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
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
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-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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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.
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-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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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
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.
http://www69.zippyshare.com/v/MJDVstW0/file.html 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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 greve@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
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.
http://www69.zippyshare.com/v/MJDVstW0/file.html 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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 greve@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
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.
http://www69.zippyshare.com/v/MJDVstW0/file.html 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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 greve@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
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...
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: mharms@wustl.edu
On 6/7/17, 10:31 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of adick@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-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_ 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-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.e 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 >> 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.e 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: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.e 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 >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli 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 >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e 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 > 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.e 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: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.e 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 > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e 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 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.e 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: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.e du_transfer_outgoing_flat_greve_&d=DwICAg&c=lhMMI368wojMYNABHh1gQQ&r=DmdQWj wCJRFVHJCqLOrjwA&m=g4_TV6MfSiXALIDKr3LpvzgYmprDf9Ko0SA7NvVK6v0&s=UqaCViRTy6 SfYcCR_BpnT5GLFyAA8wwb__5WEGyAaao&e=
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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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Harms, Michael [mharms@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: mharms@wustl.edu
On 6/7/17, 10:31 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of adick@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-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. >> >> 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-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 >>> 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 >> greve@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 > greve@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 greve@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=
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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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Harms, Michael [mharms@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: mharms@wustl.edu
On 6/7/17, 10:31 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of adick@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-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.
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-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
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-- 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:
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-- 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:
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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=
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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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Harms, Michael [mharms@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: mharms@wustl.edu
On 6/7/17, 10:31 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of adick@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-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.
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-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
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
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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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Harms, Michael [mharms@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: mharms@wustl.edu
On 6/7/17, 10:31 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anthony Dick" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of adick@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-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.
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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
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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-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.
http://www69.zippyshare.com/v/MJDVstW0/file.html 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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://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 greve@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@nmr.mgh.harvard.edu
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Anthony Dick -
Bruce Fischl -
Douglas N Greve -
Emily Rogers -
Harms, Michael