Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

Re: [Freesurfer] corpus calosum volume ?...
by Gonzalo Rojas Costa 15 Mar '11

15 Mar '11

Hi Bruce: Thanks you very much for your answer... And, how can I get the volume of the new segmentation of the CC that I got with mri_cc command ?... Sincerely, Gonzalo Rojas Costa El 15-03-2011 21:27, Bruce Fischl escribió: > I mean that if the volume is rotated in any 2d slice it can look as if > only some of the cc is properly labeled, even if the full 3d labeling is > correct > On Tue, 15 Mar 2011, Gonzalo Rojas Costa wrote: > >> Hi Bruce; >> >> I don't understand why you said that in 3D the labeling is usually >> correct... ???... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >> >> El 15-03-2011 15:33, Bruce Fischl escribió: >>> Hi Gonzalo >>> >>> mri_cc computes the optimal rotation. If the patient's head is not >>> straight this can make it look like an inconsistent labeling, but in 3d >>> it usually is correct. >>> >>> Bruce >>> >>> On Tue, 15 Mar 2011, Gonzalo Rojas Costa wrote: >>> >>>> Hi: >>>> >>>> The CC_Posterior, CC_Central, etc, volumes in "aseg.mgz" are the >>>> complete CC volume, or it includes only some sagital slices ?... >>>> >>>> How can I meassure the CC volume for some sagital slices only (5 in >>>> total for example) ?... When I tried using "mri_cc" I got an error >>>> (for example) in the case that the patient is slightly rotated >>>> (freesurfer segments only one section of the CC as CC and the other as >>>> WM)... >>>> >>>> Sincerely, >>>> >>>> >>>> >>>> Gonzalo Rojas Costa >>>> Laboratory for Advanced Medical Image Processing >>>> Department of Radiology >>>> Las Condes Clinic >>>> Lo Fontecilla 441, Las Condes, Santiago, Chile. >>>> Tel: 56-2-2105170 >>>> Cel: 56-9-97771785 >>>> www.clc.cl >>>> >>>> >>>> >>> >>> >>> 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.

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Philips DICOM format problem
by leonardo kay 15 Mar '11

15 Mar '11

Hi All I'm new in freesurfer. I have a question regards Philips DICOM format. I tried to convert from dicom to .mgz using mri_convert but i get the following error message: MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 -0.000 nan nan; 0.000 0.000 0.000 1.000; Have anyone experienced this before? Any help converting from philips dicom format? Best regards Leo.

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Re: [Freesurfer] mri_glmfit allocate memory error
by Douglas N Greve 15 Mar '11

