Re: [Freesurfer] Problematic dilated ventricles

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Victor Kovac

2 Jan 2014 2 Jan '14

12:18 p.m.

Dear Bruce,

A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1.

I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces.

Could you please advise?

Thank you. Victor

On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz

then run:

recon-all -make all -s MPS1036-1

you should be all set

Bruce

On Mon, 9 Dec 2013, Victor Kovac wrote:

I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you

...

for looking into MPS2002-3 -- it is quite the brain. And somehow, with all those morphological abnormalities, this subject has an IQ of 130. Very strange. Thanks, Victor

On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: which one? I'm still messing with MPS2002-3 in my spare time On Mon, 9 Dec 2013, Victor Kovac wrote:

        Hi Bruce,
        Is there a way for you to send the subject(s) you
        analyzed to me? I know
        it's too big for email, but could you possibly
        upload it to GoogleDrive?

        Thanks!
        Victor


        On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              p.s. the other thing I did was run the graph
        cut skull
              stripping, which removed a bunch of extraneous
        stuff
              On Wed, 4 Dec 2013, kovac081@umn.edu wrote:

              Hey!

              Victor Kovac (kovac081@umn.edu) has uploaded
        some files
              for you at the Martinos Center FileDrop:

        -> MPS2002-3.zip (292.12 MiB)
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&

f=55xjt9pflsi> -> MPS2017-1.zip (264.15 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& f=ak4v31bzu4p

        Also, they left this message for you:
        Hi Bruce,

        Here are the two subjects with ventriculomegaly that
        are causing
        the worst issues. The worst segmentation in
        MPS2002-3 is in the
        superior frontal (slices 150-180) and parietal
        (slices 50-95)
        cortical areas; this may be due to the numerous
        dilated
        Virchow-Robin spaces in his brain, which is another
        neuropathological feature of this disease.

        Thanks!
        Victor

        Please be aware, your upload will expire on December
        31st. If
        you'd like to download these files, feel free to use
        the link
        below:

        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

        Cheers,
        The NMR Team





        The information in this e-mail is intended only for
        the person to whom
        it is
        addressed. If you believe this e-mail was sent to
        you in error and the
        e-mail
        contains patient information, please contact the
        Partners Compliance
        HelpLine at
        http://www.partners.org/complianceline . If the
        e-mail was sent to you
        in error
        but does not contain patient information, please
        contact the sender
        and properly
        dispose of the e-mail.

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Bruce Fischl

2 Jan 2 Jan

1:12 p.m.

New subject: Problematic dilated ventricles

Hi Victor

you can look in the recon-all -help and run the stages that are after mri_ca_label. Not sure why -make all didn't work, perhaps Zeke and/or Nick can comment? Bruce

On Thu, 2 Jan 2014, Victor Kovac wrote:

...

Dear Bruce,

I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces.

Could you please advise?

Thank you. Victor

On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz

  then run:

  recon-all -make all -s MPS1036-1

  you should be all set

  Bruce


  On Mon, 9 Dec 2013, Victor Kovac wrote:

        I was hoping to MPS1036-1. I only got
        aseg.auto_noCCseg.new.mgz. Thank you
        for looking into MPS2002-3 -- it is quite the brain.
        And somehow, with all
        those morphological abnormalities, this subject has
        an IQ of 130. Very
        strange.
        Thanks,
        Victor


        On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              which one? I'm still messing with MPS2002-3 in
        my spare time
              On Mon, 9 Dec 2013, Victor Kovac wrote:

                    Hi Bruce,
                    Is there a way for you to send the
        subject(s) you
                    analyzed to me? I know
                    it's too big for email, but could you
        possibly
                    upload it to GoogleDrive?

                    Thanks!
                    Victor


                    On Wed, Dec 4, 2013 at 3:40 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          p.s. the other thing I did was run
        the graph
                    cut skull
                          stripping, which removed a bunch
        of extraneous
                    stuff
                          On Wed, 4 Dec 2013,
        kovac081@umn.edu wrote:

                          Hey!

