Re: [Freesurfer] Qdec - thickness-age correlation - Interpretation
Thank you Doug ! regards, alex. --- En date de : Lun 14.3.11, Douglas N Greve gr...@nmr.mgh.harvard.edu a écrit : Hi Alex, you can compute the difference in those slopes using an appropriate contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this would be an interaction between group and age). doug ___ 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] display multiple functional overlays simultaneously
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 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.bin0x0011d547
wxVTKRenderWindowInteractor::OnPaint(wxPaintEvent) + 151
9 freeview.bin0x00407b53
wxAppConsole::HandleEvent(wxEvtHandler*, void
(wxEvtHandler::*)(wxEvent), wxEvent) const + 65
10 freeview.bin0x00452f30
wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const,
wxEvtHandler*, wxEvent) + 212
11 freeview.bin0x004532d4
wxEventHashTable::HandleEvent(wxEvent, wxEvtHandler*) + 204
12 freeview.bin0x00453f5e
wxEvtHandler::ProcessEvent(wxEvent) + 240
13 freeview.bin0x003525e3
wxWindow::MacDoRedraw(void*, long) + 975
14 freeview.bin0x00353985
wxMacWindowControlEventHandler(OpaqueEventHandlerCallRef*,
OpaqueEventRef*, void*) + 815
15 freeview.bin0x00354135
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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[Freesurfer] Re-post: Fixated brain
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: ta...@gwdg.de mailto:tibor.a...@gmail.com ___ 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] Re-post: Fixated brain
Tibor, We are working to put some exvivo wm segmentation methods into the next FreeSurfer release although I'm not sure where that stands. We do process our exvivo scans with FreeSurfer but we use scripts that use different parameters than recon-all since the contrast is different and as you said there is no skull. Our scripts are specific to our scan protocol. What did you collect and on what scanner? Allison On Tue, 15 Mar 2011, Auer, Tibor MD. Ph.D. wrote: 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: ta...@gwdg.de mailto:tibor.a...@gmail.com ___ 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] display multiple functional overlays simultaneously
Hi Scott, I'm not sure what you are trying to do. How can you display
two different z-values at the same voxel at the same time? Or do you
want to merge the maps in some way?
doug
Scott Hayes wrote:
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 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 0x95953ecf
DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*,
HandlerCallRec*) + 1567
17 com.apple.HIToolbox 0x95953196
SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*,
HandlerCallRec*) + 411
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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
Re: [Freesurfer] results visualization
Hi Nadia, You can follow instructions on how to check data using our tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData and https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData Allison On Tue, 15 Mar 2011, nadia merhoum wrote: 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 ___ 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] normal vector in gm
Hi Seok, Try using --projfac .01 in the surf2vol command. doug Seok Lew wrote: Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up the wm surface by mris_convert -s 1.01 lh.white lh.white101 and then projected the normals on the volume by mri_surf2surf -- hemi lh --sval-nxyz white101 --tval wn101.mgz mri_surf2vol --surfval wn101.mgz --hemi lh --surf white101 --volreg reg2ana.dat --template vol.mgz --outvol wn101_b.mgz However, the projection seemed not in the scaled-up layers, but in the original wm layers. The scaling seemed not effective. Would you have any ideas what could project normals in the gm boundary voxels with wm? Eventually what I wanted to do is assign normal vectors in all gm voxels somehow. Thanks, Seok On Mar 9, 2011, at 5:44 PM, Douglas N Greve wrote: That is the file created by registering your orig.mgz to the mni152 brain (assuming you are using the 152). You can create this registration file with the mni152reg script. doug Seok Lew wrote: Thanks, first of all. I tried with the following scripts, but ended up with an error. I am not sure which format or file is required for the --volreg. # mri_surf2surf --s FS --hemi lh --sval-nxyz pial --tval ./ttt.mgz # mri_surf2vol --surfval ttt.mgz --hemi lh --volreg mri/transforms/talairach.xfm --outvol ooo.mgz --template mri/T1.mgz gdiagno = -1 regio_read_register(): No such file or directory Error reading inplaneres from mri/transforms/talairach.xfm Thanks, Seok On Mar 9, 2011, at 2:00 PM, Douglas N Greve wrote: Try using mri_surf2surf with the --sval-nxyz. The output have 3-frame, one