Freesurfer

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Guideline to process high resolution data using FreeSurfer and some questions
by Falk Lüsebrink 20 May '09

20 May '09

Hi FreeSurfers, Due to an accident and after several hundreds of hours of work I was finally able to completely (actually not completely, but it seems to work) process high resolution data with an isometric voxel size of 0.6mm without any manual intervention, while using the advantage of all atlases. I would like to share my experience with you and especially would like to know if and how some of my individual changes to the recon-all stream may affect the results. The data I used was acquired at 7T (Siemens), so my volumes were not very homogenous. To get rid of most of the inhomogeneities we are using a method at our lab in which two volumes are acquired, a MPRAGE and 3D gradient echo. Both volumes are co-registered and afterwards the MPRAGE is divided by the 3D GE. Everything further has been done directly using FreeSurfer. First you need to run recon-all autorecon1 cm noskullstrip s <your subject>. Using the cm flag the volumes are not conformed to 1mm^3 voxel size and 256^3, but to the smallest voxel size (in my case 0.5990mm^3 and 385^3). It is crucial to not run skullstrip using the high resolution data as this will not work! You need to go to your subject/mri folder and use mri_convert cs 1 nu.mgz nu.conformed.mgz, this creates a conformed version of the nu.mgz. Now you should run mri_em_register skull nu.conformed.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta. This has to be done using a conformed nu.mgz as in the following stage mri_watershed seems to conform the input file (Will it be really conformed? The output volume doesnt suggest this.) and if the talairach_with_skull.lta is created using a not conformed volume one gets an error stating that the WM intensity is lower than CSF intensity and the stage is exited. The nu.conformed.mgz is only used during this stage, so your high resolution volumes will never (Never? At least the output volumes are not.) be resampled, conformed or whatever to a lower resolution. After this has been done, one can use recon-all skullstrip s <your subject> and take advantage of the atlas! Though the input volume (T1.mgz) seems to be conformed during mri_watershed, the output volume (brainmask.mgz) will have the correct resolution. If the brainmask.mgz doesnt look well, try adding the wsatlas switch first, as this improved the skull stripping if only really small bits of skull and dura were still left or small pieces of the temporal lobe or cerebellum were cut off. If this doesnt help much adjust the watershed threshold using the wsthresh <value> switch (but still use wsatlas) like described in the wiki. Now run recon-all gcareg canorm careg careginv rmneck skull-lta calabel s <your subject>. Even though the aseg.mgz should look perfectly fine, one needs to stop here, as the normalization2 stage can be run only if the aseg.mgz is conformed (Why does it need to be conformed?). This is something you dont want, so go to the subject/mri folder again and run mri_normalize mask brainmask.mgz norm.mgz brain.mgz. Right now I'm running the missing stages of -autorecon2 (being at the -fix stage which will take some time) and I think it should work totally fine. Maybe the following stages using the aseg.mgz might not run as those maybe want the aseg.mgz to be conformed as well, but I don't know yet. Additionally in my case this wouldn't be a problem as I just want to measure the cortical thickness. I would highly appreciate if you could answer the questions in the brackets and how the results might be effected by the changes I have done. By the way, I tried running mri_nu_correct.mni using the T1.mgz as the input volume and running mri_normalize again afterwards to improve the inhomogeneity correction. The result looks very good, but parts of the skull and dura are not erased during the skull stripping stage (as they seem to match the intensities of GM and WM). If I adjust the watershed threshold so these are erased, pieces of the cerebellum and temporal lobes are erased additionally. Would it be possible to run mri_nu_correct using the brainmask.mgz as input volume and mri_normalize afterwards, so the inhomogeneity correction can be further improved? Will mri_nu_correct.mni work fine on a volume without skull? Thanks in advance, Regards, Falk

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brainmask volume greater than ICV
by Martin Kavec 20 May '09

20 May '09

Hi, I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of quite a few of my subjects that brain mask volume (1735600 mm^3) is greater than ICV (1701891 mm^3). The talairach failure detection passed fine: talairach.xfm OK (p=0.7556, pval=0.6675 >= threshold 0.005 ). The segstat step passed fine, with atlas_icv (eTIV) = 1701891 mm^3 (det: 1.144671). However, the mris_volmask, which followed right after the segstat exited with errors and dumped the core. I see this on about 30% of my analyzes. :( I can provide the data, if that could help. Thanks, Martin

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Re: Freesurfer Digest, Vol 63, Issue 35
by Sebastian Moeller 19 May '09

19 May '09

Hi Falk, what about you change the voxelsize to 1 mm before opening the volume in tkmedit for modifications and then change them back to the original values after you are done. I have not tried that, but it should work at least around the tkmedit problem... ahoi Sebastian On May 19, 2009, at 2:46 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Tue, 19 May 2009 11:46:00 +0200 > From: Falk L?sebrink <falk.luese(a)gmx.net> > Subject: RE: [Freesurfer] mri_fill > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <002801c9d866$9e0fcff0$da2f6fd0$@luese@gmx.net> > Content-Type: text/plain; charset="iso-8859-1" > > 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 -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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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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