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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