Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

RE: [Freesurfer] mri_fill
by Allison Stevens 19 May '09

19 May '09

The page up and page down buttons scroll through slices in both tools. If you have any problems or requests please let me know. We have abandoned scuba and probably will not be offering any support for it, however freeview is still in development. Allison -- On Tue, 19 May 2009, Falk Lüsebrink wrote: > Hi Allison and Nick, > > Thanks for the info. The wiki didn't mention that either freeview or scuba > (dev only) would be available in the current release. > > I tried both scuba and freeview and I'm wondering if there is some easy way > to browse through the slices from either the sagital, coronal or axial view. > Using scuba I could enter the RAS or index coords or is there something else > I'm missing? In freeview I think I have to switch between the navigation > tool and voxel edit tool or is there another way? > > At first glance freeview does appeal more to me in terms of simply erasing > some voxels, so I think I will stick with it. > > Thanks in advance, > Regards, > Falk > > > -----Original Message----- > From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] > Sent: Tuesday, May 19, 2009 5:38 PM > To: Nick Schmansky > Cc: Falk Lüsebrink > Subject: RE: [Freesurfer] mri_fill > > Falk, > I can help you get started with scuba or freeview. > > For freeview, you type: > freeview -v volume.mgz > > and it will load your volume. There is a help guide in there to take you > through all the tools. Let me know if you need any help. > Allison > >

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RE: [Freesurfer] mri_fill
by Falk Lüsebrink 19 May '09

19 May '09

Hi Allison and Nick, Thanks for the info. The wiki didn't mention that either freeview or scuba (dev only) would be available in the current release. I tried both scuba and freeview and I'm wondering if there is some easy way to browse through the slices from either the sagital, coronal or axial view. Using scuba I could enter the RAS or index coords or is there something else I'm missing? In freeview I think I have to switch between the navigation tool and voxel edit tool or is there another way? At first glance freeview does appeal more to me in terms of simply erasing some voxels, so I think I will stick with it. Thanks in advance, Regards, Falk -----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Tuesday, May 19, 2009 5:38 PM To: Nick Schmansky Cc: Falk Lüsebrink Subject: RE: [Freesurfer] mri_fill Falk, I can help you get started with scuba or freeview. For freeview, you type: freeview -v volume.mgz and it will load your volume. There is a help guide in there to take you through all the tools. Let me know if you need any help. Allison -- On Tue, 19 May 2009, Nick Schmansky wrote: > Falk, > > There are two tools included with freesurfer that can be used to perform > edits on hi-res data: scuba, and freeview. I do not have experience > with either. tkmedit is not setup to edit hi-res data, as it resamples > to 1mm^3. > > Nick > > On Tue, 2009-05-19 at 11:46 +0200, Falk Lüsebrink wrote: >> As mentioned in the first email somehow tkmedit seems to skip some slices if >> one tries to edit them manually and the resolution of the volume is not >> 1mm^3. Attached is a screenshot of the filled.mgz which I tried to edit on >> the left from the coronal view and on the right from the sagittal view. >> >> The resolution of the volume used in this case is 0.6mm. If I use the >> "Slice" thing to browse through the slices nearly every second slice is >> skipped. Increasing or decreasing the volume index by 1 in the direction I >> would like to move on doesn't work either. For example if I change the >> volume index from 162 338 124 to 163 338 124 the same slice is being shown. >> 161 338 124 and 164 338 124 are different as it should be, but it is not >> possible to view 163 and so it is impossible to edit this slice. >> >> Are there any other tools available to edit volumes like tkmedit does? It >> doesn't need to be included within FreeSurfer but it would be better if it >> could handle the .mgz format. >> >> Regards, >> Falk >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink >> Sent: Monday, May 18, 2009 2:36 PM >> To: 'Bruce Fischl' >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] mri_fill >> >> Hi Bruce, >> >> Actually I need to skip the whole aseg process as this is incompatible to >> the high resolution volumes I'm using. I read that prior to the aseg files >> the talairach transform was used to delete the cerebellum and that the >> cutting planes correctly. Is it possible to use this again? >> >> I also tried using seed points, though the cerebellum was never erased. >> >> Regards, >> Falk >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl >> Sent: Monday, May 18, 2009 2:07 PM >> To: Falk Lüsebrink >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] mri_fill >> >> p.s. you can pick seed points in the callosum and pons in tkmedit and see if >> that fixes your problem, but if there is something else going on then it may >> not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink >> wrote: >> >>> Hi FreeSurfers, >>> >>> >>> >>> At the end of mri_fill Iÿÿm told to check the filled volume as the >>> cerebellum may be included. It is and also the brainstem. But >>> actually I donÿÿt know how to fix this. Do I need to include the seed >>> points for cc and pons for better cutting planes? Do I need to manually >> edit the volume? >>> >>> >>> >>> If the latter is better are there any other tools available besides >> tkmedit? >>> If I try to add or delete voxels of a high resolution volume tkmedit >>> seems to skin every second slice. >>> >>> >>> >>> Regards, >>> >>> Falk >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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RE: [Freesurfer] mri_fill
by Nick Schmansky 19 May '09

