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
