Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly build of centos 6 with the hires flag only. Disk space or alike wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get working surfaces.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never occur

cheers Bruce On Sun, 29 Nov 2015, Ajay Kurani wrote:

Hello Freesurfer experts,    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error during pocessing:

Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage.  I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error:

Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag.  Are there any suggestions you have?

Thanks, Ajay

Hi Falk, Thank you very much for the suggestion! I will give it a try.

Also Bruce I sent a separate email with a link to the original image for you to download. I can also move all of my processed files for that template there if you would like so you do not have to restart from scratch?

Thanks, Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly build of centos 6 with the hires flag only. Disk space or alike wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get working surfaces.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never occur

cheers Bruce On Sun, 29 Nov 2015, Ajay Kurani wrote:

...

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing:

Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error:

Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have?

Thanks, Ajay

Hi Falk, I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh mris_topo_fixer -mgz -warning -seed 1234 ICBM lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list

Any suggestions would be appreciated.

Thanks, Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly build of centos 6 with the hires flag only. Disk space or alike wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get working surfaces.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never occur

cheers Bruce On Sun, 29 Nov 2015, Ajay Kurani wrote:

...

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing:

Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error:

Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have?

Thanks, Ajay

Hi Falk

I don't think you need to rerun the qsphere. I'm pretty sure this is a bug in mris_fix_topology for giant defects, but haven't finished tracking it down yet

cheers Bruce

On Tue, 1 Dec 2015, Falk Lüsebrink wrote:

Hi Ajay,

you should

cp ?h.orig.nofix ?h.orig

cp ?h.inflated.nofix ?h.inflated

with ? being l or r depending your hemisphere. After the fixing stage the surfaces got damaged somehow, therefore you have to recreate it them. I’m not entirely sure about the qsphere. Probably you have to run the -qsphere stage again also.

Best,

Falk

Von: Ajay Kurani [mailto:dr.ajay.kurani@gmail.com] Gesendet: Montag, 30. November 2015 21:50 An: Falk Lüsebrink Cc: Freesurfer support list; Bruce Fischl Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Falk,

I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh mris_topo_fixer -mgz -warning -seed 1234 ICBM lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym _09b/ICBM/surf/lh.orig... mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym _09b/ICBM/surf/rh.orig... mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list

Any suggestions would be appreciated.

Thanks,

Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink falk.luesebrink@ovgu.de wrote:

Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly build of centos 6 with the hires flag only. Disk space or alike wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get working surfaces.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never occur

cheers Bruce

On Sun, 29 Nov 2015, Ajay Kurani wrote:

...

Hello Freesurfer experts,    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error during pocessing:

Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage.  I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error:

Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag.  Are there any suggestions you have?

Thanks, Ajay

Hi Ajay

can you explain your entire processing stream, including the details of the acquisition? What sequence/coil/scanner was used? You could fix your problem by looking at the defects on the inflated.nofix, overlaying lh.defect_labels on it to see where they are, then figuring out what caused them in the volume. However, there is a bug in mris_fix_topology that only comes up when it encounters a large enough defect (with nvertices>200,000). The code tries to avoid running it's normal genetic algorithm as it would take days (or weeks) to finish, since it scales with the square of the number of vertices. I haven't figured out what is going wrong yet, but hopefully will have a code fix soon.

cheers Bruce

On Tue, 1 Dec 2015, Ajay Kurani wrote:

Hi Bruce,  When looking at my top slices in brain ask I noticed that the gray/white matter shows but the darker areas surrounding it are not present (this usually goes to the edge of the brain).  Could the large defects be a result of having masked this out on the input file?  I multiplied the template with the GM/WM/CSF masks they provided to get the brain extracted so I only see this missing in the very top few slices of the brain.

Thanks, Ajay

On Tuesday, December 1, 2015, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Falk

  I don't think you need to rerun the qsphere. I'm pretty sure
  this is a bug in mris_fix_topology for giant defects, but
  haven't finished tracking it down yet

  cheers
  Bruce


  On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


        Hi Ajay,

         

        you should

         

        cp ?h.orig.nofix ?h.orig

        cp ?h.inflated.nofix ?h.inflated

         

        with ? being l or r depending your hemisphere.
        After the fixing stage the
        surfaces got damaged somehow, therefore you have to
        recreate it them. I’m
        not entirely sure about the qsphere. Probably you
        have to run the -qsphere
        stage again also.

