Re: [Freesurfer] XL defect in recon-all
Hi Devika these types of huge defects usually mean something dramatic has gone wrong with e.g. the skull stripping. Even if it completes it is unlikely to generate accurate surfaces. Check the ?h.inflated.nofix and ?h.orig.nofix over the wm.mgz and you will likely find the issue quicky cheers Bruce On Fri, 31 Jan 2020, Devika K wrote: External Email - Use Caution Hi, I am running recon-all on Freesurfer version 6. Few of my subject's have XL defect error as shown below. CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0) XL defect detected... This has been running for more than a day. How can I fix this error? Please give me some commands to solve this issue. Looking forward to hearing from you Thanks and Regards Devika K ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] XL defect in recon-all
External Email - Use Caution Hi I found this tutorial helpful https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview I was able to correct a defect of similar size (18k+ vertices) corresponding to a “huge periventricular heterotopia” according to clinical colleague. In particular the paint bucket with the option to fill multiple slices make it quite easier to paint in in the whole thing. Then save the image and run commands as in the tutorial. Cheers, Marmaduke From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Devika K Sent: Friday, January 31, 2020 5:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] XL defect in recon-all External Email - Use Caution Hi, I am running recon-all on Freesurfer version 6. Few of my subject's have XL defect error as shown below. CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0) XL defect detected... This has been running for more than a day. How can I fix this error? Please give me some commands to solve this issue. Looking forward to hearing from you Thanks and Regards Devika K ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] XL defect in recon-all
External Email - Use Caution Hi, I am running recon-all on Freesurfer version 6. Few of my subject's have XL defect error as shown below. CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0) XL defect detected... This has been running for more than a day. How can I fix this error? Please give me some commands to solve this issue. Looking forward to hearing from you Thanks and Regards Devika K ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] XL defect in recon-all
no, sorry On 5/24/2019 10:19 AM, Barletta, Valeria wrote: That would be great. However, I am launching recon-all -all by entering the environment for freesurfer 6 in my terminal (we still have version 5_3 installed in our computers). So there is no way I can copy the files from the 2nd link in the folder $FREESURFER_HOME/bin (I have no access to that folder). Is there another way to apply the command -conf2hires without having version 6 installed? Thank you, Vale From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: Thursday, May 23, 2019 3:46:30 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] XL defect in recon-all You can look at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview But if you are using high res, I would run high res stream I put together for the HCP: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/23/19 2:59 PM, Barletta, Valeria wrote: > > Dear Freesurfers, > > I tried to launch "recon-all -all" for an high-resolution 7T 0.75 > isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, > numbered 54, measuring over 20,000 voxels!! > > > How do I check, and eventually fix, this defect? > > > Thank you, > > Vale > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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
Re: [Freesurfer] XL defect in recon-all
That would be great. However, I am launching recon-all -all by entering the environment for freesurfer 6 in my terminal (we still have version 5_3 installed in our computers). So there is no way I can copy the files from the 2nd link in the folder $FREESURFER_HOME/bin (I have no access to that folder). Is there another way to apply the command -conf2hires without having version 6 installed? Thank you, Vale From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, May 23, 2019 3:46:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XL defect in recon-all You can look at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview But if you are using high res, I would run high res stream I put together for the HCP: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/23/19 2:59 PM, Barletta, Valeria wrote: > > Dear Freesurfers, > > I tried to launch "recon-all -all" for an high-resolution 7T 0.75 > isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, > numbered 54, measuring over 20,000 voxels!! > > > How do I check, and eventually fix, this defect? > > > Thank you, > > Vale > > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] XL defect in recon-all
You can look at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview But if you are using high res, I would run high res stream I put together for the HCP: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/23/19 2:59 PM, Barletta, Valeria wrote: > > Dear Freesurfers, > > I tried to launch "recon-all -all" for an high-resolution 7T 0.75 > isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, > numbered 54, measuring over 20,000 voxels!! > > > How do I check, and eventually fix, this defect? > > > Thank you, > > Vale > > > ___ > 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] XL defect in recon-all
Dear Freesurfers, I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54, measuring over 20,000 voxels!! How do I check, and eventually fix, this defect? Thank you, Vale ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
