Hi Cheng
if you go to our wiki there are instructions for uploading big datasets using either ftp or our filedrop
cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote:
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 pcdulaney@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 fischl@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
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.