I apologize, I am new to linux and programming through the terminal. Would this need to be done prior to the recon command?
If my command is: "recon-all -i 00015DCM.dcm -s summer2 -all" with that being the first slice in the series, do I execute dcm2niix in the same line or before? Thanks, Emily ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Harms, Michael [mha...@wustl.edu] Sent: Wednesday, June 07, 2017 11:57 AM To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) This email contains a suspicious URL dcm2niix with the -s flag will allow you to convert a single DICOM that is part of a directory with other DICOMs cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 6/7/17, 10:31 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ad...@fiu.edu> wrote: 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-boun...@nmr.mgh.harvard.edu on behalf of Emily Rogers" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of erog...@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-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. >> >> BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=http-3A__www69[.]zippyshare[.]com_v_BLOCKED MJDVstW0_file.html&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrj wA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=ocZR0DZOeaCCHg4-JY0dFyPk byXnSqvxQR2FSAqmqYA&e= >> 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 >>> BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= >> -- >> 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: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__gate[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_filedrop2&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrjwA&m=g 4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=p-SDsa3-uDTqXPjqOoKITKQHFEBRxv ADzktTFw_0Rcs&e= >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=ftp-3A__surfer[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_transfer_outgoing_flat_greve_&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWj wCJRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=UqaCViRTy6 SfYcCR_BpnT5GLFyAA8wwb__5WEGyAaao&e= >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= >> >> >> 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 >> BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=http-3A__www[.]partners[.]org_compliBLOCKED anceline&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrjwA&m=g4_TV 6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=-BL6o_NzRJ0oLhpXoRtStG4PwDn3aubHtR Jz0KJey5o&e= . 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 >> BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= >> >> > -- > 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: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__gate[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_filedrop2&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrjwA&m=g 4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=p-SDsa3-uDTqXPjqOoKITKQHFEBRxv ADzktTFw_0Rcs&e= > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=ftp-3A__surfer[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_transfer_outgoing_flat_greve_&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWj wCJRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=UqaCViRTy6 SfYcCR_BpnT5GLFyAA8wwb__5WEGyAaao&e= > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= -- 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: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__gate[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_filedrop2&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwCJRFVHJCqLOrjwA&m=g 4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=p-SDsa3-uDTqXPjqOoKITKQHFEBRxv ADzktTFw_0Rcs&e= www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=ftp-3A__surfer[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_transfer_outgoing_flat_greve_&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWj wCJRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=UqaCViRTy6 SfYcCR_BpnT5GLFyAA8wwb__5WEGyAaao&e= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu BLOCKEDurldefense[.]proofpoint[.]com/v2/url?u=https-3A__mail[.]nmr[.]mgh[.]harvard[.]eBLOCKED du_mailman_listinfo_freesurfer&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWjwC JRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=qxTn62UAQIT6 WiILFEaa8IiBASTirJieum__uLBqgU4&e= _______________________________________________ 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. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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