                          Victor Kovac (kovac081@umn.edu)
        has uploaded
                    some files
                          for you at the Martinos Center
        FileDrop:

                    -> MPS2002-3.zip (292.12 MiB)
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi>
                    -> MPS2017-1.zip (264.15 MiB)
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p>

                    Also, they left this message for you:
                    Hi Bruce,

                    Here are the two subjects with
        ventriculomegaly that
                    are causing
                    the worst issues. The worst segmentation
        in
                    MPS2002-3 is in the
                    superior frontal (slices 150-180) and
        parietal
                    (slices 50-95)
                    cortical areas; this may be due to the
        numerous
                    dilated
                    Virchow-Robin spaces in his brain, which
        is another
                    neuropathological feature of this
        disease.

                    Thanks!
                    Victor

                    Please be aware, your upload will expire
        on December
                    31st. If
                    you'd like to download these files, feel
        free to use
                    the link
                    below:

                   
        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                    Cheers,
                    The NMR Team





                    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.

Victor Kovac

7 Jan 7 Jan

12:04 p.m.

New subject: Problematic dilated ventricles

Hi Bruce,

I ran recon-all -autorecon2-cp -autorecon3 -s MPS1036-1 but, again, this did not affect the pial or wm surfaces. I have attached the recon-all.log in case that would be helpful in diagnosing the issue.

Any advise would be greatly appreciated.

Thanks! Victor

On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

Hi Victor

you can look in the recon-all -help and run the stages that are after mri_ca_label. Not sure why -make all didn't work, perhaps Zeke and/or Nick can comment? Bruce

On Thu, 2 Jan 2014, Victor Kovac wrote:

Dear Bruce,

...

I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces.

Could you please advise?

Thank you. Victor

On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz

  then run:

  recon-all -make all -s MPS1036-1

  you should be all set

  Bruce


  On Mon, 9 Dec 2013, Victor Kovac wrote:

        I was hoping to MPS1036-1. I only got
        aseg.auto_noCCseg.new.mgz. Thank you
        for looking into MPS2002-3 -- it is quite the brain.
        And somehow, with all
        those morphological abnormalities, this subject has
        an IQ of 130. Very
        strange.
        Thanks,
        Victor


        On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              which one? I'm still messing with MPS2002-3 in
        my spare time
              On Mon, 9 Dec 2013, Victor Kovac wrote:

                    Hi Bruce,
                    Is there a way for you to send the
        subject(s) you
                    analyzed to me? I know
                    it's too big for email, but could you
        possibly
                    upload it to GoogleDrive?

                    Thanks!
                    Victor


                    On Wed, Dec 4, 2013 at 3:40 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          p.s. the other thing I did was run
        the graph
                    cut skull
                          stripping, which removed a bunch
        of extraneous
                    stuff
                          On Wed, 4 Dec 2013,
        kovac081@umn.edu wrote:

                          Hey!

                          Victor Kovac (kovac081@umn.edu)
        has uploaded
                    some files
                          for you at the Martinos Center
        FileDrop:

                    -> MPS2002-3.zip (292.12 MiB)

        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&

f=55xjt9pflsi> -> MPS2017-1.zip (264.15 MiB)

        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&

f=ak4v31bzu4p>

                    Also, they left this message for you:
                    Hi Bruce,

                    Here are the two subjects with
        ventriculomegaly that
                    are causing
                    the worst issues. The worst segmentation
        in
                    MPS2002-3 is in the
                    superior frontal (slices 150-180) and
        parietal
                    (slices 50-95)
                    cortical areas; this may be due to the
        numerous
                    dilated
                    Virchow-Robin spaces in his brain, which
        is another
                    neuropathological feature of this
        disease.

                    Thanks!
                    Victor

                    Please be aware, your upload will expire
        on December
                    31st. If
                    you'd like to download these files, feel
        free to use
                    the link
                    below:


        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                    Cheers,
                    The NMR Team





                    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.