19 May '09

Falk, There are two tools included with freesurfer that can be used to perform edits on hi-res data: scuba, and freeview. I do not have experience with either. tkmedit is not setup to edit hi-res data, as it resamples to 1mm^3. Nick On Tue, 2009-05-19 at 11:46 +0200, Falk Lüsebrink wrote: > As mentioned in the first email somehow tkmedit seems to skip some slices if > one tries to edit them manually and the resolution of the volume is not > 1mm^3. Attached is a screenshot of the filled.mgz which I tried to edit on > the left from the coronal view and on the right from the sagittal view. > > The resolution of the volume used in this case is 0.6mm. If I use the > "Slice" thing to browse through the slices nearly every second slice is > skipped. Increasing or decreasing the volume index by 1 in the direction I > would like to move on doesn't work either. For example if I change the > volume index from 162 338 124 to 163 338 124 the same slice is being shown. > 161 338 124 and 164 338 124 are different as it should be, but it is not > possible to view 163 and so it is impossible to edit this slice. > > Are there any other tools available to edit volumes like tkmedit does? It > doesn't need to be included within FreeSurfer but it would be better if it > could handle the .mgz format. > > Regards, > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink > Sent: Monday, May 18, 2009 2:36 PM > To: 'Bruce Fischl' > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] mri_fill > > Hi Bruce, > > Actually I need to skip the whole aseg process as this is incompatible to > the high resolution volumes I'm using. I read that prior to the aseg files > the talairach transform was used to delete the cerebellum and that the > cutting planes correctly. Is it possible to use this again? > > I also tried using seed points, though the cerebellum was never erased. > > Regards, > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Monday, May 18, 2009 2:07 PM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_fill > > p.s. you can pick seed points in the callosum and pons in tkmedit and see if > that fixes your problem, but if there is something else going on then it may > not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink > wrote: > > > Hi FreeSurfers, > > > > > > > > At the end of mri_fill I’m told to check the filled volume as the > > cerebellum may be included. It is and also the brainstem. But > > actually I don’t know how to fix this. Do I need to include the seed > > points for cc and pons for better cutting planes? Do I need to manually > edit the volume? > > > > > > > > If the latter is better are there any other tools available besides > tkmedit? > > If I try to add or delete voxels of a high resolution volume tkmedit > > seems to skin every second slice. > > > > > > > > Regards, > > > > Falk > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] mri_fill
by Falk Lüsebrink 19 May '09

19 May '09

As mentioned in the first email somehow tkmedit seems to skip some slices if one tries to edit them manually and the resolution of the volume is not 1mm^3. Attached is a screenshot of the filled.mgz which I tried to edit on the left from the coronal view and on the right from the sagittal view. The resolution of the volume used in this case is 0.6mm. If I use the "Slice" thing to browse through the slices nearly every second slice is skipped. Increasing or decreasing the volume index by 1 in the direction I would like to move on doesn't work either. For example if I change the volume index from 162 338 124 to 163 338 124 the same slice is being shown. 161 338 124 and 164 338 124 are different as it should be, but it is not possible to view 163 and so it is impossible to edit this slice. Are there any other tools available to edit volumes like tkmedit does? It doesn't need to be included within FreeSurfer but it would be better if it could handle the .mgz format. Regards, Falk -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink Sent: Monday, May 18, 2009 2:36 PM To: 'Bruce Fischl' Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_fill Hi Bruce, Actually I need to skip the whole aseg process as this is incompatible to the high resolution volumes I'm using. I read that prior to the aseg files the talairach transform was used to delete the cerebellum and that the cutting planes correctly. Is it possible to use this again? I also tried using seed points, though the cerebellum was never erased. Regards, Falk -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 18, 2009 2:07 PM To: Falk Lüsebrink Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_fill p.s. you can pick seed points in the callosum and pons in tkmedit and see if that fixes your problem, but if there is something else going on then it may not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink wrote: > Hi FreeSurfers, > > > > At the end of mri_fill Im told to check the filled volume as the > cerebellum may be included. It is and also the brainstem. But > actually I dont know how to fix this. Do I need to include the seed > points for cc and pons for better cutting planes? Do I need to manually edit the volume? > > > > If the latter is better are there any other tools available besides tkmedit? > If I try to add or delete voxels of a high resolution volume tkmedit > seems to skin every second slice. > > > > Regards, > > Falk > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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question abt flattening in freesurfer
by Ritobrato Datta 18 May '09

18 May '09

Hi All, My name is Ritobrato Datta and I am a post-doc at PENN. I have just started learning Freesurfer. I am trying to create occipital flatmap in freesurfer using the command mris_flatten. I followed the commands as described but am getting the following error. I created the lh.occip.patch.3d and its there in the surf directory. Following is the error- --------------------- mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat using write iterations = 0 sampling 7 neighbors out to a distance of 20 mm reading patch lh.occip.patch.3d with 1919246708 vertices (1096499.4% of total) MRISreadPatch: bad vertex # (1701060705) found in patch file No such file or directory --------------------- Any suggestions will be highly appreciated. Thanks much Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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error recon-all
by anita di iasio 18 May '09