         

        Best,

        Falk

         

         

        Von: Ajay Kurani [mailto:dr.ajay.kurani@gmail.com]
        Gesendet: Montag, 30. November 2015 21:50
        An: Falk Lüsebrink
        Cc: Freesurfer support list; Bruce Fischl
        Betreff: Re: [Freesurfer] Freesurfer 6.0 -
        Autorecon2 failure
        (mris_euler_number) using high res (0.5mm
        isotropic) T1 image

         

        Hi Falk,

           I used the command and got the following error:

        Command: ris_topo_fixer -mgz -warning -seed 1234
        ICBM lh
        mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
        INFO: assuming .mgz format
        setting seed for random number genererator to 1234
        reading inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
        lin_sym
        _09b/ICBM/surf/lh.orig...

mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn i_icbm152_nlin_sym _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

        mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
        INFO: assuming .mgz format
        setting seed for random number genererator to 1234
        reading inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
        lin_sym
        _09b/ICBM/surf/rh.orig...

mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn i_icbm152_nlin_sym _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list

        Any suggestions would be appreciated.

        Thanks,

        Ajay

         

        On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
        <falk.luesebrink@ovgu.de>
        wrote:

        Hi Ajay,

        I ran into the same error processing hires data a
        while ago using a nightly
        build of centos 6 with the hires flag only. Disk
        space or alike wasn't an
        issue. I ran mris_topo_fixer instead of
        mris_fix_topology to get working
        surfaces.

        Best,
        Falk

        -----Ursprüngliche Nachricht-----
        Von: freesurfer-bounces@nmr.mgh.harvard.edu
        [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im
        Auftrag von Bruce Fischl
        Gesendet: Sonntag, 29. November 2015 22:48
        An: Freesurfer support list
        Betreff: Re: [Freesurfer] Freesurfer 6.0 -
        Autorecon2 failure
        (mris_euler_number) using high res (0.5mm
        isotropic) T1 image

        Hi Ajay

        are you sure you didn't run out of disk space? That
        error is a sanity check
        on the surfaces that should never occur

        cheers
        Bruce

        On Sun, 29 Nov 2015, Ajay
        Kurani wrote:

        > Hello Freesurfer experts,
        >    I am trying to run Freesurfer 6.0 beta
        (downloaded 10/15/15
        > version) with the -hires flag to process an MNI
        template image which
        > is 0.5mm isotropic.  Stage 1 ran well and on
        stage 2 there is an error
        > during
        > pocessing:
        >
        > Command run:
        > recon-all -s ICBM -autorecon2 -openmp 8 -3T
        -hires -expert expert.opts
        >
        > I supplied a skull stripped brain which was nu
        corrected and so I used
        > the T1.mgz and copied it to brainmask.mgz and
        nu.mgz in autorecon1
        > stage.  I then ran autorecon2 and it was working
        well until I was at
        > the -fix stage and ran into the following error:
        >
        >
        > Error:
        > mris_euler_number ./surf/lh.orig
        > mrisFindNeighbors: ./surf/lh.orig:
        face[46196].v[0] = 24215, but face
        > 46196 not in vertex 24215 face list
        >
        >
        >
        > I am not sure if this is due to the fact that we
        have a very high
        > resolution image (template) and if there are any
        modifications needed
        > aside from the hires flag.  Are there any
        suggestions you have?
        >
        > Thanks,
        > Ajay
        >
        >

         





  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.

Hi Ajay

I have found the problem that messed up the surfaces and fixed it. We can get you an updated mris_fix_topology that will not generate corrupted surfaces. However, the underlying problem is huge topological defects caused by low gray/white contrast in this data. For example in the left hemi, there is on in the insula (e.g. voxels around 362, 213, 200 and 364, 229, 207 and in the temporal lobe (351, 286, 282, 283, 309, 258).

Basically the gray/white contrast isn't high enough for us to accurately segment the wm with our default procedures. Control points may help a bit, but you may also need to manually edit the wm.mgz to remove the largest defects. The easiest way to do this is to visualize them on the lh.inflated.nofix surface with the lh.defect_labels overlaid to show you where the defects are, then go into the volume in the wm.mgz and either add control points or erase wm to fix things.

Let us know if you want a new mris_fix_topology. I'm not sure it is worth the trouble since while it will now generate topologically correct surfaces for this dataset, they will not be geometrically acccurate in the vicinity of the huge (>200,000 vertices!) defects.

cheers Bruce

On Wed, 2 Dec 2015, Ajay Kurani wrote:

Hi Bruce,

The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which I downloaded from the McGills site (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).%C2%A0 The template has a range of values from 0-100.  Then I combined the csf/wm/gm masks (derived from the 2009c template which is 1mm isotropic) and resampled to 0.5 mm to mask the brain.  Subsequently I rescaled the data to have a range of 0-255 and used this output as my input T1 for Freesurfer.  Thank you very much for looking into this matter, it is much appreciated!  I will look at the file as you suggested.