Bruce Fischl

12:19 p.m.

New subject: Problematic dilated ventricles

Hi Victor

for each subject I think you want to run:

set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz

then run recon-all from normalization2 forward (check the recon-all -help for these steps)

cheers Bruce

On Tue, 7 Jan 2014, Victor Kovac wrote:

...

Hi Bruce,

Any advise would be greatly appreciated.

Thanks! Victor

On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Victor

  you can look in the recon-all -help and run the stages that are
  after mri_ca_label. Not sure why -make all didn't work, perhaps
  Zeke and/or Nick can comment?
  Bruce


  On Thu, 2 Jan 2014, Victor Kovac wrote:

        Dear Bruce,

        A few weeks ago you made code mods to
        mri_em_register and got recon-all to
        process a subject of mine, MPS1036-1. You sent me
        the new
        aseg.auto_noCCseg.mgz and told me to run recon-all
        -make all -s MPS1036-1.

        I did this but I get the message
        make: Nothing to be done for 'all'
        and when I visualize the segmentation with tkmedit,
        there appears to be no
        change to the pial or wm surfaces.

        Could you please advise?

        Thank you.
        Victor


        On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              if you rename aseg.auto_noCCseg.new.mgz to be
              aseg.auto_noCCseg.mgz

              then run:

              recon-all -make all -s MPS1036-1

              you should be all set

              Bruce


              On Mon, 9 Dec 2013, Victor Kovac wrote:

                    I was hoping to MPS1036-1. I only got
                    aseg.auto_noCCseg.new.mgz. Thank you
                    for looking into MPS2002-3 -- it is
        quite the brain.
                    And somehow, with all
                    those morphological abnormalities, this
        subject has
                    an IQ of 130. Very
                    strange.
                    Thanks,
                    Victor


                    On Mon, Dec 9, 2013 at 2:03 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          which one? I'm still messing with
        MPS2002-3 in
                    my spare time
                          On Mon, 9 Dec 2013, Victor Kovac
        wrote:

                                Hi Bruce,
                                Is there a way for you to
        send the
                    subject(s) you
                                analyzed to me? I know
                                it's too big for email, but
        could you
                    possibly
                                upload it to GoogleDrive?

                                Thanks!
                                Victor


                                On Wed, Dec 4, 2013 at 3:40
        PM, Bruce
                    Fischl
                                <fischl@nmr.mgh.harvard.edu>
                                wrote:
                                      p.s. the other thing I
        did was run
                    the graph
                                cut skull
                                      stripping, which
        removed a bunch
                    of extraneous
                                stuff
                                      On Wed, 4 Dec 2013,
                    kovac081@umn.edu wrote:

                                      Hey!

                                      Victor Kovac
        (kovac081@umn.edu)
                    has uploaded
                                some files
                                      for you at the
        Martinos Center
                    FileDrop:

                                -> MPS2002-3.zip (292.12
        MiB)
                               
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi>
                                -> MPS2017-1.zip (264.15
        MiB)
                               
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p>

                                Also, they left this message
        for you:
                                Hi Bruce,

                                Here are the two subjects
        with
                    ventriculomegaly that
                                are causing
                                the worst issues. The worst
        segmentation
                    in
                                MPS2002-3 is in the
                                superior frontal (slices
        150-180) and
                    parietal
                                (slices 50-95)
                                cortical areas; this may be
        due to the
                    numerous
                                dilated
                                Virchow-Robin spaces in his
        brain, which
                    is another
                                neuropathological feature of
        this
                    disease.

                                Thanks!
                                Victor

                                Please be aware, your upload
        will expire
                    on December
                                31st. If
                                you'd like to download these
        files, feel
                    free to use
                                the link
                                below:

                               
                   
        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                                Cheers,
                                The NMR Team





                                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.

Victor Kovac

27 Feb 27 Feb

5:59 p.m.

