[Freesurfer] mni_paths

Dear Nick and colleagues, after solving the first problem with nu_correct (fix_mni_paths ... the way you suggested, thanks) we face the fact that the mni paths have to be fixed again after every 2nd, 3rd subject if we try to preprocess a number of subjects data. We run freesurfer with a CentOS

RE: [Freesurfer] problem with mris_anatomical_stats

that s works! Cheers! At 01:51 18/08/2006, Nick Schmansky wrote: Abdel, I don't think there is a matlab alternative to mris_anatomical_stats. However, there is a suspicious line of code in mris_anatomical_stats that I have fixed, and I'm wondering if you can give a new binary a try. It is fo

RE: [Freesurfer] problem with mris_anatomical_stats

Abdel, Thanks for testing this. The bug fix will appear in an upcoming release, but you can continue using the mris_anatomical_stats that you have now. For those interested in the perils of testing a multi-platform app, the buggy line of code was: sprintf(fname,"%s.mgz",fname) Here the sourc

[Freesurfer] thickness maps

Dear all, When I load ?h.thick files as an overlay in tksurfer I notice that values at the thickest points are all listed as having a thickness of exactly 5. Is this a max cutoff in the actual values, or is it just that tksurfer won't display larger values? Is there a better way to visualize th

Re: [Freesurfer] thickness maps

Hi Sasha, the thickness values aren't allowed to be more than 5. Usually there aren't many places where this happens. Do you see a lot of them? Bruce On Fri, 18 Aug 2006, Sasha Wolosin wrote: Dear all, When I load ?h.thick files as an overlay in tksurfer I notice that values at the thicke

Re: [Freesurfer] thickness maps

p.s. you can run mris_thickness -max to recompute the thickness maps with whatever threshold you want, but I don't think the true thickness is ever that much except in pathological cases like dysplasias. cheers, Bruce On Fri, 18 Aug 2006, Bruce Fischl wrote: Hi Sasha, the thickness v

[Freesurfer] Converting .dcm to COR files

Hi Freesurfer help, I am trying to convert my .dcm files to COR format. I use: mri_convert -ot cor 003DCM 003 I get the following error: mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/cont

RE: [Freesurfer] Converting .dcm to COR files

Hi Camilo, You need to give it the path and filename for the first dicom in the series, I think 003DCM is the directory, so you'll need to include the file name for one of the dicoms. Also, you should consider converting to a .mgz file - as that is the input for most everything that Freesurfer is

Re: [Freesurfer] Converting .dcm to COR files

Does the output directory exist and do you have permission to it? btw, why are you using cor? We're trying to get people to stop :). doug [EMAIL PROTECTED] wrote: Hi Freesurfer help, I am trying to convert my .dcm files to COR format. I use: mri_convert -ot cor 003DCM 003 I get the foll

Re: [Freesurfer] Converting .dcm to COR files

do you mean 003.DCM? What is the name of the input volume? Is it dicom? On Fri, 18 Aug 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer help, I am trying to convert my .dcm files to COR format. I use: mri_convert -ot cor 003DCM 003 I get the following error: mri_convert -ot cor 003DCM 003 read

Re: [Freesurfer] Intel Mac

Four months. Time to check in. Any developments on this front? See you in four months at Christmas. Hopefully Santa has a Mac Pro in his sleigh for Bruce. :-) Ray On Apr 23, 2006, at 10:52 PM, Ray Fix wrote: Hello, Any plans for a Mac OS X Tiger Intel release? ___