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
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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/
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