Re: [Freesurfer] mris_volmask

Hi Ipek, do you mean mri_mask? What are you trying to do? And what hardware/software platform are you using? cheers Bruce On Thu, 19 Jul 2007, Ipek Oguz wrote: Hi, Where can I get the mris_volmask tool? I've seen that it was on the ftp server under pub/dist at some point, but it seems to

[Freesurfer] mris_volmask

Hi, Where can I get the mris_volmask tool? I've seen that it was on the ftp server under pub/dist at some point, but it seems to have disappeared. Thanks a lot! -ipek ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

[Freesurfer] recon-all Is-Running

I've just added a new feature to the dev version of recon-all to help you manage your processes. When you launch recon-all, it will create a file called IsRunning.lh+rh in your subject/scripts folder. When recon-all finishes (with or without errors), this file will be deleted. So, the prese

[Freesurfer] gca file format

I got some question about gca file format. What does totaltraining means? GIBBS_NEIGHBORS is more 6 neighboring voxels. What is relationship between them? From 1:6 , which one is left, right etc? thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] opening aseg.stats file

Try this lovely piece of code: grep -v # aseg.stats | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > aseg.xls Lindsay Casmaer wrote: Hello all, I am finally gearing up to look at the stats generated from processing. Though when I open the stats file as a tab/spac

[Freesurfer] one list thing

if you could include the funding source (particularly NIH institutes!) that would be great. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mris_wm_volume

Morgan, I've posted mris_wm_volume for the various platforms at this location: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev Nick On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: > Would it be possible to post binaries of mris_wm_volume again? I believe > this is t

[Freesurfer] mri_glmfit

Hi, Please ignore my previous mail, I did not see that "external" on the y axis means dependent variable (blame it on the early morning blues...) -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

[Freesurfer] clarification

Two more thing: please include the # of subjects that you have analyzed, and any clinically relevant study that uses FreeSurfer can be included (included DTI and fMRI). thanks again, Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_glmfit

Hi, I ran mri_glmfit with a fsgdf looking (in principle) like this: GroupDescriptorFile 1 Title MyTitle Class Group1 plus blue Class Group2 circle green Variables ICV Input subjid1 Group1 1 Input subjid2 Group22 Dependent variable iscortical thickness. When I "lo

[Freesurfer] mris_wm_volume

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] clinically relevant morphometry

Hi All, we've been asked by NCRR to quantify our impact in clinical conditions. If all of you using FreeSurfer to study something relevant to human health (e.g. aging, AD, etc...) could send me a brief email containing: name and PI of the study subject processed to date 1 sentence describing

Re: [Freesurfer] Segmentation

we have some prototypes for this, but nothing ready for distribution On Thu, 19 Jul 2007, Mehul Sampat wrote: Hi Bruce, Thanks for the quick response. Are there plans to add functionality to label sulcal CSF from T2 images? (Or can I do this easily using some existing script ?) My intuition i

Re: [Freesurfer] Segmentation

Hi Bruce, Thanks for the quick response. Are there plans to add functionality to label sulcal CSF from T2 images? (Or can I do this easily using some existing script ?) My intuition is that this would be helpful since as brain tissue atrophy occurs in a given neurological disorder (Multiple Scler

Re: [Freesurfer] Segmentation

Hi Mehul, We explicitly label ventricular CSF, but not sulcal CSF (which you pretty much can't do from only a T1 volume). The ICV would give you an approximation of the sum of it all, so yes I think what you are doing is a reasonable approach. cheers, Bruce On Thu, 19 Jul 2007, Mehul Sampat

Re: [Freesurfer] Segmentation

Hi I am interested in measuring the Brain Parenchymal Fraction (BPF) which is defined as follows: BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF volume) I think I get the White and Gray Matter V

[Freesurfer] opening aseg.stats file

Hello all, I am finally gearing up to look at the stats generated from processing. Though when I open the stats file as a tab/space delimited in excel, it really looks messy. Any other programs that would be good to view the tables with? Thanks. -Lindsay _