Hi, Bruce:
I attached the file with an email and sent it to you an hour ago and received
an automatic reply saying it's pending for approval due to the size of the
email. Is there another way to upload my image or it's getting processed? I
don't want to spam you guys since i already sent it twice and got the same
result.
Thanks!
Cheng Peng
On Wednesday, July 23, 2014 9:39 AM, Cheng Peng <pcdula...@yahoo.com> wrote:
Hi, Bruce,
I attached the nu.mgz file with this email, i'm at home right now and would
upload T1.mgz later if need to. As far as i know individual recon-all runs were
completed without error (two scans on one subject, two hours apart), really
appreciate the help!
Cheng Peng
Maryland Neuroimaging Center
On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Cheng
do the cross-sectional runs look okay? The base? If so, does the first
intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you
can't track it down, upload the subject and we will take a look
cheers
Bruce
On Wed, 23
Jul 2014, Cheng Peng wrote:
> Hi, Freesurfer experts:
>
>
>
> I encountered an error message while i was attempting to run a longitudinal
> study (following the instructions from
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2
> under workflow summary)
>
> egister_mri: find_optimal_transform
> find_optimal_transform: nsamples 2185, passno 0, spacing 8
> GCAhistoScaleImageIntensities: could not find wm peak
> resetting wm mean[0]: 102 --> 107
> resetting gm mean[0]: 64 --> 64
> input volume #1 is the most T1-like
> using real data threshold=0.0
> skull bounding box =
(0, 0, 0) --> (255, 255, 255)
> using (85, 85, 128) as brain centroid...
> mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI
> wm
> WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1
> before smoothing, mri peak at 0
> WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1
> after smoothing, mri peak at 0, scaling input intensities by inf
>
> It appears that the skull strip step has failed as brainmask.mgz is
> completely blank. I tried to look up the error message online but found
> little help there. I would really appreciate it if someone can explain the
> problem or where to look for an explaination. I attached the recon-all error
> log with this email, i would also include nu.mgz but the last email attached
> with that was blocked due to the size of the image.
>
> Thanks!
>
> Best Regards,
>
> Cheng Peng
>
> Maryland Neuroimaging Center
>
>
>
>
>
>
>
>
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