[Freesurfer] Freesurfer output question
Hi, I have some questions (sent to me by someone else, actually) about freesurfer output from make_cortex_table.csh. 1. Do integrated_rectified_mean_curvature integrated_rectified_Gaussian_curvature refer to the shape/arc of the surface of the cortex either before or after inflation? Or are they descriptors of the distribution of the individual thickness measures... as might indicate if the measures were normally distributed (within an area) or skewed to the left or right? 2. Does the num_of_vertices represent the number of measures of thicknesses made for that region? 3. Would be possible to examine the distribution of thickness measures to identify focal regions of skewing... as might occur if there were micro-foci of atrophy within some areas? For example, values for the thicknesses corresponding to the 10th, 25th, 50th, 75th, and 90th percentile values within an area? Or even a median thickness, in addition to the mean? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mgz format
nothing unless you specify -conform. On Mon, 26 Sep 2005, Fornito, Alexander wrote: Hi, Just wandering if someone could tell me what converting to mgh or mgz actually does to the image. COR changed it to 256x256x256, 1mm3, what happens with mgz/mgh? Thanks, Alex ___ 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] Freesurfer output question
1. Of whatever surface you specify (white by default I think). 2. Yes. 3. Easy enough to do in matlab I guess. Bruce On Mon, 26 Sep 2005, Michele Perry wrote: Hi, I have some questions (sent to me by someone else, actually) about freesurfer output from make_cortex_table.csh. 1. Do integrated_rectified_mean_curvature integrated_rectified_Gaussian_curvature refer to the shape/arc of the surface of the cortex either before or after inflation? Or are they descriptors of the distribution of the individual thickness measures... as might indicate if the measures were normally distributed (within an area) or skewed to the left or right? 2. Does the num_of_vertices represent the number of measures of thicknesses made for that region? 3. Would be possible to examine the distribution of thickness measures to identify focal regions of skewing... as might occur if there were micro-foci of atrophy within some areas? For example, values for the thicknesses corresponding to the 10th, 25th, 50th, 75th, and 90th percentile values within an area? Or even a median thickness, in addition to the mean? ___ 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] Scuba/recon-all
I see the following statement printed several times through the recon-all processing and when I try to manipulate images in scuba. Is this something I can safely ignore? INFO: Volume /tmp/mritotal_5799/nu_8_dxyz.mnc cannot be found. Thanks, Satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject error?
Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error?
I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: if person = brian; exit 0 Brian From: Doug Greve [EMAIL PROTECTED] Date: Mon, 26 Sep 2005 16:40:48 -0400 To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] anatomical stats
HI, I'm finishing a study I completed using an older version of freesurfer (20040218), and have noticed that I get different values for surface area and grey matter volume when using mris_anatomical_stats for my labels depending on whether I use the mris_anatomical_stats that it is part of this older distribution, or the one packaged as part of the newer dev release (20050905). I noticed on a previous posting that Doug Greve identified an error with respect to how surface area was calculated (I've included it below) and was wandering if this is the reason for the discrepancy. Should I believe the figures calculated using the newer version, or will this also be associated with errors, since the surfaces were generated using the older version? Thanks, Alex I have just fixed a bug in FreeSurfer that involves computing the area of some surface structures. For those of you who care, this was a bug that emerged after converting our surface meshes from quadralaterals to triangles. This change was made a few years ago. This change should have little effect on the reconstruction. It will have an effect on programs that report the area of subsections of cortex (but not total cortical area). At least three such programs that are affected are: mris_compute_overlap, mris_label_area, and mri_surfcluster. The bug causes the reported area to appear to be 1.5 times what it really is. For example, in mri_surfcluster, a cluster threshold of 300 mm^2 would actually be a threshold of 200 mm^2. For those in the NMR center, these three programs have been updated. For those outside, you can get these programs from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve New versions of freesurfer will, of course, have the update. Sorry for any inconvenience. doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
