[Freesurfer] subcortical gray matter segmentation

when conducting a subcortical gray matter segmentation, the volume of the cerebral cortex is also measured . how this is performed? is it also based upon the probabilistic atlas ? thank you Asaf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] {Disarmed} Re: mgz file is tilted

those are fine. Jay Ives wrote: > Thanks Doug. > > Here are some images from tkmedit. > > J > > - Original Message - > From: "Douglas N Greve" > > To: > > Cc: > > Sent: Wednesday, October 21, 2009 12:43 AM > Subject: Re: [Freesurfer] mgz file is tilted > > > > probably not (though suppl

Re: [Freesurfer] TIV corrected

We don't have software to do it, but the estimated TIV is reported in the stats file, so you can do it yourself (see the Randy Buckner paper on it). Guang Zeng wrote: > Hello, Dr. Greve, > > Is there a method to calculate the TIV corrected volume of ROIs using FS. > > > Thanks a lot! > > Guang >

Re: [Freesurfer] TIV corrected

Hello, Dr. Greve, Is there a method to calculate the TIV corrected volume of ROIs using FS. Thanks a lot! Guang > Date: Tue, 20 Oct 2009 13:04:44 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TIV correc

Re: [Freesurfer] transverse gyrus and intermediate sulcus

Narly, v3.0 uses the aparc.a2005s atlas. to use the a2002s atlas in v3.0, edit the recon-all script and replace instances of '2005' with '2002', which only appear in the cortparc2 stage. i havent tried this, so i dont know if the atlas will work though. Nick On Tue, 2009-10-20 at 18:03 +0100,

Re: [Freesurfer] out of space

How do I increase the size of my vmware disk image? I managed to get enough space on the desktop for the time being (after deleting the duplicate freesurfer folder) but for future reference, it'd be good to know how to increase the space should I need to. Thanks -Original Message- Fr

Re: [Freesurfer] T1 scanning parameters and mean curvature

yes, it's definitely not recommended. On Tue, 20 Oct 2009, Narly A Golestani wrote: > > Hello all, > > I would like to know whether the T1 parameters such as TR, TE, TI, and > flip angle can systematically influence mean curvature values obtained by > recon-all -all. > > I have processed 2 data s

[Freesurfer] T1 scanning parameters and mean curvature

Hello all, I would like to know whether the T1 parameters such as TR, TE, TI, and flip angle can systematically influence mean curvature values obtained by recon-all -all. I have processed 2 data sets with the following T1 parameters, and am noticing that the mean curvature values systematically

Re: [Freesurfer] optseq2 tnullmax

By using tr=2, delta psd = 2 (ie, --pwdwin 0 20 2), and tnullmax=2, you are forcing each null to be exactly 0 or 2 sec, and optseq is having a hard time with such a hard constraint. You can try changing delta psd to 1. doug Kathrin Herbst wrote: > Hi, > I am having a related problem: > I don't

Re: [Freesurfer] Mri_label2vol memory error

I just created a ribbon.mgz (link below). Copy this into fsaverage/mri and see if it works. doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ribbon.mgz Alex Fornito wrote: > Thanks, that did the trick. > The only problem is that I would also like to do the same for fsaverage,

Re: [Freesurfer] TIV corrected

No. They are the volumes in the subject's native space. -MH > > Hi, there, > > Have those volume of ROIs in aseg.stats been TIV corrected? > > > > > Thanks a lot! > > Guang > > _ > Hotmail: Free, trusted and rich email service. > h

Re: [Freesurfer] transverse gyrus and intermediate sulcus

Hello all, Thanks Chistophe for your answers. I have not heard back regading some of the other points. I would like to know: 1) The fs release in which ?h.aparc.a2005s.annot replaced ?h.aparc.a2002s.annot. I assume it was before 2007 (I used version 3.0.5 in 2007). 2a) *** If it is possible

Re: [Freesurfer] TIV corrected

no. douig Guang Zeng wrote: > Hi, there, > > Have those volume of ROIs in aseg.stats been TIV corrected? > > > > > Thanks a lot! > > Guang > > > Hotmail: Free, trusted and rich email service. Get it now. >

Re: [Freesurfer] optseq2 questions

I think this is partially a bug in optseq and partially a problem with your design. You have a total amount of stimulation time = 12*9+13*8+14*8+12*9+13*8+14*8 = 648 sec. Your run lasts 500*2 = 1000 sec, so the total amount of fixation time is 1000-648 = 352 sec. You have 8*4+9*2 = 50 stimuli,

