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





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