Thanks again Douglas! Your time and help is greatly appreciated!
Best, Silas
________________________________
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: Thursday, August 25, 2016 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] I receive an error when running recon-all with T1 and
lesions from FLAIR
MRIwrite() writes out the image as a float, whereas FS insists that it
be UCHAR or INT. To get this, run
mri_convert aseg.mgz -odt int --no_scale 1 aseg.mgz
View aseg.mgz to make sure it looks right, then rerun recon-all
-autorecon2-cp -autorecon3
On 08/24/2016 05:51 PM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> I'm doing a structural analysis with 50 MS patients and 50 healthy
> controls (T1, T2 and FLAIR). The MS patients have multiple lesions
> mainly in white matter. My co-worker did manual editing (bullet
> points) in the FLAIR images, and i would like to use these edits when
> running recon-all in order to avoid further manual editing.
>
>
> _Steps in analysis:_
>
>
> 1) First steps of recon-all:
>
> recon-all -autorecon1 -autorecon2
>
>
> 2) Reslicing the FLAIR images:
>
> The aseg.auto.mgz (256x256x256) didn't have the same size as the
> FLAIR (resliced to 1mm, co-registered in MNI-space and with manually
> drawn binary lesion masks (218x182x182)). I overcome this problem by
> reslicing the FLAIR images using aseg.auto.nii as the image defining
> space. This was done in SPM8, and prior to this the aseg.auto.mgz was
> converted to a .nii using mri_convert.
>
>
> 3) Insert lesions from the resliced FLAIR images to aseg.mgz:
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so
> make a backup
>
>
> 4) The last steps of recon-all:
>
> recon- all -autorecon2-cp -autorecon3
>
> When running the following command i get this error:
>
> /depot64/freesurfer/freesurfer.5.3.0/bin/recon-all -s 01MS
> -autorecon2-cp -autorecon3 subjid 01MS
>
> ............
>
>
> '#@# Intensity Normalization2 Mon Aug DATE
> /.../subjects_FLAIR/01MS/mri
>
> mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> using segmentation for initial intensity normalization
> using MR volume brainmask.mgz to mask input volume...
> reading from norm.mgz...
> Reading aseg aseg.mgz
> normalizing image...
> processing with aseg
> removing outliers in the aseg WM...
> 5361 control points removed
> Building bias image
> mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR or MRI_INT
> building Voronoi diagram...
> Numerical argument out of domain
> Linux big28 3.13.0-66-generic #108-Ubuntu SMP Wed Oct 7 15:20:27 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 01MS exited with ERRORS at Mon Aug 8 15:31:32 CEST 2016
>
> *The lesions looks alright (as if they are in the right place). Do you
> have any suggestions what to do if they are not? And what could be the
> problem if they are placed correctly?*
>
> *What is the advantage of starting by running autorecon-1 and 2 and
> then inserting the lesions from the FLAIR?*
>
>
> Thanks a lot for all your help!
>
>
> Best, Silas
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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