New subject: Problematic dilated ventricles

Dear Bruce,

Have you had any time to try to analyze our subject MPS2002-3? I believe you mentioned you would give it a shot in your free time a couple of months ago.

Also, you were kind enough to analyze a subject for me, MPS1036-1, and sent me aseg.auto_noCCseg.new.mgz. I replaced the original file and removed thee "new" within the title, and then, to re-create the pial and wm surfaces, I ran:

set mdir=$SUBJECTS_DIR/MPS1036-1/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta MPS1036-1 cp aseg.auto.mgz aseg.mgz

and then: recon-all -autorecon2-cp -autorecon3, which I believe starts the recon-all pipeline at normalization2, as you suggested. However, this has yielded no effect that I can see when I visualize the subject with

tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

Any advice would be greatly appreciated! Attached is the recon-all.log for this subject. Let me know if I should cc the group.

Thank you. Victor

On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

Hi Victor

for each subject I think you want to run:

set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz

then run recon-all from normalization2 forward (check the recon-all -help for these steps)

cheers Bruce

On Tue, 7 Jan 2014, Victor Kovac wrote:

Hi Bruce,

...

Any advise would be greatly appreciated.

Thanks! Victor

On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

...

wrote: Hi Victor

  you can look in the recon-all -help and run the stages that are
  after mri_ca_label. Not sure why -make all didn't work, perhaps
  Zeke and/or Nick can comment?
  Bruce


  On Thu, 2 Jan 2014, Victor Kovac wrote:

        Dear Bruce,

        A few weeks ago you made code mods to
        mri_em_register and got recon-all to
        process a subject of mine, MPS1036-1. You sent me
        the new
        aseg.auto_noCCseg.mgz and told me to run recon-all
        -make all -s MPS1036-1.

        I did this but I get the message
        make: Nothing to be done for 'all'
        and when I visualize the segmentation with tkmedit,
        there appears to be no
        change to the pial or wm surfaces.

        Could you please advise?

        Thank you.
        Victor


        On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              if you rename aseg.auto_noCCseg.new.mgz to be
              aseg.auto_noCCseg.mgz

              then run:

              recon-all -make all -s MPS1036-1

              you should be all set

              Bruce


              On Mon, 9 Dec 2013, Victor Kovac wrote:

                    I was hoping to MPS1036-1. I only got
                    aseg.auto_noCCseg.new.mgz. Thank you
                    for looking into MPS2002-3 -- it is
        quite the brain.
                    And somehow, with all
                    those morphological abnormalities, this
        subject has
                    an IQ of 130. Very
                    strange.
                    Thanks,
                    Victor


                    On Mon, Dec 9, 2013 at 2:03 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          which one? I'm still messing with
        MPS2002-3 in
                    my spare time
                          On Mon, 9 Dec 2013, Victor Kovac
        wrote:

                                Hi Bruce,
                                Is there a way for you to
        send the
                    subject(s) you
                                analyzed to me? I know
                                it's too big for email, but
        could you
                    possibly
                                upload it to GoogleDrive?

                                Thanks!
                                Victor


                                On Wed, Dec 4, 2013 at 3:40
        PM, Bruce
                    Fischl
                                <fischl@nmr.mgh.harvard.edu>
                                wrote:
                                      p.s. the other thing I
        did was run
                    the graph
                                cut skull
                                      stripping, which
        removed a bunch
                    of extraneous
                                stuff
                                      On Wed, 4 Dec 2013,
                    kovac081@umn.edu wrote:

                                      Hey!

                                      Victor Kovac
        (kovac081@umn.edu)
                    has uploaded
                                some files
                                      for you at the
        Martinos Center
                    FileDrop:

                                -> MPS2002-3.zip (292.12
        MiB)


        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&

f=55xjt9pflsi> -> MPS2017-1.zip (264.15 MiB)

        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&

f=ak4v31bzu4p>

                                Also, they left this message
        for you:
                                Hi Bruce,

                                Here are the two subjects
        with
                    ventriculomegaly that
                                are causing
                                the worst issues. The worst
        segmentation
                    in
                                MPS2002-3 is in the
                                superior frontal (slices
        150-180) and
                    parietal
                                (slices 50-95)
                                cortical areas; this may be
        due to the
                    numerous
                                dilated
                                Virchow-Robin spaces in his
        brain, which
                    is another
                                neuropathological feature of
        this
                    disease.