15 Mar '11

So you re-ran mris_preproc and you still get the error? If so, try running mris_preproc --debug <Your Options> |& tee mris_preprog.err.log Send me the mris_preprog.err.log, but don't email it as it will likely be huge. Instead drop it to me a the file drop listed at the end of this email. doug Andrew Mendlowitz wrote: > The mri_prepoc runs fine still but the glmfit still says can not > allocate memory, there is 8gb of ram and very little disk space is > used up, there is 876.1 gb still free. > > On Fri, Mar 11, 2011 at 12:49 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > If you re-run mris_preproc does the same thing happen? Are you > running out of disk space? > doug > > Andrew Mendlowitz wrote: > > The code for the lh.paired-diff.thickness.mgh file is > mris_preproc --target fsaverage --hemi lh \ > > --meas thickness --out lh.paired-diff.thickness.mgh \ > > --fsgd pairss.fsgd --paired-diff > > > On Thu, Mar 10, 2011 at 10:13 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > There appears to be something wrong with the > lh.paired-diff.thickness.mgh file. How was it created? > doug > > Andrew Mendlowitz wrote: > > Hello All, > I get the following error while trying to run > mri_glmfit. I am > running a 2.93 ghz imac with 8gb of ram. I am also running > freesurfer version 5.0.0 on Snow > Leopard OS version 10.6. > > > /Applications/freesurfer/subjects/qdec$ mri_glmfit > --glmdir > lh.paired-diff --fsgd paired-diff.fsgd --C mean.mtx --y > lh.paired-diff.thickness.mghgdfReadHeader: reading > paired-diff.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT > be done. > Continuous Variable Means (all subjects) > 0 Age 1.5 > Class Means of each Continuous Variable > 1 Main 1.5000 > INFO: gd2mtx_method is dods > > $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve > Exp $ > cwd /Applications/freesurfer/subjects/qdec > cmdline mri_glmfit --glmdir lh.paired-diff --fsgd > paired-diff.fsgd --C mean.mtx > --y lh.paired-diff.thickness.mgh > sysname Darwin > hostname larry > machine i386 > user amend > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y > /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh > logyflag 0 > usedti 0 > FSGD paired-diff.fsgd > glmdir lh.paired-diff > IllCondOK 0 > DoFFx 0 > Creating output directory lh.paired-diff > Loading y from > > /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh > mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed > (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIallocIndices: could not allocate 1714511945 elt > index array > Cannot allocate memory > > The mri_info for the file is : > > > mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh, > -1): could not > open file > amend@larry /Applications/freesurfer/subjects/qdec$ > mri_info > > /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh > Volume information for > > /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh > type: MGH > dimensions: 1714510945 x 1853057372 x 1634628457 x > 1668310833 > voxel sizes: 72950800688805540228332034981888.0000, > 0.0000, > 70387746064971392794503413760.0000 > type: UNKNOWN (842347100) > fov: inf > dof: 1668244335 > xstart: -inf, xend: inf > ystart: -39.8, yend: 39.8 > zstart: > -57528904905339976080461439864148066304.0, zend: > 57528904905339976080461439864148066304.0 > TR: 71446969504754118412748034408448.00 > msec, TE: > 17862977898376175754203558313984.00 msec, TI: > 4464583905807213894543171649536.00 msec, flip angle: > 4128358109894647822155776.00 degrees > nframes: 1668310833 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = > 19441367164500690594879212879872.0000, y_r = > 282670772483715414097920.0000, z_r = > 4630517930517356511053742080.0000, c_r = > 18179207505345150839094025125888.0000 > : x_a = > 72953300747400503281465327353856.0000, y_a = > 71756401321839400437789128392704.0000, z_a = > 4721224652433019196440490016768.0000, c_a = 0.0000 > : x_s = 0.0000, y_s = > 208210237828607676252160.0000, z_s = > 4286666299869639999488.0000, c_s = > 4622889417339745644740714954752.0000 > > talairach xfm : > Orientation : AAA > Primary Slice Direction: coronal > > voxel to ras transform: > inf 12133604733747200.0000 inf > -inf > inf 3080133850722982464323584.0000 > inf > -inf > 36752183205510726549504.0000 > 8937395835633664.0000 inf -inf > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant nan > > ras to voxel transform: > mat = NULL! > Invalid argument > MatrixFree: NULL mat POINTER! > > Invalid argument > > -Andrew > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel: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> > > -- 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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display multiple functional overlays simultaneously
by Scott Hayes 15 Mar '11

15 Mar '11

Hi, I have 2 functional maps (Patient > Controls and Controls > Patients) and I would like to view both maps simultaneously on the surface (one with "normal" values and the other using the "inverse" values so that I get a "warm" and "cool" map simultaneously displayed on the surface). I'm using FS 5.0 and mac os 10.6.6 command from the mac terminal: > tksurfer fsaverage/ lh inflated -overlay PCC_nosmooth_level3_FE_8matched_vs_MA016.gfeat/cope1.feat/thresh_zstat1.nii.gz -overlay PCC_nosmooth_level3_FE_8matched_vs_MA016.gfeat/cope1.feat/thresh_zstat2.nii.gz Both maps load, but I have to click on one or the other (rather than both being overlaid simultaneously), and the options (selecting inverse) seem to be applied to both layers (even though I have not selected "apply changes to all layers"). Is it possible to view these maps at the same time using tksurfer and apply normal values to one map and inverse values to the other? It was also suggested that freeview *might* be able to do this, but this does not launch from the command line (FS, tkmedit and tksurfer all work fine). I've copied the first few lines from the freeview crash if that helps. Any suggestions/guidance would be appreciated. Thanks, Scott Process: freeview.bin [36175] Path: /Applications/freesurfer/bin/Freeview.app/Contents/MacOS/freeview.bin Identifier: freeview.bin Version: 'latest trunk' ('latest trunk') Code Type: X86 (Native) Parent Process: bash [30033] Date/Time: 2011-03-15 08:57:43.954 -0400 OS Version: Mac OS X 10.6.6 (10J567) Report Version: 6 Interval Since Last Report: 1791542 sec Crashes Since Last Report: 39 Per-App Crashes Since Last Report: 3 Anonymous UUID: E5903541-C168-4ED7-92B6-6741CD098D1A 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 0x95953ecf DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1567 17 com.apple.HIToolbox 0x95953196 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411

