Hi Douglas,
It seems that the lesions are in the right place. Do you have other suggestions? I just want to make sure; when you wrote: ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0); -> you meant: ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol ~= 0); 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: Wednesday, August 10, 2016 11:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR did you look at the aseg.mgz to see if the lesions were in the right place? On 08/10/2016 03:28 AM, Silas wrote: > > Thank you very much for your help Douglas! > > > I had a few problems running these commands. > > 1) recon-all -autorecon1 -autorecon2 -> no problems > > > 2) The matlab script > > 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 image and 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. > > This seemed to solve the problem! > > > 3) 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 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting' BugReporting - Free Surfer Wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> surfer.nmr.mgh.harvard.edu top. Bug Reporting. Submitting a request for help . When submitting a request for help with your problems please be aware that the developers will try and repeat your ... > > *How can i solve this problem?* > > > Best, Silas > > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > *Sent:* Tuesday, August 2, 2016 4:06 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR > > That recon-all command will not work as the FLAIR input should be a > simple FLAIR image. The FLAIR will only correct the pial surface and > will have nothing to do with lesion segmentation. Emily Lindermer has > a tool that can take a T1 and FLAIR and produce a lesion map; but > given that you already have manual segmentations, maybe that is not so > helpful. One thing you can do is to edit the aseg.mgz to insert your > lesions. First run recon-all with -autorecon1 -autorecon2 instead of > -all. Then, in matlab, > > > 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 > > > Then run recon-all with -autorecon2-cp -autorecon3 > > > > On 8/1/16 7:35 AM, 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. >> >> >> The data i'm working with is already resliced to 1 mm and >> co-registered in MNI-space. >> >> 1) Can i use this data or would it be preferable to use the original >> T1's? >> >> >> My thought was to run the following command: >> >> recon-all -subject subjectname -i /path/to/input_volume -FLAIR >> /path/to/FLAIR_volume_with_edits-FLAIRpial -all >> 2) Does this look correct? Is there anything i should be aware of? -> >> update: Does this command only improve the pial surface? How can i >> also improve the white mater segmentation (white) using FLAIR >> corrections? >> >> 3) Does it make a difference running recon-all -all with the FLAIR >> image - compared to running recon-all -autorecon3 with the FLAIR >> after running recon-all -all with only the T1? >> >> 4) I've also thought about using the lesion segmentation toolbox for >> SPM and completely avoid manual editing - is this preferable to using >> the FLAIR with manual editing? >> >> 5) How is the general strength of analysing corpus callosum >> structurally in MS patients using FreeSurfer? >> >> >> Best, Silas >> >> >> >> _______________________________________________ >> 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://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 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.
