Hello Emily,
The easiest free way (that I know of) is using Osirix (http://www.osirix-viewer.com/). In that program, there are a number of export functions. You may want to view in that and export to DICOM. You can then use dicom2nii (http://people.cas.sc.edu/rorden/mricron/dcm2nii.html) to convert to a single .nii file for input into Freesurfer. You may be able to skip the Osirix step with what you have.
Anthony
On 6/7/17, 11:26 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Rogers" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of erogers@wakehealth.edu> 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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. >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www69.zippyshare.com_v_M... >> I've uploaded it here >> >> Thanks, >> Emily >> >> >> >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed... >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed... > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...