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30086 discussions

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

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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(???) <9CFF48CC-4852-4D06-17AC-3C947C824159> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib 0x9480a000 - 0x948d4fef com.apple.CoreServices.OSServices 357 (357) <CF9530AD-F581-B831-09B6-16D9F9283BFA> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x948d5000 - 0x948e3fe7 libz.1.dylib 1.2.3 (compatibility 1.0.0) <3CE8AA79-F077-F1B0-A039-9103A4A02E92> /usr/lib/libz.1.dylib 0x94c93000 - 0x94ca7fe7 libbsm.0.dylib ??? (???) <14CB053A-7C47-96DA-E415-0906BA1B78C9> /usr/lib/libbsm.0.dylib 0x94ca8000 - 0x94d43ff7 com.apple.ApplicationServices.ATS 275.11.1 (???) <5FF65EC7-F512-530A-7771-3DE240EE6E43> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS 0x94e8a000 - 0x94f67ff7 com.apple.vImage 4.0 (4.0) <64597E4B-F144-DBB3-F428-0EC3D9A1219E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x94fb3000 - 0x9505cff7 com.apple.CFNetwork 454.9.8 (454.9.8) <DB2A5C33-E833-1B3A-4DE0-5FF172B2048B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork 0x95134000 - 0x95136ff7 com.apple.securityhi 4.0 (36638) <38D36D4D-C798-6ACE-5FA8-5C001993AD6B> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI 0x95137000 - 0x951f0fe7 libsqlite3.dylib 9.6.0 (compatibility 9.0.0) <16CEF8E8-8C9A-94CD-EF5D-05477844C005> /usr/lib/libsqlite3.dylib 0x9521d000 - 0x9539ffe7 libicucore.A.dylib 40.0.0 (compatibility 1.0.0) <2314BD12-0821-75BB-F3BC-98D324CFD30A> /usr/lib/libicucore.A.dylib 0x953a0000 - 0x953a0ff7 com.apple.Cocoa 6.6 (???) <EA27B428-5904-B00B-397A-185588698BCC> /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 0x9541a000 - 0x95594fe3 com.apple.CoreFoundation 6.6.3 (550.29) <00373783-3744-F47D-2191-BEEA658F0C3D> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 0x95617000 - 0x95686ff7 libvMisc.dylib 268.0.1 (compatibility 1.0.0) <2FC2178F-FEF9-6E3F-3289-A6307B1A154C> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x9568c000 - 0x95693ff7 com.apple.agl 3.0.12 (AGL-3.0.12) <6877F0D8-0DCF-CB98-5304-913667FF50FA> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x95897000 - 0x95cccff7 libLAPACK.dylib 219.0.0 (compatibility 1.0.0) <5E2D2283-57DE-9A49-1DB0-CD027FEFA6C2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x95d67000 - 0x95d72ff7 libGL.dylib ??? 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(???) <7601D717-236D-8F4E-91F5-E69BB2920478> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib 0x991f7000 - 0x9923aff7 libGLU.dylib ??? (???) <2093A1FB-67BD-39E0-CDE5-A97A77BDDBCE> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x9941e000 - 0x99461ff7 com.apple.NavigationServices 3.5.4 (182) <753B8906-06C0-3AE0-3D6A-8FF5AC18ED12> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/Versions/A/NavigationServices 0x99500000 - 0x99500ff7 com.apple.Carbon 150 (152) <9252D5F2-462D-2C15-80F3-109644D6F704> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 0x99501000 - 0x99545fe7 com.apple.Metadata 10.6.3 (507.10) <630494FA-3BB3-EDD3-E10B-8DAAF4831E26> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata 0x99546000 - 0x99551ff7 libCSync.A.dylib 543.50.0 (compatibility 64.0.0) <4FA0CE4A-BDE5-0E3D-37F0-03B41F0C2637> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dylib 0x99552000 - 0x99596ff3 com.apple.coreui 2 (114) <29F8F1A4-1C96-6A0F-4CC2-9B85CF83209F> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0x99597000 - 0x9959bff7 libGFXShared.dylib ??? (???) <2D32BDBF-C941-93FD-E233-F03D28DB9E94> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x9959c000 - 0x9959dff7 com.apple.TrustEvaluationAgent 1.1 (1) <6C04C4C5-667E-2EBE-EB96-5B67BD4B2185> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x996cb000 - 0x99781ffb libFontParser.dylib ??? 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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

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

15 Sep '10

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groups stats doubts
by Gabriel Go.Es. 15 Sep '10

15 Sep '10

I'm going to run some analyses and have some doubts with respect to the general approach that I should follow. We want to evaluate differences in cortical thickness in three different groups. Shoud I perform an ANOVA (to know if there is a group effect) followed by pairwise comparisons (to localize the difference)? If so, what should I do if results from the ANOVA and pairwise comparisons are localized in different regions? Shoud I restrict the pairwise contrasts to regions where ANOVA revealed significant differences? Many thanks in advance. Best Regards Gabriel