for each component in the normal. Then use mri_surf2vol to stuff this back into a volume. doug Seok Lew wrote: Hello users, My colleagues and I are trying to create a gray matter electric conduction model where a preferable conduction direction is aligned with the normal direction induced from the pial and white surface normals. Freesurfer reconstruction already gives pial and white matter surface normals and correspondences between them. Now I want to have the freesurfer surface normals projected on the mri volumes and interpolated for gray matter voxels (regions between the pial surface and the white surface), such that each voxel of gray matter can have a normal direction. Is it possible to do the job with freesurfer scripts ? If so, what scripts might work for this? Thanks in advance, Seok ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu -- 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 Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu -- 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 ___ 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] CUDA installation
Hi: I tried to install CUDA to use with freesurfer, but I got some errors that I sent to freesurfer list sometime ago... Could you please send how can I install CUDA and freesurfer in a Ubuntu platform ?... 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 ___ 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] Homologous Right Left ROIs
Hi Lena, we don't have tools released yet to do this. They should be available in the spring. dopug Lena Palaniyappan wrote: Hi all I have a ROI label on left hemisphere – I need to map this ROI onto right hemisphere to get a homologous region (for testing hemispheric differences). What is the best way for doing this? Cheers Lena -- *Lena Palaniyappan *Clinical Lecturer Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 ___ 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] display multiple functional overlays simultaneously
No, you'll have to merge them into one map (and you'll probably want it
to be an annotation). To do this, you'll need to run several programs.
1. mri_binarize -- threshold your two raw maps, give one a --binval 1
the other --binval 2
2. Add them together: fscalc binmap1.nii add binmap2.nii -o binmap12.nii
This will cause voxels only in binmap1 to be one, only in binmap2 to
be 2, and voxels in both to be 3
3. Create a lookup table like $FREESURFER_HOME/FreeSurferColorLUT.txt
with 4 entries (0, 1, 2, 3), and give them the color you want.
4. mri_seg2annot --seg binmap12.nii --ctab yourcolortable ...
doug
Scott Hayes wrote:
Hi Doug,
I was trying to load the maps so I could examine each map and the
overlap, as in the attached example (in this image, red is one map,
blue is the other, and pink is the overlap--done in MRICRON. I think
it's a nice way to view similarities and differences in activation for
different groups. Although this might be achievable by merging the
maps as you suggest, I was wondering if it was possible to view them
in tksurfer without trying to merge them into a single map.
Thanks,
Scott
On Tue, Mar 15, 2011 at 11:09 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Hi Scott, I'm not sure what you are trying to do. How can you display two
different z-values at the same voxel at the same time? Or do you want to
merge the maps in some way?
doug
Scott Hayes wrote:
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 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.bin0x0011d547
wxVTKRenderWindowInteractor::OnPaint(wxPaintEvent) + 151
9 freeview.bin0x00407b53
wxAppConsole::HandleEvent(wxEvtHandler*, void
(wxEvtHandler::*)(wxEvent), wxEvent) const + 65
10 freeview.bin0x00452f30
wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const,
wxEvtHandler*, wxEvent) + 212
11 freeview.bin0x004532d4
wxEventHashTable::HandleEvent(wxEvent, wxEvtHandler*) + 204
12 freeview.bin0x00453f5e
wxEvtHandler::ProcessEvent(wxEvent) + 240
13 freeview.bin0x003525e3
wxWindow::MacDoRedraw(void*, long) + 975
14 freeview.bin0x00353985
Re: [Freesurfer] mri_mask problem
Hello Bruce and Nick, I've tryed these options you said and still not works, I
must say that is not in all my subjects,
I've tryed both brain.mgz and brainmask.mgz.
The commands I've used are:
A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz
--regheader
A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz
outbrain.mgz
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the
mri_mask the image apperars with no edits.
B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz brainmask2raw.mgz
outbrain2.mgz
I've ran the mri_mask command with and without the -keep_mask_deletion_edits
flag
and again appears to be the mri_mask command the one that is not doing the
work, actually the outputs from mri_convert and mri_vol2vol, looks pretty
similar, any ideas?
