7 Jan
2014
7 Jan
'14
12:19 p.m.
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.