Hi Emily Doug is saying that if you give recon-all a single slice in a dicom series in which the rest of the slices are present in the same directory, we will figure out which they are and build the volume from them. You cannot use FreeSurfer on just a single slice - the rest of the data has to be present (but not specified on the command line)
cheers Bruce On Wed, 7 Jun 2017, Emily Rogers wrote: > Do you have any recommendations for programs to convert to a single DICOM > file? It seems that even using a single slice in the series is causing errors > and telling me the file does not exist even when it is in the correct > directory. > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, June 06, 2017 5:48 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] (no subject) > > I did not mean for you to send them to me. You should use one of them > (any one of them) as input to recon-all > > > On 06/06/2017 05:14 PM, Emily Rogers wrote: >> Yes I have the original 160 files, attached. >> >> Thanks for your help, >> Emily >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, June 06, 2017 5:11 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] (no subject) >> >> I don't think we can read that. Do you have access to the orignal dicoms? >> >> >> On 06/06/2017 04:58 PM, Emily Rogers wrote: >>> It was converted to a single dicom from individual slice files using MIPAV >>> image viewer. It is a single subject structural MRI. >>> >>> http://www69.zippyshare.com/v/MJDVstW0/file.html >>> I've uploaded it here >>> >>> Thanks, >>> Emily >>> >>> >>> >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Tuesday, June 06, 2017 4:43 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] (no subject) >>> >>> mri_convert is having a problem reading 1400composite.dcm. It is not >>> even recognizing it as a dicom. Where did it come from and what is in it? >>> >>> >>> On 06/06/2017 04:35 PM, Emily Rogers wrote: >>>> Apologies-- This email contains attachment. Thank you. >>>> >>>> ____________________________________________________ >>>> >>>> Hello, >>>> >>>> I am trying to implement using Freesurfer segmentation in my analysis for >>>> MEG data. I am trying to segment this structural MRI (1400composite.dcm) >>>> and I keep getting errors. I have attached the log file. Any help is >>>> appreciated. >>>> >>>> Thank you, >>>> Emily >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> 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 >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