18 May '09

Hi All, I have a problem. I run recon-all on f-MRI of a group of children (3-12 years). In some of them I have this error in recon-all imgrege: no voxels in register ERROR: 'imgreg_4dfp /opt/freesurfer/average/711-2C_as_mni_average_305 /opt/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux node6 2.6.18-5-amd64 #1 SMP Tue Oct 2 20:37:02 UTC 2007 x86_64 GNU/Linux recon-all exited with ERRORS at Wed May 13 18:48:05 CEST 2009 Do you know what this problem is? Which is the origin of this problem? Do you konw how to fix it? thanks, Anita di Iasio

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SPM coreg error
by Rodrigo Zepeda 18 May '09

18 May '09

While trying to coregister a ct.nii and a orig.mgz file using the following command: spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig I get the following error: >> >> >> ERROR: spm_coreg >> ??? Undefined function or variable 'x'. >> Finished after 0.023302 sec >> >> Parameters >> ??? Undefined function or variable 'x'. >> >> >> >> >> ??? Undefined function or variable 'x'. >> >> Using spm_get_space ??? Undefined variable "VF" or class "VF.fname". >> >> >> ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg The SPM package used to work a few weeks ago. Did something change? Do I need to install something? Thanks! Rodrigo

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(no subject)
by Campanella Martina 18 May '09

18 May '09

Hi freesurfer, We would make a new LUT to create an annot file with personalized names and colours.. How is it possible? Thanks, Martina Campanella

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RE: [Freesurfer] Measuring cortical thickness with high resolution data
by Falk Lüsebrink 18 May '09

18 May '09

Hi Jürgen, We are using a 7T from Siemens and we acquire two volumes with an MPRAGE and 3D GE sequence. Using SPM both volumes are co-registered and afterwards the MPRAGE is divided by the 3D GE. Attached is a sample *.jpg showing the results. In our case the temporal lobes are still not very homogeneous due to some problems with the coil or gradient system (currently a new gradient is being installed, so it probably will help). Also Im further improving the volumes by running mri_nu_correct.mni on the T1.mgz created by the normalization stage (like mri_nu_correct.mni stop 0.001 distance 25 i T1.mgz o nu.mgz) and running mri_normalize again afterwards. The volume normally looks very homogeneous afterwards, even the temporal lobes. But Im facing problems in the following stages, mainly everything based on the aseg files as I need to skip the process. I cant recall exactly during which stage, but recon-all exists with the error that the aseg.mgz needs to be conformed, so it needs to be skipped. But by skipping these stages I currently have issues during mri_fill as the cerebellum is not erased as it should be. Also the skull stripping isnt very good in most cases. The only solution I had was using a brainmask created by Slicer or to run recon-all normally (conforming the data) and resampling the brainmask to the original resolution (using mri_vol2vol). Then masking the T1.mgz to get a fairly good looking brainmask. Hope this helps, Regards, Falk From: Jürgen Hänggi [mailto:j.haenggi@psychologie.uzh.ch] Sent: Monday, May 18, 2009 3:30 PM To: Falk Lüsebrink Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data Hi Falk We are also struggling with 7T images and Freesurfer. In your email (see below) you wrote that you have find a way to get ride of the inhomogeneities inherent in the 7T images. Which other sequence did you use for that? Do you also use a 7T scanner from Philips? Do you use an adiabatic pulse sequence? Thanks in advance Best regards Jürgen On [DATE], "Falk Lüsebrink" <[ADDRESS]> wrote: Hi Freesurfers, Im trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore. My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the cm and noaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags. The error I receive is occurring after the WM Segmentation and states as follows: #-------------------------------------------- #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands.... 20 segments, 4813 filled 10270 bright non-wm voxels segmented. 5589 diagonally connected voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320. The dimensions of the data Im trying to process is 320 x 320 x 224 and is changed to 320 x 320 x 320 while using the cm flag. It seems the mri_segment process cant handle any dimensions above 256 or Im missing another flag. Does someone has any ideas about that issue? Regards, Falk _____ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] mri_fill
by Bruce Fischl 18 May '09

18 May '09

p.s. you can pick seed points in the callosum and pons in tkmedit and see if that fixes your problem, but if there is something else going on then it may not (e.g. if the aseg is badly wrong) On Mon, 18 May 2009, Falk Lüsebrink wrote: > Hi FreeSurfers, > > > > At the end of mri_fill Im told to check the filled volume as the cerebellum > may be included. It is and also the brainstem. But actually I dont know > how to fix this. Do I need to include the seed points for cc and pons for > better cutting planes? Do I need to manually edit the volume? > > > > If the latter is better are there any other tools available besides tkmedit? > If I try to add or delete voxels of a high resolution volume tkmedit seems > to skin every second slice. > > > > Regards, > > Falk > >

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