Bests
Gabriel
Date: Mon, 14 Mar 2011 08:57:16 -0400
From: fis...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_mask problem
Hi Gabriel,
did you convert the brain.mgz so it is in the same space as the
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try
mri_mask -t threshold. The default is 1e-10 so pretty much anything
non-zero is dept. Try changing it to 2 (voxels edited to be turned off are
1).
cheers
Bruce
On Mon, 14 Mar 2011,
Gabriel Go.Es. wrote:
Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it,
but I think is gonna be hard to send it to through the e-mail.
Bests,
Gabriel.
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
i'd have to try to replicate this myself, although it will have to wait
till monday (i'm with the freesurfer group three days a week).
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
actually not there (zeroed).
n.
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
Bests,
Gabriel
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
Than you Nick,
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
thank you again,
Gabriel
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
hi, not sure what you are trying to do, as the commands below
seem
to do
what i expect them to do, which is to create a masked
(skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then perhaps you need to
add
the
flag -keep_mask_deletion_edits to mri_mask to transfer those
voxels
('deleted' voxels actually have a special value to indicate
deleted).
n.
On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
Hello everybody,
Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the
brainmask.mgz
and
using mri_vol2vol and mri_mask commands to apply these changes
to
the
rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
retains all changed made by me, but when I use the mri_mask
command
over the rawavg.mgz no segmentation seems to be donne in the
final
output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz
--regheader
mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
Thanks in advanced,
Gabriel
Re: [Freesurfer] mri_mask problem
Have you checked brainmask2raw.mgz? It looks like you've checked
brain2raw.mgz, but you're not using it for some reason. Make sure the
background has values less than 2.
doug
Gabriel Go.Es. wrote:
Hello Bruce and Nick, I've tryed these options you said and still not
works, I must say that is not in all my subjects,
I've tryed both brain.mgz and brainmask.mgz.
The commands I've used are:
A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz --regheader
A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz
outbrain.mgz
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when
apply the mri_mask the image apperars with no edits.
B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz
brainmask2raw.mgz outbrain2.mgz
I've ran the mri_mask command with and without the
-keep_mask_deletion_edits flag
and again appears to be the mri_mask command the one that is not doing
the work, actually the outputs from mri_convert and mri_vol2vol, looks
pretty similar, any ideas?
Bests
Gabriel
Date: Mon, 14 Mar 2011 08:57:16 -0400
From: fis...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_mask problem
Hi Gabriel,
did you convert the brain.mgz so it is in the same space as the
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you
can try
mri_mask -t threshold. The default is 1e-10 so pretty much anything
non-zero is dept. Try changing it to 2 (voxels edited to be turned
off are
1).
cheers
Bruce
On Mon, 14 Mar 2011,
Gabriel Go.Es. wrote:
Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't
worked,
I'm guessing you'll need my data, to see if there is something
wrong on it, but I think is gonna be hard to send it to through the
e-mail.
Bests,
Gabriel.
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
i'd have to try to replicate this myself, although it will have
to wait
till monday (i'm with the freesurfer group three days a week).
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but
their
actually not there (zeroed).
n.
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the
flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but
there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
Bests,
Gabriel
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
Than you Nick,
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
thank you again,
Gabriel
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
hi, not sure what you are trying to do, as the commands below
seem
to do
what i expect them to do, which is to create a masked
(skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then perhaps you need to
add
the
flag -keep_mask_deletion_edits to mri_mask to transfer those
voxels
('deleted' voxels actually have a special value to indicate
deleted).
n.
