > Subject: [Freesurfer] substract clusters > To: <greve(a)nmr.mgh.harvard.edu> > Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SNT124-W62EE767CFAEA3007C6C24ADC790(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello > > > > I'm wondering about how to create a label from a cluster wich is > significant from a group comparison, I mean, I have made group somparisons > and i get some significant clusters, and I want to susbtract that > significative cluster and transform it to a label file. > > > > Best Regards > > Gabriel > > > > > > > >

2 2

Version conflict in FS-FAST or unpacksdcmdir?
by raij＠nmr.mgh.harvard.edu 15 Sep '10

15 Sep '10

Dear Free Surfers, I wonder if something went wrong with transitioning FS-FAST and/or unpacksdcmdir from 4.5 to 5.0. Our functional analysis stream is set to work in 4.5 and it was working fine. However, since the default version was changed to 5.0, our analyses have stopped working despite that we source /space/freesurfer/nmr-stable4-env We receive multiple errors (see ERROR 1 and ERROR 2 below) that start already at preprocessing (ERROR 1 below). For example, functional data from Bay 4 that was unpacked with unpacksdcmdir before the version shift goes through preprocessing just fine (even today), whereas if I re-unpack the exact same raw data the preprocessing fails. Details: cd /space/avml/3/users/bletham/ADA_fMRI/AD003/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT AD003_FSvs4.5 nmr-std-env # this takes us to version 5.0 of course so we also give source /space/freesurfer/nmr-stable4-env ****************** **** ERROR 1: **** ****************** preproc-sess -sf subjectname -df sessdir -fwhm 6 -sliceorder siemens -inorm -force ... some messages ... >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Error using ==> fmri_svbfile Too many output arguments. Error in ==> fast_svbslice at 71 err = fmri_svbfile(yslice,fname); Error in ==> MRIwrite at 83 err = fast_svbslice(mri.vol,fstem,[],outbext,bmri); >> >> ------------------------------------------ ERROR: output not created ERROR: mc-sess failed ****************** **** ERROR 2: **** ****************** For data that was unpacked before the version change, now when we try to run analyses under vs 4.5 we also receive another type of error at selxavg3-sess that seems to be related to version numbers: ... Computing CES Magnitude AV8VT-REST J=13 ------------- Computing CES Magnitude Saving h.dat to /autofs/space/avml_003/users/bletham/ADA_fMRI/AD003/bold/FIRsm6pf2_taumax20/h.dat ??? Reference to non-existent field 'Version'. Error in ==> fmri_svdat3 at 35 if(hd.Version == 2) Error in ==> fast_selxavg3 at 1039 fmri_svdat3(fname,hd); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Any suggestions? Anything and everything of course most welcome! Best regards, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

1 0

fs 5.0 Longitudinal Fix
by Martin Reuter 15 Sep '10

15 Sep '10

Hi, in the meantime the 5.0 longitudinal stream has been fixed and tested. See: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalChangeLog for links to download the fixed binaries and updated recon-all script. Note, that we recommend to wait with any large scale longitudinal processing for the 5.1 release this fall, that will include several improvements (see link above). Detailed bug description: mri_robust_template and mri_robust_register make use of a shared FreeSurfer library to transform/resample images. A non-related, last minute, 'bug-fix' in that transformation library introduced a new bug: Instead of taking the target geometry information from the LTA, it was incorrectly copied from the source image if no specific target is passed. This broke the robust tools and thus the longitudinal stream. Cheers, Martin Enjoy the free longitudinal surfin' ...

1 0

mri_convert with Nifti1 files
by roberto.viviani＠uni-ulm.de 15 Sep '10

15 Sep '10

Dear list, I am using mri_convert to prepare my pipeline for FreeSurfer, and, yes, I have been struggling for a couple of days to get it done. After conversion, I have no problem using tkmedit to display the file; however, the Volume RAS coordinates are swapped -- the numbers aren't wrong, they are just swapped in place and/or inverted, while the image is always displayed fine (left on the right, up is up, front is front etc, which shows, I assume, that the coordinates are right in the header). By 'always' I mean that if I reslice the image, and then convert it, then mri_convert will always produce an mgz file that will be displayed correctly in tkmedit, but will also produce a new permutation of the swapping in the Volume RAS coordinates. Even if a reslice my image in axial slices (it was originally the usual sagittal MPRAGE thing from Siemens), I get the wrong swapping. Can anyone tell me how to reslice my image to get it right? Thank you in advance, Roberto Viviani University of Ulm, Germany

2 1

Which volumes
by Ed Gronenschild 15 Sep '10

15 Sep '10

Hi, In the wmparc.stats file a large number of ctx structures and the corresponding volumes, like ctx-lh-parahippocampal. For some of these structures the volumes are also listed in the ?h.aparc.stats files. Which volumes are correct? Ed

2 1

how to fix the this problem when I open freeview
by Rahyeong Juh 15 Sep '10

15 Sep '10

1 0

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Freesurfer September 2010