Sincerely, Ajay

On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ajay

  can you explain your entire processing stream, including the details of the
  acquisition? What sequence/coil/scanner was used? You could fix your problem by looking
  at the defects on the inflated.nofix, overlaying
  lh.defect_labels on it to see where they are, then figuring out what caused them in the
  volume. However, there is a bug in mris_fix_topology that only comes up when it
  encounters a large enough defect (with nvertices>200,000). The code tries to avoid
  running it's normal genetic algorithm as it would take days (or weeks) to finish, since
  it scales with the square of the number of vertices. I haven't figured out what is
  going wrong yet, but hopefully will have a code fix soon.

  cheers
  Bruce


  On Tue, 1 Dec 2015, Ajay Kurani wrote:

        Hi Bruce,  When looking at my top slices in brain ask I noticed that the
        gray/white matter shows but the darker areas surrounding it are not present
        (this usually goes to the edge of the brain).  Could the large defects be a
        result of having masked this out on the input file?  I multiplied the
        template with the GM/WM/CSF masks they provided to get the brain extracted
        so I only see this missing in the very top few slices of the brain.

        Thanks,
        Ajay

        On Tuesday, December 1, 2015, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Falk

              I don't think you need to rerun the qsphere. I'm pretty sure
              this is a bug in mris_fix_topology for giant defects, but
              haven't finished tracking it down yet

              cheers
              Bruce


              On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


                    Hi Ajay,

                     

                    you should

                     

                    cp ?h.orig.nofix ?h.orig

                    cp ?h.inflated.nofix ?h.inflated

                     

                    with ? being l or r depending your hemisphere.
                    After the fixing stage the
                    surfaces got damaged somehow, therefore you have to
                    recreate it them. I’m
                    not entirely sure about the qsphere. Probably you
                    have to run the -qsphere
                    stage again also.

                     

                    Best,

                    Falk

                     

                     

                    Von: Ajay Kurani [mailto:dr.ajay.kurani@gmail.com]
                    Gesendet: Montag, 30. November 2015 21:50
                    An: Falk Lüsebrink
                    Cc: Freesurfer support list; Bruce Fischl
                    Betreff: Re: [Freesurfer] Freesurfer 6.0 -
                    Autorecon2 failure
                    (mris_euler_number) using high res (0.5mm
                    isotropic) T1 image

                     

                    Hi Falk,

                       I used the command and got the following error:

                    Command: ris_topo_fixer -mgz -warning -seed 1234
                    ICBM lh
                    mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
                    INFO: assuming .mgz format
                    setting seed for random number genererator to 1234
                    reading
        inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                    lin_sym
                    _09b/ICBM/surf/lh.orig...
        mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                    i_icbm152_nlin_sym
                    _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
                    but face 46196 not in
                    vertex 24215 face list

                    mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
                    INFO: assuming .mgz format
                    setting seed for random number genererator to 1234
                    reading
        inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                    lin_sym
                    _09b/ICBM/surf/rh.orig...
        mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                    i_icbm152_nlin_sym
                    _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903,
                    but face 35822 not in
                    vertex 18903 face list

                    Any suggestions would be appreciated.

                    Thanks,

                    Ajay

                     

                    On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
                    <falk.luesebrink@ovgu.de>
                    wrote:

                    Hi Ajay,

                    I ran into the same error processing hires data a
                    while ago using a nightly
                    build of centos 6 with the hires flag only. Disk
                    space or alike wasn't an
                    issue. I ran mris_topo_fixer instead of
                    mris_fix_topology to get working
                    surfaces.

                    Best,
                    Falk

                    -----Ursprüngliche Nachricht-----
                    Von: freesurfer-bounces@nmr.mgh.harvard.edu
                    [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im
                    Auftrag von Bruce Fischl
                    Gesendet: Sonntag, 29. November 2015 22:48
                    An: Freesurfer support list
                    Betreff: Re: [Freesurfer] Freesurfer 6.0 -
                    Autorecon2 failure
                    (mris_euler_number) using high res (0.5mm
                    isotropic) T1 image

                    Hi Ajay

                    are you sure you didn't run out of disk space? That
                    error is a sanity check
                    on the surfaces that should never occur

                    cheers
                    Bruce

                    On Sun, 29 Nov 2015, Ajay
                    Kurani wrote:

