Re: [Freesurfer] different rotation matrix from same DICOM

Probably the AA matlab file is using dicom coordinates which are LPS whereas my software uses RAS. On Thu, 15 Jul 2010, Xu, Jun wrote: Hi, I found out something that I do not understand when I was trying to create rotation matrix from scratch. I have used two methods and hope they

[Freesurfer] question: gray matter segmentation

Hi, I am a new user of FreeSurfer and trying to figure out gray matter segmentation. A volume that I extracted from aparc+aseg.mgz using mri_segstats did not match the volume reported in /stats/ text files (for example, aseg.stats, rh.aparc.stats). Even without specifying a mask in

Re: [Freesurfer] question: gray matter segmentation

The stats files are computed with partial volume correction. doug On Thu, 15 Jul 2010, Yunjo Lee wrote: Hi, I am a new user of FreeSurfer and trying to figure out gray matter segmentation. A volume that I extracted from aparc+aseg.mgz using mri_segstats did not match the volume

Re: [Freesurfer] Pial edits?

Hi Brianna, what kind of acquisition do you have? And in what part of the brain are you having issues? What version are you using? We have a newer skull stripping contributed by Mike Chee and Vitali Zagorodnov in Singapore that you could try - it is better at stripping the dura. Current

[Freesurfer] problem converting .ima files

Hi, I am trying to convert .ima files, and my command seems to work fine for some series: mri_convert -it siemens -ot nii 523-2-4.ima ../srs2.nii but not others: mri_convert -it siemens -ot nii 523-3-132.ima ../srs3.nii These are series collected from the same scan session. The data were

Re: [Freesurfer] problem converting .ima files

wow, I have no clue. You can tar up the data and drop it to me at the file drop. But I just want to warn you that it might take me a while to get to. doug On Thu, 15 Jul 2010, Scott Hayes wrote: Hi, I am trying to convert .ima files, and my command seems to work fine for some series:

Re: [Freesurfer] problem converting .ima files

can you try it on a linux machine and see if you are still having problems? On Thu, 15 Jul 2010, Doug Greve wrote: wow, I have no clue. You can tar up the data and drop it to me at the file drop. But I just want to warn you that it might take me a while to get to. doug On Thu, 15 Jul

[Freesurfer] overlay registration

Hi, I'm trying to use a registration file while overlaying my functional volume on the surface. I'm getting this warning -iMac1-2:~ aarslan$ tksurfer KS02sess1 lh inflated –ovreg $V1/register.dat -overlay $V1/spmT_0001.mgz WARNING: flag –ovreg unrecognized WARNING: flag

[Freesurfer] FDR Calculations

Hello- Does the built-in FDR function in tksurfer and QDEC run the calculations upon the actual values in the .mgh files, or does it take the exponent of those -log10(p) values first? -- Jim Porter, M.A. Graduate Student Clinical Science Psychopathology Research University of Minnesota

Re: [Freesurfer] FDR Calculations

It computes the p-values first. doug On Thu, 15 Jul 2010, James Porter wrote: Hello- Does the built-in FDR function in tksurfer and QDEC run the calculations upon the actual values in the .mgh files, or does it take the exponent of those -log10(p) values first? -- Douglas N. Greve,

[Freesurfer] mri_ca_normalize hanging on a case

Hi there, We're processing some new 3T cases in FreeSurfer, and one case has been hanging just after it begins mri_ca_normalize: #...@# CA Normalize Wed Jul 14 17:16:05 EDT 2010 /home/pnlstaff/freesurfer/subjects/case01264/mri mri_ca_normalize -mask brainmask.mgz nu.mgz

Re: [Freesurfer] mri_ca_normalize hanging on a case

Hi Diandra, can you try running it with the current dev version and see if the problem goes away? Krish can get you a binary. cheers Bruce On Thu, 15 Jul 2010, Diandra Lucia wrote: Hi there, We're processing some new 3T cases in FreeSurfer, and one case has been hanging just after it

Re: [Freesurfer] A region loss in the ?h.aparc.stats

Hi Doug, Maybe I can't give clear information about my problem in the previous post. Please allow me report it again. My question is that I can't find the insula in the averaged ?h.aparc.annot obtained from the command make_average_surface. I check ?h.aparc.annot of each subject and find

Re: [Freesurfer] A region loss in the ?h.aparc.stats

Liang, make_average_surface is not using the latest atlas when creating the .annot files. i've attached a fixed version of make_average_surface which you should copy to your $FREESURFER_HOME/bin directory. n. On Thu, 2010-07-15 at 14:36 -0700, liang wang wrote: Hi Doug, Maybe I can't give

[Freesurfer] Mixing fs 4.3.1 with fs 4.5.0 longitudinally

Hello, I processed a 200 subject dataset cross-sectionally using fs 4.3.1 with the intention of running them longitudinally. I now read that the longitudinal stream in 4.3.1 is biased towards the initial timepoint and the 4.5.0 is the recommended version to do longitudinally. Can I just send my

Re: [Freesurfer] Mixing fs 4.3.1 with fs 4.5.0 longitudinally

Hi Jeff, sorry, but you are probably better off rerunning your cross sectional with 4.5 or whatever verion you use (5.0 is coming out soon). Note that this is probably just compute time as we will keep whatever manual edits you had to make cheers Bruce On Thu, 15 Jul 2010, Jeff Sadino wrote:

[Freesurfer] mri_convert question: converting dicom to mgz

Hello, all. I have not been able to convert dicom files to a mgz file using mri_convert. Could you tell me how to use mri_convert to do that and the example? I typed the following command and run: mri_convert -it dicom -ot mgz 001/ 001.mgz Then I got the following message: mri_convert -it dicom

Re: [Freesurfer] mri_convert question: converting dicom to mgz

Give one slice of the correct dicom series as input On Jul 15, 2010, at 10:09 PM, Kenichiro Tanaka ktan...@j-adni.org wrote: Hello, all. I have not been able to convert dicom files to a mgz file using mri_convert. Could you tell me how to use mri_convert to do that and the example? I typed