Hi Emily
if the dicoms are there you wanted to put the FS output in .../freesurfer/subjects/summerMRI_recon you would do recon-all -s summerMRi_recon \ -sd .../freesurfer/subjects \ -i .../freesurfer/subjects/summerMRI/00015DCM \ -all no need to run dcm2nii at all I don't think, unless for some reason we can read your dicoms cheers Bruce On Wed, 7 Jun 2017, Emily Rogers wrote: > Okay, so if all of my DICOM files are in the folder summerMRi (with > 00015DCM being the first of the series) my command would look like.. > > $export SUBJECTS_DIR=.../freesurfer/subjects/summerMRI/00015DCM > $ dcm2niix 00015DCM.dcm -s sum2 -all > > or is the directory the folder? > > Thank you so much for the help. > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, June 07, 2017 1:47 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] (no subject) > > that should work if th erest of the slices are in your current directory. > Mike is suggestion you could instead run dcm2niix first, then give the > resulting .nii file to recon-all with -i instead of the dicom file. Note > that this will *not* work with a single slice - you need the entire series > > cheers > Bruce > > > On Wed, 7 Jun 2017, Emily Rogers wrote: > >> 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 >> >> >> > _______________________________________________ > 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