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Re: [Freesurfer] How to access host files in the freesurfer virtualBox.
by Darren Gitelman 14 Sep '10

14 Sep '10

Nevermind. I was able to install the additions, and then with disabling 3D acceleration freesurfer works. Darren

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How to access host files in the freesurfer virtualBox.
by Darren Gitelman 14 Sep '10

14 Sep '10

Hi Does anyone know how to access the host's drive when using VirtualBox? The problem is (I don't think) that one can install the VirtualBox Guest Additions as it messes up the graphics for freesurfer (at least it did for me). However the VirtualBox guest additions contain the kernel extensions to mount the host's drives. Is there any way to just install access to the virtual drives or to access the drives in some other way? I am running Freesurfer VirtualBox on a windows 7 system. Thanks, Darren

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Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45
by Darren Gitelman 14 Sep '10

14 Sep '10

I have figured out how to increase the size of the Freesurfer Virtualbox disk. This turned out to be non-trivial and was greatly facilitated by the CloneVDI tool. I tried a number of methods before using this tool but they did not result in a bootable virtual disk for reasons that remain unclear to me. Those methods include creating a new larger virtual disk, then using gparted to copy the old disk contents to the new disk contents and then expanding the disk to fill the new larger space. I also tried using the unix dd utility to copy the old to new disk and using the VBoxManage command line program to try to clone the disk. The instructions below require some familiarity with using unix tools such as gparted to setup the disk. If you have no experience with this find someone who does. I should probably add that your virtual box should be shutdown before you do any of this and you should have made a backup copy in case you select the wrong virtual disk in this process and mess it up. (The usual disclaimer applies- i.e., if you mess up your freesurfer virtual disk with all your data, and don't have a backup, it's your problem.) The CloneVDI tool, (get it here: http://forums.virtualbox.org/viewtopic.php?f=6&t=22422) works like a charm. Start the tool and you will see a GUI for cloning your freesurfer vdi disk. You just select your current freesurfer vdi file as the source, and then a new destination vdi file. I generated a new UUID for the new disk and increased the virtual drive size to 25 GB (but you can choose whatever size you want). Then click proceed. Once the new disk is generated you will need to fix it up a bit with gparted. The overview is that when you examine the disk in gparted you will notice that the old filesystem occupies only a portion of the disk (the first partition). This is followed by an extended partition that contains a linux swap partition. In order to expand the size of the freesurfer installation you will need to delete the linux swap and the extended partition, enlarge the primary partition and then recreate the extended partition and the linux swap. The steps are as follows: Download the gparted-live iso ( http://sourceforge.net/projects/gparted/files/gparted-live-stable/) Start virtualbox, open the virtual media manager and add the gparted-live iso under CD/DVD images. Also add the new cloned hard disk. Now open the virtual box settings. Under storage you will need to add the new virtual hard disk and change it to be the primary master. (You will have to change the old freesurfer virtual disk to be the secondary slave and then you can select the new disk as the primary master. Also make sure the gparted-live disk (iso) is selected as the CD/DVD device. Now boot the virtualbox and immediately press F12 which allows you to select the boot device. Choose the gparted-live CD. Once gparted starts it should recognize your visual disks and show them in the GUI. Make sure you have selected your new visual disk and NOT the old one. If you have properly designated the new virtual disk as the primary master it should be identified as /dev/sda. You should notice that there is a primary partition (/dev/sda1) which is your freesurfer installation. There will also be an extended partition (/dev/sda2) that contains the swap partition (/dev/sda5). Delete the swap partition and then the extended partition. Now expand the primary partition consistent with your new disk size BUT remember to leave room for the swap partition. (You must have a swap partition on linux or the installation definitely won't work properly.) The old swap was 400 MB but if you increase the RAM on your virtual disk you may want the swap to be 2 GB. So for a 25 GB disk your primary partition will be about 23 GB and swap will be 2 GB. After expanding the primary partition, recreate the extended partition as /dev/sda2 and then within that recreate the linux-swap partition- it will be /dev/sda5. Apply the changes, and then shutdown gparted. Now unmount the gparted-disk and you can also unmount your old freesurfer installation. Reboot and voila (if everything worked correctly) you will have the your freesurfer installation and oodles (or GB) of additional disk space. Happy freesurfing, Darren P.S: I don't monitor the freesurfer list so email both the list and me (d DOT gitelman AT gmail DOT com) if there are questions about this. I will try to answer, but no promises as to when.

