We ran the following command, but the clarity improved minimally. Therefore, is there another command that you would recommend.

Thanks,

Gaurang

On 6/9/16, 5:30 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:

That tells you there is one "series" in that folder. The series here means a volume, though there are many dicom files. dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm is just one in the series. To use this, you can run

recon-all -s yoursubject -all -i dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm

or

mri_convert dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm output.nii.gz

On 06/09/2016 05:11 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:

...

Hello All,

We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we can perform morphometric analysis using FreeSurfer. What is the optimal way to convert the DICOM files so we can use them with FreeSurfer tools? Specifically, what command line do you recommend for dcmunpack?

When running the command: dcmunpack ­src dicomdir we get the following output: Found 1 unique series: 6 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm Not sure how to interpret this.

Thanks.

Gaurang Limachia

---

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.