                                Thanks!
                                Victor

                                Please be aware, your upload
        will expire
                    on December
                                31st. If
                                you'd like to download these
        files, feel
                    free to use
                                the link
                                below:



        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                                Cheers,
                                The NMR Team





                                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.

Bruce Fischl

2 Mar 2 Mar

10:07 a.m.

New subject: Problematic dilated ventricles

Hi Victor

hmmm, I'm not sure why that didn't work. Perhaps someone else can comment? Doug or Nick: if the aseg.mgz is recreated and you start with -autorecon2-cp shouldn't it propagate the effects of the new aseg forward?

cheers Bruce

On Thu, 27 Feb 2014, Victor Kovac wrote:

...

Dear Bruce, Have you had any time to try to analyze our subject MPS2002-3? I believe you mentioned you would give it a shot in your free time a couple of months ago.

set mdir=$SUBJECTS_DIR/MPS1036-1/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta MPS1036-1 cp aseg.auto.mgz aseg.mgz

tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

Any advice would be greatly appreciated! Attached is the recon-all.log for this subject. Let me know if I should cc the group.

Thank you. Victor

On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Victor

  for each subject I think you want to run:


  set mdir=$SUBJECTS_DIR/$subject/mri
  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \
  -lta $mdir/transforms/cc_up.lta  $subject
  cp aseg.auto.mgz aseg.mgz


  then run recon-all from normalization2 forward (check the
  recon-all -help for these steps)

  cheers
  Bruce

  On Tue, 7 Jan 2014, Victor Kovac wrote:

        Hi Bruce,

        I ran recon-all -autorecon2-cp -autorecon3 -s
        MPS1036-1 but, again, this did
        not affect the pial or wm surfaces. I have attached
        the recon-all.log in
        case that would be helpful in diagnosing the issue.

        Any advise would be greatly appreciated.

        Thanks!
        Victor


        On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Victor

              you can look in the recon-all -help and run
        the stages that are
              after mri_ca_label. Not sure why -make all
        didn't work, perhaps
              Zeke and/or Nick can comment?
              Bruce


              On Thu, 2 Jan 2014, Victor Kovac wrote:

                    Dear Bruce,

                    A few weeks ago you made code mods to
                    mri_em_register and got recon-all to
                    process a subject of mine, MPS1036-1.
        You sent me
                    the new
                    aseg.auto_noCCseg.mgz and told me to run
        recon-all
                    -make all -s MPS1036-1.

                    I did this but I get the message
                    make: Nothing to be done for 'all'
                    and when I visualize the segmentation
        with tkmedit,
                    there appears to be no
                    change to the pial or wm surfaces.

                    Could you please advise?

                    Thank you.
                    Victor


                    On Mon, Dec 9, 2013 at 2:11 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          if you rename
        aseg.auto_noCCseg.new.mgz to be
                          aseg.auto_noCCseg.mgz

                          then run:

                          recon-all -make all -s MPS1036-1

                          you should be all set

                          Bruce


                          On Mon, 9 Dec 2013, Victor Kovac
        wrote:

                                I was hoping to MPS1036-1. I
        only got
                                aseg.auto_noCCseg.new.mgz.
        Thank you
                                for looking into MPS2002-3
        -- it is
                    quite the brain.
                                And somehow, with all
                                those morphological
        abnormalities, this
                    subject has
                                an IQ of 130. Very
                                strange.
                                Thanks,
                                Victor


                                On Mon, Dec 9, 2013 at 2:03
        PM, Bruce
                    Fischl
                                <fischl@nmr.mgh.harvard.edu>
                                wrote:
                                      which one? I'm still
        messing with
                    MPS2002-3 in
                                my spare time
                                      On Mon, 9 Dec 2013,
        Victor Kovac
                    wrote:

                                            Hi Bruce,
                                            Is there a way
        for you to
                    send the
                                subject(s) you
                                            analyzed to me?
        I know
                                            it's too big for
        email, but
                    could you
                                possibly
                                            upload it to
        GoogleDrive?