On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
Hello everybody,
Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the
brainmask.mgz
and
using mri_vol2vol and mri_mask commands to apply these changes
to
the
rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
retains all changed made by me, but when I use the mri_mask
command
over the rawavg.mgz no
[Freesurfer] V1 prediction
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 ___ 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] Label Orientation
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 ___ 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] Label Orientation
So the difference is that one label was created from the ROI resampled in the T1 space and the other was created from the original ROI volume? If so, then this behavior is as expected. Why not use the first label? doug Tyler Blazey wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 ___ 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] mri_mask problem
Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or brainmask2raw.gz to mask the rawavg.gz on the mri_mask. mri_mask -T 2 -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz And actually the brain.mgz and brainmask.mgz have values of one on edited voxels, but after mri_vol2vol or mri_convert -rl the voxel values appear with bigger values, and some of these values are like ventricles values, so I can not just put a high threshold; new values on edited voxels range from 1 to 40 approximately, and yes, the background has values less than 2. Gabriel Date: Tue, 15 Mar 2011 13:30:40 -0400 From: gr...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_mask problem Have you checked brainmask2raw.mgz? It looks like you've checked brain2raw.mgz, but you're not using it for some reason. Make sure the background has values less than 2. doug Gabriel Go.Es. wrote: Hello Bruce and Nick, I've tryed these options you said and still not works, I must say that is not in all my subjects, I've tryed both brain.mgz and brainmask.mgz. The commands I've used are: A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the mri_mask the image apperars with no edits. B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz brainmask2raw.mgz outbrain2.mgz I've ran the mri_mask command with and without the -keep_mask_deletion_edits flag and again appears to be the mri_mask command the one that is not doing the work, actually the outputs from mri_convert and mri_vol2vol, looks pretty similar, any ideas? Bests Gabriel Date: Mon, 14 Mar 2011 08:57:16 -0400 From: fis...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_mask problem Hi Gabriel, did you convert the brain.mgz so it is in the same space as the rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try mri_mask -t threshold. The default is 1e-10 so pretty much anything non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 1). cheers Bruce On Mon, 14 Mar 2011, Gabriel Go.Es. wrote: Hello Nick I'm wondering if you're able to verify my data today, I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked, I'm guessing you'll need my data, to see if there is something wrong on it, but I think is gonna be hard to send it to through the e-mail. Bests, Gabriel. Subject: RE: [Freesurfer] mri_mask problem From: ni...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com Date: Thu, 10 Mar 2011 21:38:50 -0500 i'd have to try to replicate this myself, although it will have to wait till monday (i'm with the freesurfer group three days a week). i wonder if you can use the brain.mgz as your mask instead of brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their actually not there (zeroed). n. On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote: Hello Nick, good mornig for you, when you read this, Now I have tryed the flag in the mri_mask command but it seems too similar to what was doing before, it says that will transfer 1 voxel edits to dst vol, but there many more voxels edited, I have also tryed mri_vol2vol in the brainmask.mgz intead of brain.mgz but the result is exactly the same (the output from mri_vol2vol has the voxel 'deletions', but the mri_mask ignore them. Now i have no idea how to solve this, do you? Bests, Gabriel Subject: RE: [Freesurfer] mri_mask problem From: ni...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com Date: Wed, 9 Mar 2011 18:00:37 -0500 we've improved some of the help text for the next version (5.1), which is the only reason i noticed it this time. On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote: Than you Nick, Actually that was exactly what i did, delete some voxels from the brainmask, I will try adding the flag and let you know, I dind't saw that this option exist in the mri_mask. thank you again, Gabriel Subject: Re: [Freesurfer] mri_mask problem From: ni...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Wed, 9 Mar 2011 17:52:34 -0500 hi, not sure what you
Re: [Freesurfer] mri_mask problem
For mri_vol2vol try using --interp nearest doug Gabriel Go.Es. wrote: Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or brainmask2raw.gz to mask the rawavg.gz on the mri_mask. mri_mask -T 2 -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz And actually the brain.mgz and brainmask.mgz have values of one on edited voxels, but after mri_vol2vol or mri_convert -rl the voxel values appear with bigger values, and some of these values are like ventricles values, so I can not just put a high threshold; new values on edited voxels range from 1 to 40 approximately, and yes, the background has values less than 2. Gabriel Date: Tue, 15 Mar 2011 13:30:40 -0400 From: gr...