[Freesurfer] TIV corrected

Hi, there, Have those volume of ROIs in aseg.stats been TIV corrected? Thanks a lot! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/

Re: [Freesurfer] Creating FSGD file

I'm skeptical that openoffice is going to work. It has to be a simple text ascii file. Try using emacs or nedit. You don't have to put the fsgd file anywhere special on the file system, you just need to give mris_preproc the path to the file. doug Weisinger, Brian (NIH/OD) [E] wrote: > I am t

Re: [Freesurfer] mgz file is tilted

probably not (though supplying images would have been helpful). When viewing in tkmedit, tkmedit aligns the view port axes along the scanner coordinates, not the image coords. doug Jay Ives wrote: > My nii files look straight in FSLView, but after converting them to > mgz with mri_convert, the

Re: [Freesurfer] optseq2 tnullmax

Hi, I am having a related problem: I don't want 0-events that last longer than a normal trial (2 sec) and lead to the fact that the number of a TR (2sec) in the run is not equal to the number of trials. Setting --tnullmax 2 produces an error: ERROR: could not enforce tNullMax (ntries=10)

Re: [Freesurfer] myaverage

what's the command line? Can you send the log file? What version are you using? Oertel, Viola wrote: > Hello, > > during the creation of my average brain with freesurfer, I got the > following ERROR message. > > getpwdcmd: command not found > > ERROR: format for rh.orig.avg.area.mgh not recogniz

Re: [Freesurfer] mri_motion_correction to average DTI sequences?

the right way to do this is to analyze each set separately to get beta maps, register each set to a common template, resample the beta maps to the template (inclucing proper rotation), then average them together, then recompute the tensor from the betas. Sorry, we don't have anything that will

[Freesurfer] optseq2 questions

Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2

[Freesurfer] Creating FSGD file

I am trying to follow the directions to create a FSGD file put I am having trouble. I used open office to make the file which looks like the one in the example. Is this where I am supposed to create it? Do I create it in as a text file? Do I save it as an .odt file? If all this is correct I have

[Freesurfer] mgz file is tilted

My nii files look straight in FSLView, but after converting them to mgz with mri_convert, they are tilted a bit to one side and slightly forwards when viewed with tkmedit. Have I done something wrong, or omitted a necessary command? Thx ___ Freesurfe

Re: [Freesurfer] Mri_label2vol memory error

Thanks, that did the trick. The only problem is that I would also like to do the same for fsaverage, but in this case mri_aparc2aseg fails because it is looking for ribbon.mgz (see below). Is there a work around for this? Thanks again, Alex mri_aparc2aseg --s fsaverage/ --rip-unknown --annot 1000

Re: [Freesurfer] out of space

are they both full installs? If so, you certainly don't need both. cheers, Bruce On Tue, 20 Oct 2009, Ahmed, F, Me wrote: > Hello, > > I'm trying to get my dicom images into my VMware desktop but I have run out > of space so can't continue to copy files over. I am trying desperately to > make

Re: [Freesurfer] The uncertainty of final stats from repeated runs on the same subject

these look like normal variations of the measures with repeated runs. Certainly 2% test/retest is nothing to worry about. I think that randomness is now off by default, but Nick can confirm. cheers, Bruce On Tue, 20 Oct 2009, leemon albert wrote: > Hi, > > We run the freesurfer stable v4.4.0 o

[Freesurfer] myaverage

Hello, > during the creation of my average brain with freesurfer, I got the following > ERROR message. > getpwdcmd: command not found > ERROR: format for rh.orig.avg.area.mgh not recognized. > ERROR: make_average_surface > > Would you be so kind and help me with the solution for this problem? > Th

[Freesurfer] mri_motion_correction to average DTI sequences?

Hi all, I want to get the average DTI from 2 DTI sequences (obtained from the same subject with the same configuration data). I am using mri_motion_correct to get it but I wonder whether I can apply the original diffusion direction file to this average image or I need to rotate the diffusion direc

[Freesurfer] out of space

Hello, I'm trying to get my dicom images into my VMware desktop but I have run out of space so can't continue to copy files over. I am trying desperately to make space on the desktop and had a question regarding that. I have 2 freesurfer folders; 1 is on my desktop and 1 is located in /usr/loca

[Freesurfer] The uncertainty of final stats from repeated runs on the same subject

Hi, We run the freesurfer stable v4.4.0 on our Linux computer (Ubuntu 9.04). The program finishes without any error. However, we find the stats files (in the /subject/stats) from repeated runs on the same subject vary widely in final outcome. Meanwhile, we notice the item of the stable v4.5.0 rel