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corpus calosum volume ?...
by Gonzalo Rojas Costa 15 Mar '11

15 Mar '11

Hi: The CC_Posterior, CC_Central, etc, volumes in "aseg.mgz" are the complete CC volume, or it includes only some sagital slices ?... How can I meassure the CC volume for some sagital slices only (5 in total for example) ?... When I tried using "mri_cc" I got an error (for example) in the case that the patient is slightly rotated (freesurfer segments only one section of the CC as CC and the other as WM)... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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V1 prediction
by Thesen, Thomas 15 Mar '11

15 Mar '11

Dear Freesurfer List, I ran the script for predicting V1 location on the surface: http://surfer.nmr.mgh.harvard.edu/fswiki/V1 According to the paper, the output should be a probability map, but the script only seems to produce a label file: $SUBJECT_DIR/label/?h.v1.prob.label . When I load this file (it only loads as 'label') it is a binary label, with no probability values associated with it. That means it is a pretty generous description of predicted V1. How can I get probability values and trim it to, let's say, >80% probability? Thanks for your input. Thomas </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

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tksurfer error
by Don Hagler 15 Mar '11

15 Mar '11

Hi, In response to the message below, I have been getting the exact same error when running tksurfer on a particular workstation. tksurfer does display correctly, but the drawing is very slow, as if running remotely (or not using the video card). This happens with versions 3.0.5 and 4.5.0. I tried uninstalling and reinstalling the nvidia driver, but that didn't help. glxgears and glxinfo work fine, no warnings or error messages. In Xorg.0.log, there is one warning: (WW) NVIDIA(0): UBB is incompatible with the Composite extension. Disabling (WW) NVIDIA(0): UBB. After googling, I found that UBB stands for Unified Back Buffer. http://http.download.nvidia.com/XFree86/Linux-x86/1.0-8178/README/appendix-… This only applies to Quadro GPUs. This particular workstation has this type: NVIDIA GPU Quadro FX 580 I haven't yet found a solution. Evan, do you have a Quadro GPU? Did you find a solution? Don _________________________________________________________________________ Dear freesurfer community, I am currently trying to view one of the surfaces generated by recon-all command in tksurfer but when I enter the command: tksurfer LuceHR_FS_SURF lh inflated.nofix I receive a series of errors that look like this: Received X error! Error code : 1 Request code : 147 Minor code : 181 Error text : 'BadRequest (invalid request code or no such operation)' Subsequently the surface window does not display what I would believe is the surface I am trying to view and then the only way I can exit the tksurfer environment is by exiting the terminal that I invoked it in. Any ideas or solutions? Thank you very much, Evan Luther

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results visualization
by nadia merhoum 15 Mar '11

15 Mar '11

Hello I have just started using FreeSurfer (version 4.5) and performed the following script: “recon-all -i tpidN.nii -subjid tpidN -all” I would like to know how to check the obtained results for any errors; what script is used to visualize the image below? Thank you for your help Sincerely Nadia

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Label Orientation
by Tyler Blazey 15 Mar '11

15 Mar '11

Hi, I am having a bit of a problem with the orientation of a label produced by mri_cor2label. I have an old analyze ROI that I have converted to a nifti volume and then registered to T1.mgz. When I load the ROI volume in tkmedit , the registration looks fine. The label and T1.mgz are in the same orientation and everything matches up. This occurs whether I load the ROI volume as the aux volume or as the main volume. I then have tried to run mri_cor2label on the ROI volume in order to convert it to a label. When I look at the label with T1.mgz as the main volume, the z and y axises of the label are flipped and so is the left/right orientation. The strange thing is when I load the ROI volume as the main volume and T1.mgz as the aux volume, the label has the correct orientation. Is there a reason why the label only has the correct orientation when its source volume is used as the main volume? Is there any way I can correct this issue? I am sorry if any of this is unclear. Thanks in advance for any help. Thanks, - Tyler

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Re-post: Fixated brain
by Auer, Tibor MD. Ph.D. 15 Mar '11

15 Mar '11

Dear Users, Is there a way to process fixated brain (after autopsy) with Freesurfer? I have read somewhere that I should just "invert" the image, but what does it mean? And would it not increase the noise and the signal from the CSF? Of course, the brain is without any skull, pia and dura mater. Does it cause no problem for Freesurfer? Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Mobile: +49-(0)176-8012-7921 E-Mail: tauer(a)gwdg.de <mailto:tibor.auer@gmail.com>

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Freesurfer March 2011