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_mask problem Have you checked brainmask2raw.mgz? It looks like you've checked brain2raw.mgz, but you're not using it for some reason. Make sure the background has values less than 2. doug Gabriel Go.Es. wrote: Hello Bruce and Nick, I've tryed these options you said and still not works, I must say that is not in all my subjects, I've tryed both brain.mgz and brainmask.mgz. The commands I've used are: A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the mri_mask the image apperars with no edits. B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz brainmask2raw.mgz outbrain2.mgz I've ran the mri_mask command with and without the -keep_mask_deletion_edits flag and again appears to be the mri_mask command the one that is not doing the work, actually the outputs from mri_convert and mri_vol2vol, looks pretty similar, any ideas? Bests Gabriel Date: Mon, 14 Mar 2011 08:57:16 -0400 From: fis...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_mask problem Hi Gabriel, did you convert the brain.mgz so it is in the same space as the rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try mri_mask -t threshold. The default is 1e-10 so pretty much anything non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 1). cheers Bruce On Mon, 14 Mar 2011, Gabriel Go.Es. wrote: Hello Nick I'm wondering if you're able to verify my data today, I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked, I'm guessing you'll need my data, to see if there is something wrong on it, but I think is gonna be hard to send it to through the e-mail. Bests, Gabriel. Subject: RE: [Freesurfer] mri_mask problem From: ni...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com Date: Thu, 10 Mar 2011 21:38:50 -0500 i'd have to try to replicate this myself, although it will have to wait till monday (i'm with the freesurfer group three days a week). i wonder if you can use the brain.mgz as your mask instead of brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their actually not there (zeroed). n. On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote: Hello Nick, good mornig for you, when you read this, Now I have tryed the flag in the mri_mask command but it seems too similar to what was doing before, it says that will transfer 1 voxel edits to dst vol, but there many more voxels edited, I have also tryed mri_vol2vol in the brainmask.mgz intead of brain.mgz but the result is exactly the same (the output from mri_vol2vol has the voxel 'deletions', but the mri_mask ignore them. Now i have no idea how to solve this, do you? Bests, Gabriel Subject: RE: [Freesurfer] mri_mask problem From: ni...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com Date: Wed, 9 Mar 2011 18:00:37 -0500 we've improved some of the help text for the next version (5.1), which is the only reason i noticed it this time. On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote: Than you Nick, Actually that was exactly what i did, delete some voxels from the brainmask, I will try adding the flag and let you know, I dind't saw that this option exist in the mri_mask. thank you again, Gabriel Subject: Re:
Re: [Freesurfer] Re-post: Fixated brain
we do have a procedure but it involved a fair amount of manual intervention and isn't terribly well documented (and it's evolving). It depends on Andre van der Kouwe's multi-echo flash sequence, which you would need to get as well cheers Bruce On Tue, 15 Mar 2011, Auer, Tibor MD. Ph.D. wrote: 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: ta...@gwdg.de mailto:tibor.a...@gmail.com ___ 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] Label Orientation
Hi Doug, Thanks for your reply. There is actually only one label, which was created from the ROI resampled in T1 space. The problem is that the label only has the correct orientation in tkmedit when the resampled ROI is loaded as the main volume. When I load T1.mgz as the main volume, the label orientation is incorrect. Does this make sense? Sorry for being unclear in previous post. Thanks, - Tyler On Mar 15, 2011, at 1:17 PM, Douglas N Greve wrote: So the difference is that one label was created from the ROI resampled in the T1 space and the other was created from the original ROI volume? If so, then this behavior is as expected. Why not use the first label? doug Tyler Blazey wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] results visualization
try: tkmedit tpidNtpidN norm.mgz lh.white -aux wm.mgz -aseg -aux-surface rh.white cheers Bruce On Tue, 15 Mar 2011, nadia merhoum wrote: 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 ___ 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 error
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-k.html 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 ___ 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] V1 prediction
Hi Thomas, there is a tksurfer menu item to transfer the label stat field to an overlay, and you can go from there. cheers Bruce On Tue, 15 Mar 2011, Thesen, Thomas wrote: 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 ___ 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] corpus calosum volume ?...
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 ___ 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] display multiple functional overlays simultaneously
Thanks Doug. Does mri_seg2annot come w/ the latest FS distribution?
It doesn't seem to be available (I can't launch the help and receive
command not found when I try to run the command). mri_binarize
worked fine.
On Tue, Mar 15, 2011 at 12:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
No, you'll have to merge them into one map (and you'll probably want it to
be an annotation). To do this, you'll need to run several programs.
1. mri_binarize -- threshold your two raw maps, give one a --binval 1 the
other --binval 2
2. Add them together: fscalc binmap1.nii add binmap2.nii -o binmap12.nii
This will cause voxels only in binmap1 to be one, only in binmap2 to be 2,
and voxels in both to be 3
3. Create a lookup table like $FREESURFER_HOME/FreeSurferColorLUT.txt with 4
entries (0, 1, 2, 3), and give them the color you want.
