Re: [Freesurfer] mri_segstats error

Hi Doug, Thanks for the quickly reply. The new version of mri_segstats works fine. I noticed after running it though that all the volumes are slightly different than those reported by previous version. I think it might have something to do with the partial volume correction, as the results are

[Freesurfer] mri_segstats error

Hi, I recently installed the updated mri_segstats (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux). This seems to work fine for recalculating the supratentorial volume. However, it is causing my new recons to fail (see example error below). Any suggestions? Th

[Freesurfer] Freeview NIH Color Map

Hi, Is there any way to prevent the NIH color map in Freeview from displaying values higher than the max as black? I can only seem to find this option for the Heat color map. Thanks for any help, -Tyler The material in this message is private and may contain

Re: [Freesurfer] Tracula: Small Tracts

t'd happen, the mask >>> being >>> only one of them. >>> >>> If you could find the dmri_paths command line in trac-all.log, add >>> "--debug" to it and run it again and send the log file, I can try to >>> track >>> down wha

Re: [Freesurfer] Tracula: Small Tracts

yler - Sometimes this happens if the brain mask (which will come either > from the FS recon or from the DWIs themselves, depending on your settings) is > missing part of that tract (usually one of the end region). Have you checked > your brain masks? > > a.y > > On Wed, 30 N

[Freesurfer] Tracula: Small Tracts

Hi List, I recently ran a group of around 70 subjects through trac-all. I have started to check the results, and have noticed that Tracula will often produce a tract with a really small volume and a posterior distribution that consists of just 0s and 1000s. When this occurs, the end point image

[Freesurfer] Tksurfer Time Course Correlation

Hi, I have a couple of questions about Tksurfer's time course correlation option. First, what type of correlation does it show? Does it use Pearson's r or something else? Second, is there any way to get the same output from the command line? From previous list discussions, it looks like it migh

Re: [Freesurfer] Label Orientation

om the original ROI volume? If so, then > this behavior is as expected. Why not use the first label? > > doug > > Tyler Blazey wrote: >> Hi, >> >> I am having a bit of a problem with the orientation of a label produced by >> mri_cor2label. I have an old analyze RO

[Freesurfer] Label Orientation

Hi, I am having a bit of a problem with the orientation of a label produced by mri_cor2label. I have an old analyze ROI that I have converted to a nifti volume and then registered to T1.mgz. When I load the ROI volume in tkmedit , the registration looks fine. The label and T1.mgz are in the sam

Re: [Freesurfer] Volume for a range of slices

ertainly won't be the same > for the split volumes > > On Wed, 5 Jan 2011, Tyler Blazey wrote: > >> Hi, >> >> Is there any way to return the volume for a specific range of slices using >> the tools offered by FreeSurfer? I tried using mri_convert on ase

[Freesurfer] Volume for a range of slices

there a better way to do all this? Thanks, as always, for any replies. - Tyler Blazey ___ 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

[Freesurfer] Using mri_segstats

Hi, I have two questions about using mri_segstats. First, I notice that on the individual dti tutorial, you don't use the --pvol option to correct for partial voluming. Is there a reason for this? Second, would there be any disadvantage to using mri_segstats with aparc+aseg.mgz to get volume/ t

Re: [Freesurfer] Space of FreeSurfer Stats

Doug, You understood correctly. Thanks for your help! - Tyler > Hi Tyler, I'm not sure what you mean by the stats being in a particular > space. I had understood it to mean the space that volumes would be > measured in. Is that right? If so, then the volumes will be measured in > the space of th

[Freesurfer] Space of FreeSurfer Stats

Hi All, Are the volume stats outputted by FreeSurfer in native space or in FreeSurfer's space? According to some older mailing list questions, they are in native space, but I wanted to make sure that this was still the case. Thanks in advance for any help. - Tyler ___

[Freesurfer] Linux Unix Comparisons

Hi, I recently ran several subjects through both a Linux version of FreeSurfer (4.5, 64bit) and a Mac version (4.5, 64 bit processors), and noticed some differences in the results. I know that you advise against comparing across different versions of FreeSurfer, but I wasn't sure about differen

[Freesurfer] Across Scanner Comparisons

will help reduce the variability seen between the two scanners? Thanks in advance for any help. - Tyler Blazey ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Qdec Error Question

x27;t been able to find any documentation about using these flags. It would be great is someone could either show me where the documentation is, or give me a brief explanation as to how to use these flags. Thanks in advance for any help. - Tyler B