                                            Thanks!
                                            Victor


                                            On Wed, Dec 4,
        2013 at 3:40
                    PM, Bruce
                                Fischl
                                           
        <fischl@nmr.mgh.harvard.edu>
                                            wrote:
                                                  p.s. the
        other thing I
                    did was run
                                the graph
                                            cut skull
                                                  stripping,
        which
                    removed a bunch
                                of extraneous
                                            stuff
                                                  On Wed, 4
        Dec 2013,
                                kovac081@umn.edu wrote:

                                                  Hey!

                                                  Victor
        Kovac
                    (kovac081@umn.edu)
                                has uploaded
                                            some files
                                                  for you at
        the
                    Martinos Center
                                FileDrop:

                                            -> MPS2002-3.zip
        (292.12
                    MiB)
                                           
                               
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi>
                                            -> MPS2017-1.zip
        (264.15
                    MiB)
                                           
                               
                   
        <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p>

                                            Also, they left
        this message
                    for you:
                                            Hi Bruce,

                                            Here are the two
        subjects
                    with
                                ventriculomegaly that
                                            are causing
                                            the worst
        issues. The worst
                    segmentation
                                in
                                            MPS2002-3 is in
        the
                                            superior frontal
        (slices
                    150-180) and
                                parietal
                                            (slices 50-95)
                                            cortical areas;
        this may be
                    due to the
                                numerous
                                            dilated
                                            Virchow-Robin
        spaces in his
                    brain, which
                                is another
                                           
        neuropathological feature of
                    this
                                disease.

                                            Thanks!
                                            Victor

                                            Please be aware,
        your upload
                    will expire
                                on December
                                            31st. If
                                            you'd like to
        download these
                    files, feel
                                free to use
                                            the link
                                            below:

                                           
                               
                   
        http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                                            Cheers,
                                            The NMR Team





                                            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

Douglas N Greve

3 Mar 3 Mar

11:53 a.m.

New subject: Problematic dilated ventricles

I think that it should. To be safe, I would "cp aseg.auto.mgz aseg.mgz" otherwise aseg.mgz will not change (any differences will be interpreted as manual changes) doug

On 03/02/2014 10:07 AM, Bruce Fischl wrote:

...

Hi Victor

cheers Bruce

On Thu, 27 Feb 2014, Victor Kovac wrote:

...

Dear Bruce, Have you had any time to try to analyze our subject MPS2002-3? I believe you mentioned you would give it a shot in your free time a couple of months ago.

set mdir=$SUBJECTS_DIR/MPS1036-1/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta MPS1036-1 cp aseg.auto.mgz aseg.mgz

tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation wmparc.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

Any advice would be greatly appreciated! Attached is the recon-all.log for this subject. Let me know if I should cc the group.

Thank you. Victor

On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Victor

  for each subject I think you want to run:


  set mdir=$SUBJECTS_DIR/$subject/mri
  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \
  -lta $mdir/transforms/cc_up.lta  $subject
  cp aseg.auto.mgz aseg.mgz


  then run recon-all from normalization2 forward (check the
  recon-all -help for these steps)

  cheers
  Bruce

  On Tue, 7 Jan 2014, Victor Kovac wrote:

        Hi Bruce,

        I ran recon-all -autorecon2-cp -autorecon3 -s
        MPS1036-1 but, again, this did
        not affect the pial or wm surfaces. I have attached
        the recon-all.log in
        case that would be helpful in diagnosing the issue.

        Any advise would be greatly appreciated.