                    > Hello Freesurfer experts,
                    >    I am trying to run Freesurfer 6.0 beta
                    (downloaded 10/15/15
                    > version) with the -hires flag to process an MNI
                    template image which
                    > is 0.5mm isotropic.  Stage 1 ran well and on
                    stage 2 there is an error
                    > during
                    > pocessing:
                    >
                    > Command run:
                    > recon-all -s ICBM -autorecon2 -openmp 8 -3T
                    -hires -expert expert.opts
                    >
                    > I supplied a skull stripped brain which was nu
                    corrected and so I used
                    > the T1.mgz and copied it to brainmask.mgz and
                    nu.mgz in autorecon1
                    > stage.  I then ran autorecon2 and it was working
                    well until I was at
                    > the -fix stage and ran into the following error:
                    >
                    >
                    > Error:
                    > mris_euler_number ./surf/lh.orig
                    > mrisFindNeighbors: ./surf/lh.orig:
                    face[46196].v[0] = 24215, but face
                    > 46196 not in vertex 24215 face list
                    >
                    >
                    >
                    > I am not sure if this is due to the fact that we
                    have a very high
                    > resolution image (template) and if there are any
                    modifications needed
                    > aside from the hires flag.  Are there any
                    suggestions you have?
                    >
                    > Thanks,
                    > Ajay
                    >
                    >

                     





              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.

sure Zeke can get it to you if you tell himn your hardware/software env, but as I said if you have defects that are that big they are unlikelly to be corrected to produce geometrically accurate surfaces.

cheers Bruce On Thu, 3 Dec 2015, Ajay Kurani wrote:

Hi Bruce,   If it isn't too much trouble could you send the program update?  I have another set of images (2009c template) which I can contrast enhance for GM/WM regions so I can try this set of images to process along with the images I sent you.

Thanks, Ajay

On Thursday, December 3, 2015, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ajay

  I have found the problem that messed up the surfaces and fixed it. We can get you an
  updated mris_fix_topology that will not generate corrupted surfaces. However, the
  underlying problem is huge topological defects caused by low gray/white contrast in
  this data. For example in the left hemi, there is on in the insula (e.g. voxels around
  362, 213, 200 and 364, 229, 207 and in the temporal lobe (351, 286, 282, 283, 309,
  258).


  Basically the gray/white contrast isn't high enough for us to accurately segment the wm
  with our default procedures. Control points may help a bit, but you may also need to
  manually edit the wm.mgz to remove the largest defects. The easiest way to do this is
  to visualize them on the lh.inflated.nofix surface with the lh.defect_labels overlaid
  to show you where the defects are, then go into the volume in the wm.mgz and either add
  control points or erase wm to fix things.

  Let us know if you want a new mris_fix_topology. I'm not sure it is worth the trouble
  since while it will now generate topologically correct surfaces for this dataset, they
  will not be geometrically acccurate in the vicinity of the huge (>200,000 vertices!)
  defects.

  cheers
  Bruce


  On Wed, 2 Dec 2015, Ajay Kurani wrote:

        Hi Bruce,

          The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which
        I downloaded from the
        McGills site
        (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  The
        template has a
        range of values from 0-100.  Then I combined the csf/wm/gm masks (derived
        from the 2009c template
        which is 1mm isotropic) and resampled to 0.5 mm to mask the brain. 
        Subsequently I rescaled the
        data to have a range of 0-255 and used this output as my input T1 for
        Freesurfer.  Thank you very
        much for looking into this matter, it is much appreciated!  I will look at
        the file as you
        suggested.

        Sincerely,
        Ajay

        On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Ajay

              can you explain your entire processing stream, including the details
        of the
              acquisition? What sequence/coil/scanner was used? You could fix your
        problem by looking
              at the defects on the inflated.nofix, overlaying
              lh.defect_labels on it to see where they are, then figuring out what
        caused them in the
              volume. However, there is a bug in mris_fix_topology that only comes
        up when it
              encounters a large enough defect (with nvertices>200,000). The code
        tries to avoid
              running it's normal genetic algorithm as it would take days (or
        weeks) to finish, since
              it scales with the square of the number of vertices. I haven't
        figured out what is
              going wrong yet, but hopefully will have a code fix soon.

              cheers
              Bruce


              On Tue, 1 Dec 2015, Ajay Kurani wrote:

                    Hi Bruce,  When looking at my top slices in brain ask I noticed
        that the
                    gray/white matter shows but the darker areas surrounding it are
        not present
                    (this usually goes to the edge of the brain).  Could the large
        defects be a
                    result of having masked this out on the input file?  I
        multiplied the
                    template with the GM/WM/CSF masks they provided to get the
        brain extracted
                    so I only see this missing in the very top few slices of the
        brain.

