[Freesurfer] Spikes in the inflated surface

Hi everybody. I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions. I have uploaded some images of the surfaces and segmentations of a su

Re: [Freesurfer] Spikes in the inflated surface

Hi Nikolas the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate

Re: [Freesurfer] Spikes in the inflated surface

You can also run the defect-seg program to help locate the places where the automatic topology fixer fixed defects. Run it with --help to get more info. doug Bruce Fischl wrote: > Hi Nikolas > > the spiked by themselves aren't a problem, it's only if the surface isn't > accurately following th

Re: [Freesurfer] loading data to matlab?

There are a couple of things you can do. To get info on the coordinate systems, look at the power points slides we have on the wiki (search for coordinates). The other thing you can do is to sample your functional data onto the surface and then load that into matlab. Then each anatomical vertex

Re: [Freesurfer] mri_convert problem

There is a tag in this file that our DICOM reader does not recognize: 280092 DCM Unrecognized VR code (??) in readVRLength Unfortunately, we're using a 3rd party dicom reader that is quite brittle, and I don't know a way around it. Can you convert to nifti using MRIcro and then use mri_convert

Re: [Freesurfer] Spikes in the inflated surface

Thanks for the fast reply. I have uploaded the entire subject directory and would appreciate if you could take a look. /Nikolas On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl wrote: > Hi Nikolas > > the spiked by themselves aren't a problem, it's only if the surface isn't > accurately following th

Re: [Freesurfer] Spikes in the inflated surface

what did you call it? On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote: > Thanks for the fast reply. I have uploaded the entire subject directory and > would appreciate if you could take a look. > > /Nikolas > > On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl > wrote: > >> Hi Nikolas >> >> the spiked

Re: [Freesurfer] Spikes in the inflated surface

subj1dir.tar.gz in the outermost directory. On Tue, Feb 1, 2011 at 5:28 PM, Bruce Fischl wrote: > what did you call it? > > On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote: > > Thanks for the fast reply. I have uploaded the entire subject d

[Freesurfer] How to cite DOSS / DODS?

Dear all, does anyone know one or two good method papers to cite when describing the difference of DOSS and DODS? I have already screened Pubmed and Co. but did not really find anything convincing. Any help greatly appreciated! Best wishes, Christian Scheel ___

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

Hi Allison, Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow. Thanks, Cheryl On 1/31/11 7:05 PM, "Allison Stevens" wrote: > Hi

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

I'm not actually sure. What are the files that appeared there? On Tue, 1 Feb 2011, Cheryl McCreary wrote: > Hi Allison, > > Is there a way into incorporate these files into the brainmask without > having to redo the edits? I processed a number of subjects this way, using > 'save main volume as'

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

and what wiki page were you following? (some of our wiki pages are no longer used but still exist on the site) On Tue, 2011-02-01 at 15:59 -0500, Allison Stevens wrote: > I'm not actually sure. What are the files that appeared there? > > On Tue, 1 Feb 2011, Cheryl McCreary wrote: > > > Hi Alli

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

More questions regarding aseg.stats ... Are these results corrected for partial voluming? Are the total GM and WM volumes calculated by summing the segment volumes or using surfaces? Is the cerebellum included in the GM and WM volumes reported in the header of the aseg.stats file? Is ICV reporte

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

For instructions I used the link FS Tutorial/SkullStripFix on http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction The files that appeared in the subject mri directory were COR-info and COR-001, COR-002 ... COR-256. I assumed that these refer to the number of segments in the 3D MRI

Re: [Freesurfer] How to cite DOSS / DODS?

It really is just a matter of justifying and explaining your chosen statistical model. If you believe that two groups have the same regression slope for a parameter (but possibly different offsets/intercepts), then you would use a "DOSS" model -- this is akin to a model in SPSS/SAS in which you m

Re: [Freesurfer] mri_convert problem

Thanks Doug, The answer is yes, I can convert to NIfTY with using MRIcro (DCM2nii) and then use mri_convert to convert to mgz but, how can I be sure that this will not change the handedness???' Bests, Gabriel > Date: Tue, 1 Feb 2011 10:59:56 -0500 > From: gr...@nmr.mgh.harvard.edu > To

Re: [Freesurfer] How to cite DOSS / DODS?

Thank you Michael for your explanations, that is exactly the way I understood DODS and DOSS. I am planning to present DOSS and DODS results in comparison and wanted to explain both models in a similar manner that you have done it here. But as these DOSS and DODS terms are kind of unique to Free

Re: [Freesurfer] How to cite DOSS / DODS?

Hi Christian, yes, these are unique! I came up with them in about 30 seconds when I wrote mri_glmfit about 10 years ago. If I had known they were going to last this long, I would have spent more time coming up with a good name for them! doug Christian Scheel wrote: > Thank you Michael for you

Re: [Freesurfer] mri_convert problem

If MRIcro gets the orientation right, then that will be stored in the nifti file and be inherited by the mgz. doug Gabriel Go.Es. wrote: > Thanks Doug, > > The answer is yes, I can convert to NIfTY with using MRIcro (DCM2nii) > and then use mri_convert to convert to mgz but, how can I be sure t

Re: [Freesurfer] How to cite DOSS / DODS?

Hi Doug, OK, I see. Honestly, I think the names could be much worse! Really not bad for 30 seconds... ;-) But as I understand there is no paper of you naming DOSS and DODS that I could cite, correct? I will try to find a different solution then. Thanks for your infos! Best wishes, Christian Sc

Re: [Freesurfer] How to cite DOSS / DODS?

right, there is no paper. As Michael points out, these are fairly standard stats models. doug Christian Scheel wrote: > Hi Doug, > > OK, I see. Honestly, I think the names could be much worse! Really not > bad for 30 seconds... ;-) > But as I understand there is no paper of you naming DOSS and

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

what are the files? Is it COR*? If so, you could mri_convert them to the brainmask. From the mri dir do: mri_convert . brainmask.mgz but save the old brainmask first of course. cheers Bruce On Tue, 1 Feb 2011, Cheryl McCreary wrote: > Hi Allison, > > Is there a way into incorporate these file