1 0

problem with mri_fill
by SM Chita 14 Sep '10

14 Sep '10

Hello gentle readers and experts of FreeSurfer, I am using the FS software package to calculate the gyrification index for premature baby brain. Of course in order to get to this step I do need to run the previous autorecon steps to obtain the pial surface. So far I've run the first sequence for one of my test subjects, recon-all -autorecon1, and encountered no errors. For the second step autorecon2 I have decided to run every subsequent step, firstly, because if I understand correctly from the wiki-webpage the flag -noaseg is necessary if the subjects cannot use an aseg, like baby brain. Secondly, due to the poor T1,T2 intensity contrast in my baby-scans the FS default segmentation step was not performed correctly (large portions of white matter were not counted). So I include my own segmented white matter volume. To include my WM volume I have used "mri_convert -c" to convert analyze data into .mgz format. The steps from the second sequence that I ran without getting any errors are: "-gcareg", "-canorm", "-careg", "-careginv", "- rmneck", "-skull-lta", "-normalization2 -noaseg", "-maskbfs" . At the step "-fill -noaseg" the errors are: min_slice = -1, min_area = 65536 mri_fill: could not find corpus callosum find_cutting_plane:seed point not in structure! Searching neighborhood... recon-all -s blob2test exited with ERRORS at Tue Sep 14 13:18:14 CEST 2010 After this error I used the command: "recon-all -fill -cc-crs -pons-crs -lh-crs -rh-crs -noaseg -s blob2test" and got a bus error: /Applications/freesurfer/subjects/blob2test/mri \n mri_fill -a ../scripts/ponscc.cut.log -Cv -pons-crs -lh-crs -rh-crs -xform transforms/talairach.lta wm.mgz filled.mgz \n logging cutting plane coordinates to ../scripts/ponscc.cut.log... using voxel position ( 0, 0, 0) as corpus callosum seed point INFO: Using transforms/talairach.lta and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 2.694 0.124 -0.276 -194.089; -0.311 2.259 -0.788 -3.124; 0.090 0.794 2.183 -266.051; 0.000 0.000 0.000 1.000; Bus error recon-all -s blob2test exited with ERRORS at Tue Sep 14 13:20:58 CEST 2010 My suspicion is that the way I have converted my WM volume is not correct and since the -fill uses the wm.mgz I do get error on this step. However I also tried to "align" my wm.mgz with brain.mgz using: "mri_convert mywm.mgz mynewwm.mgz --like brain.mgz". The "--apply_transform" option is not really clear to me and I do not get any good results if I apply that to mywhitematter.mgz. I also used tkregister2 to align the two volumes: my white matter with brain.mgz for example. But the wm.mgz file I've saved after registration to brain.mgz it could not be opened in tkmedit anymore so I decided not to use it as wm.mgz further. I do want to use my white matter segmentation and continue with the steps in order to calculate with FS a pial surface, inflated surface, gyrification index, etc. for both hemispheres. I am also aware of the fact that using an adult atlas for baby scans is not correct so this might be also causing errors. One next step would probable be to make a baby brain atlas and include that instead of the */average/*.gca files. What do you suggest as first starting point in solving the errors? Thanks a million for your answer !! Best regards, Sabina

2 1

Re: [Freesurfer] Re-run FreeSurfer with V.5.0
by Douglas N Greve 14 Sep '10

14 Sep '10

Hi Jordi, The edits will automatically be incorporated when you run version 5. Assuming that the edits you made were correct (eg, control points are in white matter), then the edits that you made in previous versions will be valid for version 5 (though you might not have had to have made those edits if you had run v5 from scratch). doug Jordi Delgado wrote: > Hi, > > I have a question related to this thread. If we have made manual > modifications using tkmedit (control points, pial, wm) with 4.3.1 > version and now we would like to run these subjects with version 5, is > it posible? What implications we will have to take into account, or > maybe for each new freesurfer version we have to start from scratch? > > I assume that the transfer of the manual modifications from an old > version to the 5 version, doesn't make sense because for every > processing with a new version the result will not be the same and we > have to modify the images according to the 5 version results. > > Thank you, > > 2010/9/13 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > yes (but make sure to make backups). > > doug > > Gina Caetano wrote: > > Hello, > > > > Version 4.2.0 was used to start processing data for a 3-years > project. > > We are still acquiring data for the project, and would like to start > > using version 5.0. > > > > For some of the subjects already processed, manual talairach > alignment > > was performed with tkregister2, and as I understood when recon-all > > -autorecon1 is run it will not overwrite this alignment. Former > > processing also contains manual edits to the brainmsak.mgz, > wm.mgz as > > well as control points, and as I understood when re-running > autorecon2 > > the manual edits will be saved by default. > > > > Thus, I am thinking to re-run all the recon-all steps when changing > > from v4.2 to v.5.0. Would you advise it? > > > > Thank you all in advance, > > > > > > Gina > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Jordi Delgado Mengual > PIC (Port d'Informació Científica) > Campus UAB, Edifici D > E-08193 Bellaterra, Barcelona > Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 > http://www.pic.es > Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- 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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