        Thanks!
        Victor


        On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Victor

              you can look in the recon-all -help and run
        the stages that are
              after mri_ca_label. Not sure why -make all
        didn't work, perhaps
              Zeke and/or Nick can comment?
              Bruce


              On Thu, 2 Jan 2014, Victor Kovac wrote:

                    Dear Bruce,

                    A few weeks ago you made code mods to
                    mri_em_register and got recon-all to
                    process a subject of mine, MPS1036-1.
        You sent me
                    the new
                    aseg.auto_noCCseg.mgz and told me to run
        recon-all
                    -make all -s MPS1036-1.

                    I did this but I get the message
                    make: Nothing to be done for 'all'
                    and when I visualize the segmentation
        with tkmedit,
                    there appears to be no
                    change to the pial or wm surfaces.

                    Could you please advise?

                    Thank you.
                    Victor


                    On Mon, Dec 9, 2013 at 2:11 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          if you rename
        aseg.auto_noCCseg.new.mgz to be
                          aseg.auto_noCCseg.mgz

                          then run:

                          recon-all -make all -s MPS1036-1

                          you should be all set

                          Bruce


                          On Mon, 9 Dec 2013, Victor Kovac
        wrote:

                                I was hoping to MPS1036-1. I
        only got
                                aseg.auto_noCCseg.new.mgz.
        Thank you
                                for looking into MPS2002-3
        -- it is
                    quite the brain.
                                And somehow, with all
                                those morphological
        abnormalities, this
                    subject has
                                an IQ of 130. Very
                                strange.
                                Thanks,
                                Victor


                                On Mon, Dec 9, 2013 at 2:03
        PM, Bruce
                    Fischl

fischl@nmr.mgh.harvard.edu wrote: which one? I'm still messing with MPS2002-3 in my spare time On Mon, 9 Dec 2013, Victor Kovac wrote:

                                            Hi Bruce,
                                            Is there a way
        for you to
                    send the
                                subject(s) you
                                            analyzed to me?
        I know
                                            it's too big for
        email, but
                    could you
                                possibly
                                            upload it to
        GoogleDrive?

                                            Thanks!
                                            Victor


                                            On Wed, Dec 4,
        2013 at 3:40
                    PM, Bruce
                                Fischl

        <fischl@nmr.mgh.harvard.edu>
                                            wrote:
                                                  p.s. the
        other thing I
                    did was run
                                the graph
                                            cut skull
                                                  stripping,
        which
                    removed a bunch
                                of extraneous
                                            stuff
                                                  On Wed, 4
        Dec 2013,
                                kovac081@umn.edu wrote:

                                                  Hey!

                                                  Victor
        Kovac
                    (kovac081@umn.edu)
                                has uploaded
                                            some files
                                                  for you at
        the
                    Martinos Center
                                FileDrop:

                                            -> MPS2002-3.zip
        (292.12
                    MiB)

http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi -> MPS2017-1.zip (264.15 MiB)

http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p

                                            Also, they left
        this message
                    for you:
                                            Hi Bruce,

                                            Here are the two
        subjects
                    with
                                ventriculomegaly that
                                            are causing
                                            the worst
        issues. The worst
                    segmentation
                                in
                                            MPS2002-3 is in
        the
                                            superior frontal
        (slices
                    150-180) and
                                parietal
                                            (slices 50-95)
                                            cortical areas;
        this may be
                    due to the
                                numerous
                                            dilated
                                            Virchow-Robin
        spaces in his
                    brain, which
                                is another

        neuropathological feature of
                    this
                                disease.

                                            Thanks!
                                            Victor

                                            Please be aware,
        your upload
                    will expire
                                on December
                                            31st. If
                                            you'd like to
        download these
                    files, feel
                                free to use
                                            the link
                                            below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep

                                            Cheers,
                                            The NMR Team





                                            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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

4474

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freesurfer@nmr.mgh.harvard.edu

6 comments

3 participants

tags (0)

participants (3)

Bruce Fischl
Douglas N Greve
Victor Kovac