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 <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 > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