                    Thanks,
                    Ajay

                    On Tuesday, December 1, 2015, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          Hi Falk

                          I don't think you need to rerun the qsphere. I'm pretty
        sure
                          this is a bug in mris_fix_topology for giant defects, but
                          haven't finished tracking it down yet

                          cheers
                          Bruce


                          On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


                                Hi Ajay,

                                 

                                you should

                                 

                                cp ?h.orig.nofix ?h.orig

                                cp ?h.inflated.nofix ?h.inflated

                                 

                                with ? being l or r depending your hemisphere.
                                After the fixing stage the
                                surfaces got damaged somehow, therefore you have to
                                recreate it them. I’m
                                not entirely sure about the qsphere. Probably you
                                have to run the -qsphere
                                stage again also.

                                 

                                Best,

                                Falk

                                 

                                 

                                Von: Ajay Kurani [mailto:dr.ajay.kurani@gmail.com]
                                Gesendet: Montag, 30. November 2015 21:50
                                An: Falk Lüsebrink
                                Cc: Freesurfer support list; Bruce Fischl
                                Betreff: Re: [Freesurfer] Freesurfer 6.0 -
                                Autorecon2 failure
                                (mris_euler_number) using high res (0.5mm
                                isotropic) T1 image

                                 

                                Hi Falk,

                                   I used the command and got the following error:

                                Command: ris_topo_fixer -mgz -warning -seed 1234
                                ICBM lh
                                mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
                                INFO: assuming .mgz format
                                setting seed for random number genererator to 1234
                                reading
                   
        inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                                lin_sym
                                _09b/ICBM/surf/lh.orig...
                   
        mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                                i_icbm152_nlin_sym
                                _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
                                but face 46196 not in
                                vertex 24215 face list

                                mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
                                INFO: assuming .mgz format
                                setting seed for random number genererator to 1234
                                reading
                   
        inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                                lin_sym
                                _09b/ICBM/surf/rh.orig...
                   
        mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                                i_icbm152_nlin_sym
                                _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903,
                                but face 35822 not in
                                vertex 18903 face list

                                Any suggestions would be appreciated.

                                Thanks,

                                Ajay

                                 

                                On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
                                <falk.luesebrink@ovgu.de>
                                wrote:

                                Hi Ajay,

                                I ran into the same error processing hires data a
                                while ago using a nightly
                                build of centos 6 with the hires flag only. Disk
                                space or alike wasn't an
                                issue. I ran mris_topo_fixer instead of
                                mris_fix_topology to get working
                                surfaces.

                                Best,
                                Falk

                                -----Ursprüngliche Nachricht-----
                                Von: freesurfer-bounces@nmr.mgh.harvard.edu
                                [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im
                                Auftrag von Bruce Fischl
                                Gesendet: Sonntag, 29. November 2015 22:48
                                An: Freesurfer support list
                                Betreff: Re: [Freesurfer] Freesurfer 6.0 -
                                Autorecon2 failure
                                (mris_euler_number) using high res (0.5mm
                                isotropic) T1 image

                                Hi Ajay

                                are you sure you didn't run out of disk space? That
                                error is a sanity check
                                on the surfaces that should never occur

                                cheers
                                Bruce

                                On Sun, 29 Nov 2015, Ajay
                                Kurani wrote:

                                > Hello Freesurfer experts,
                                >    I am trying to run Freesurfer 6.0 beta
                                (downloaded 10/15/15
                                > version) with the -hires flag to process an MNI
                                template image which
                                > is 0.5mm isotropic.  Stage 1 ran well and on
                                stage 2 there is an error
                                > during
                                > pocessing:
                                >
                                > Command run:
                                > recon-all -s ICBM -autorecon2 -openmp 8 -3T
                                -hires -expert expert.opts
                                >
                                > I supplied a skull stripped brain which was nu
                                corrected and so I used
                                > the T1.mgz and copied it to brainmask.mgz and
                                nu.mgz in autorecon1
                                > stage.  I then ran autorecon2 and it was working
                                well until I was at
                                > the -fix stage and ran into the following error:
                                >
                                >
                                > Error:
                                > mris_euler_number ./surf/lh.orig
                                > mrisFindNeighbors: ./surf/lh.orig:
                                face[46196].v[0] = 24215, but face
                                > 46196 not in vertex 24215 face list
                                >
                                >
                                >
                                > I am not sure if this is due to the fact that we
                                have a very high
                                > resolution image (template) and if there are any
                                modifications needed
                                > aside from the hires flag.  Are there any
                                suggestions you have?
                                >
                                > Thanks,
                                > Ajay
                                >
                                >

                                 





                          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.