Re: [Freesurfer] mris_fix_topology stops with two T1-s
Many thanks Bruce, I will choose the best one in this case. The command line was: recon-all -s B_06 -qcache -measure thickness -all (I already had copied by hand the /mri/orig/001.mgz and 002.mgz) Just in case I repeated the process with the original files, but I had exactly the same results. This was the command line: recon-all -i /home/glerma/glerma/freesurfer/subjects/BERTSO_MRI/BS3_06/58153751 -i /home/glerma/glerma/freesurfer/subjects/BERTSO_MRI/SESION2/06_BERTSOLARI_IEA/54336388 -s B_06c -qcache -measure thickness -all thanks! Gari On 2012-08-10, at 19:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what was your command line (now I sound like Doug)? Including structurals from different days may not work as you may have large differential distortions due to differences in e.g. shimming, gradient nonlinearities, etc... that will preclude an accurate motion correction. Certainly it failed in this case. cheers Bruce On Fri, 10 Aug 2012, Garikoitz Lerma Usabiaga wrote: Thanks for the answer Bruce, it is still running, so I killed the process. When using two individual structural images separately, the recon-all process was OK. When I tried to use both structurals, I can check that the T1.mgz has some strange distortions (please check image attached). When it is ok using two structurals (different days, same subject)? In this is case, is there something we can do to fix it or should be use just one of them? Many thanks, Gari On 2012-08-05, at 23:25, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gari is it still running? The time it takes is square in the convex hull of the largest defect, so that can take a long time. A 45K defect is too big and typically means something is dramatically wrong, like the cerebellum or skull is attached. cheers Bruce On Sun, 5 Aug 2012, Garikoitz Lerma Usabiaga wrote: Hi FS experts, I've run recon-all -i file -s subject -qcache -measure thickness -all to: - 18 subjects, session 1 T1 - same 18 subjects, session 2 T1 and everything went well. Then I copied the subject_id_session/mri/orig/001.mgz-s to subject_id/mri/orig/001.mgz and 002.mgz, and run the same command again: recon-all -s subject_id -qcache -measure thickness -all Half of the subjects are failing when trying to correct the topology. Please find below the outputs of two of the subjects. Should I use the -i and the original files instead of the already created 001.mgz files? What should I check in order to avoid this error or what should I do in order to correct it? thank you very much, Gari * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-956 (nv=167898, nf=337708, ne=506562, g=479) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 127705 ambiguous faces found in tessellation segmenting defects... 125 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 1 -merging segment 9 into 1 -merging segment 21 into 1 -merging segment 24 into 1 -merging segment 26 into 1 -merging segment 29 into 1 -merging segment 44 into 1 -merging segment 56 into 1 -merging segment 2 into 1 -merging segment 65 into 1 -merging segment 67 into 1 -merging segment 71 into 1 -merging segment 4 into 1 -merging segment 12 into 1 -merging segment 34 into 18 -merging segment 30 into 19 -merging segment 38 into 35 -merging segment 61 into 47 -merging segment 107 into 106 -merging segment 115 into 113 105 defects to be corrected 0 vertices coincident reading input surface /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_16/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.9838 (-3.9919) -vertex loglikelihood: -5.7349 (-2.8674) -normal dot loglikelihood: -3.5106 (-3.5106) -quad curv loglikelihood: -6.1770 (-3.0885) Total Loglikelihood : -23.4063 CORRECTING DEFECT 0 (vertices=23, convex hull=21) After retessellation of defect 0, euler #=-32 (96640,274187,177515) : difference with theory (-102) = -70 CORRECTING DEFECT 1 (vertices=44927, convex hull=14482) Topology Correction Parametersretessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0
[Freesurfer] Averaging overlays/labels across subjects
Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the subjects (or fsaverage) using mri_surf2surf, and in the process also converted the format from .w to .mgh (as I understand .w is pretty much legacy). Now, I would just need to compute an average across these overlays. I would greatly appreciate any suggestions which FS tools to use for this. Thank you in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ 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.
Re: [Freesurfer] Averaging overlays/labels across subjects
Hi Tommi, to compute an average, all you need to do is run mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh doug On 8/12/12 7:50 PM, r...@nmr.mgh.harvard.edu wrote: Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the subjects (or fsaverage) using mri_surf2surf, and in the process also converted the format from .w to .mgh (as I understand .w is pretty much legacy). Now, I would just need to compute an average across these overlays. I would greatly appreciate any suggestions which FS tools to use for this. Thank you in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ 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 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] (no subject)
Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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.
Re: [Freesurfer] (no subject)
The values are in the ?h.sulc file doug On 8/12/12 10:12 PM, Hugh Pemberton wrote: Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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 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.
Re: [Freesurfer] (no subject)
What are the units of that measure? Thanks, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Sunday, August 12, 2012 9:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) The values are in the ?h.sulc file doug On 8/12/12 10:12 PM, Hugh Pemberton wrote: Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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 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.
Re: [Freesurfer] (no subject)
They are the integrated dot product of the surface normal and the movement vector during inflation. On Aug 12, 2012, at 10:28 PM, Matt Glasser m...@ma-tea.com wrote: What are the units of that measure? Thanks, Matt. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Sunday, August 12, 2012 9:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) The values are in the ?h.sulc file doug On 8/12/12 10:12 PM, Hugh Pemberton wrote: Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ 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 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.