4. mri_seg2annot --seg binmap12.nii --ctab yourcolortable ...
doug
Scott Hayes wrote:
Hi Doug,
I was trying to load the maps so I could examine each map and the
overlap, as in the attached example (in this image, red is one map,
blue is the other, and pink is the overlap--done in MRICRON. I think
it's a nice way to view similarities and differences in activation for
different groups. Although this might be achievable by merging the
maps as you suggest, I was wondering if it was possible to view them
in tksurfer without trying to merge them into a single map.
Thanks,
Scott
On Tue, Mar 15, 2011 at 11:09 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Hi Scott, I'm not sure what you are trying to do. How can you display two
different z-values at the same voxel at the same time? Or do you want to
merge the maps in some way?
doug
Scott Hayes wrote:
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 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
[Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain
Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed through FreeSurfer? Thanks, -Andrew ___ 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] Philips DICOM format problem
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. ___ 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] display multiple functional overlays simultaneously
Sorry, it should be mris_seg2annot (not mri_seg2annot).
doug
Scott Hayes wrote:
Thanks Doug. Does mri_seg2annot come w/ the latest FS distribution?
It doesn't seem to be available (I can't launch the help and receive
command not found when I try to run the command). mri_binarize
worked fine.
On Tue, Mar 15, 2011 at 12:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
No, you'll have to merge them into one map (and you'll probably want it to
be an annotation). To do this, you'll need to run several programs.
1. mri_binarize -- threshold your two raw maps, give one a --binval 1 the
other --binval 2
2. Add them together: fscalc binmap1.nii add binmap2.nii -o binmap12.nii
This will cause voxels only in binmap1 to be one, only in binmap2 to be 2,
and voxels in both to be 3
3. Create a lookup table like $FREESURFER_HOME/FreeSurferColorLUT.txt with 4
entries (0, 1, 2, 3), and give them the color you want.
4. mri_seg2annot --seg binmap12.nii --ctab yourcolortable ...
doug
Scott Hayes wrote:
Hi Doug,
I was trying to load the maps so I could examine each map and the
overlap, as in the attached example (in this image, red is one map,
blue is the other, and pink is the overlap--done in MRICRON. I think
it's a nice way to view similarities and differences in activation for
different groups. Although this might be achievable by merging the
maps as you suggest, I was wondering if it was possible to view them
in tksurfer without trying to merge them into a single map.
Thanks,
Scott
On Tue, Mar 15, 2011 at 11:09 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Hi Scott, I'm not sure what you are trying to do. How can you display two
different z-values at the same voxel at the same time? Or do you want to
merge the maps in some way?
doug
Scott Hayes wrote:
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 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.bin0x0011d547
wxVTKRenderWindowInteractor::OnPaint(wxPaintEvent) + 151
9 freeview.bin0x00407b53
wxAppConsole::HandleEvent(wxEvtHandler*, void
(wxEvtHandler::*)(wxEvent), wxEvent) const + 65
10 freeview.bin0x00452f30
wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const,
wxEvtHandler*, wxEvent) + 212
11
Re: [Freesurfer] mri_glmfit allocate memory error
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 gr...@nmr.mgh.harvard.edu mailto:gr...@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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., 0., 70387746064971392794503413760. 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:
Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain
After you've gone into MNI space with all of your subjects, then visualizing the results on the surface are of questionable value. If you just want to take a peek, then it's not a big deal, but I would not recommend reporting them in a publication. If your results are in the mni152 space, you can try tksurfer fsaverage lh inflated -aparc -mni152reg yourfile.img doug Andrew Jahn wrote: Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed through FreeSurfer? Thanks, -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 ___ 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] Philips DICOM format problem
Hi Leo: I have faced this problem before. Philips scanner's default output format is the PAR/REC format - but it also outputs in Dicom format. What I believe is the problem is that the images are oriented wrongly. Take a look at this in MRICRO and see how the images are oriented. You may need to reorient the images to be acceptable to FS. hope this helps! Alan On Tue, Mar 15, 2011 at 4:01 PM, leonardo kay leonardo@gmail.comwrote: 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. ___ 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 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] corpus calosum volume ?...
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Is there a way to obtain the thickness of every vertex of the whole brain?
Hi,all: Just as the title says,I wonder if there is a method to obtain the thickness of each vertex in the whole brain,and so,if we can,how do we kown which of the area is the vertex belong to? I am using the freesurfer 5.0. thanks in advance! wang___ 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.
