Re: [Freesurfer] sulcal depth/cortical folding

HI Doug, I tried the mris_anatomical_stats and may well be doing it wrong but got this as the result: hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a ABM/surf/lh.sulc -b ABM lh computing statistics for each annotation in ABM/surf/lh.sulc. reading volume /home/hughp/freesurfer/subj

Re: [Freesurfer] aparc2aseg

Hi Megan you are correct - you shouldn't need to edit those voxels if the surface is correct. cheers Bruce On Tue, 14 Aug 2012, Herting, Megan wrote: Hello, I am new to FreeSurfer and had a quick question about the calculation of cortical volumes using the aparc2aseg. In the aseg images, "c

Re: [Freesurfer] aparc2aseg

Hi Megan, you do not need to worry about the voxels in the aseg where dura is labeled as cortex as long as the pial surface does not extend into the dura. doug On 08/14/2012 05:44 PM, Herting, Megan wrote: > Hello, > > I am new to FreeSurfer and had a quick question about the calculation > of

[Freesurfer] aparc2aseg

Hello, I am new to FreeSurfer and had a quick question about the calculation of cortical volumes using the aparc2aseg. In the aseg images, "cortical volume" is sometimes assigned to extra dura at the superior midline of the brain. My understanding is that this dura will not impact my final gray

Re: [Freesurfer] T-value intensity overlayed onto 2009 Destrieux Parcellations

Try touching ?h.orig.nofix, ie, touch rh.orig.nofix lh.orig.nofix then re-running with -make all doug On 08/14/2012 05:08 PM, David Vazquez wrote: > > Hi, > > We would like to visually display some t-values onto a brain using the > 2009 Destrieux freesurfer parcellations. We have our own t-val

[Freesurfer] T-value intensity overlayed onto 2009 Destrieux Parcellations

Hi, We would like to visually display some t-values onto a brain using the 2009 Destrieux freesurfer parcellations. We have our own t-values for each parcellation. We would like to display a color-coded spm map for all parcellations, and would like each parcellation to represent the same intensi

Re: [Freesurfer] recon-all error

After you ran -autorecon2-wm you skipped a couple of the autorecon3 steps (-pial, -surfvolume, -segstats). On Tue, 14 Aug 2012, Douglas N Greve wrote: > It means that your subject is out of synch. This usually happens when > you've edited a subject and re-run recon-all, but the re-run did not ge

Re: [Freesurfer] recon-all error

It means that your subject is out of synch. This usually happens when you've edited a subject and re-run recon-all, but the re-run did not get far enough either because it failed for some reason or you did not run it all the way through to the end. You can run recon-all -s subject -make all an

Re: [Freesurfer] Edits to aparc+aseg.mgz

For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stat

Re: [Freesurfer] Edits to aparc+aseg.mgz

Doug, Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a

[Freesurfer] Problems with ICV calculations in fs5.1.0?

Dear fs Experts, In the most recent Freesurfer Digest (vol102, Issue13), a question regarding ICV calculations in version 5.1.0 was raised (message 4). Can you please expand on the problems with this? I am using version 5.1.0 and the estimate of ICV is of interest. Thanks, Cheryl McCreary

Re: [Freesurfer] Talairach coordinates

There's not an automated way to do this. You can run tkmedit fsaverage orig.mgz -aparc+aseg then put in the talairach coordinate in the control panel and see where the cursor goes. doug On 08/14/2012 11:53 AM, peka Savayan wrote: > Hi FreeSurfer, > > My fMRI time series come from Brain Voyager an

[Freesurfer] Talairach coordinates

Hi FreeSurfer, My fMRI time series come from Brain Voyager and x,y,z-coordinates are in Talairach space. Thank you. Peka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

Re: [Freesurfer] sulcal depth/cortical folding

Hi Hugh, you can run mris_anatomical_stats passing it the sulc file as input. This will give you averages within aparc. I'm not sure what you mean by "measuring cortical folding". What measure would you accept? There's the sulcal depth and then there's curvature (?h.curv). There are two types o

Re: [Freesurfer] Talairach coordinates

What are you using the to the fMRI analysis? What coordinate system do you have the fMRI xyz coordinates in? Eg, RAS, col-row-slice, etc doug On 08/14/2012 10:12 AM, peka Savayan wrote: > Hi FreeSurfer, > I would like to know the x,y,z- coordinates of all atlas ROIs in > Talairach space. > I hav

[Freesurfer] analyzeto4dfp to get a talsrcimg.4dfp.ifh file

Hi,I have run talairach_avi with the template I have made, and an input file that is manually skull stripped. I ran: talairach_avi --i .nii.gz --atlas --xfm talairach_avitest.xfmI had put the .nii.gz file in the average folder in freesurfer for this to work. I also have .4dfp.hdr , .4dfp

Re: [Freesurfer] Edits to aparc+aseg.mgz

Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: > Doug, > > I looked at the surface files by using the command

Re: [Freesurfer] Creating and using an atlas from scratch‏

Hi,I have run talairach_avi with the template I have made, and an input file that is manually skull stripped. I ran: talairach_avi --i .nii.gz --atlas --xfm talairach_avitest.xfmI had put the .nii.gz file in the average folder in freesurfer for this to work. I also have .4dfp.hdr , .4dfp

Re: [Freesurfer] Edits to aparc+aseg.mgz

Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear

[Freesurfer] Talairach coordinates

Hi FreeSurfer, I would like to know the x,y,z- coordinates of all atlas ROIs in Talairach space. I have the x, y z coordinates of the voxel  time series of an fMRI task. I would like to know which of these voxels belong to a particular ROI. Can you give me advice, please? Thank you. Peka ___

Re: [Freesurfer] mri_cnr

Hi Paul, nothing fancy. Just a Gaussian noise model and the CNR is the average of the gray/white and gray/csf cnr: gray_white_cnr = SQR(gray_mean - white_mean) / (gray_var+white_var) ; gray_csf_cnr = SQR(gray_mean - csf_mean) / (gray_var+csf_var) ; cheers Bruce On Tue, 14 Aug 2012, prasser

Re: [Freesurfer] Problems with ICV

I think nick has a patch he can distribute before we release 5.2 Bruce On Aug 14, 2012, at 3:13 AM, "Wisse, L.E.M." wrote: > Hi Bruce, > Thanks for the quick response. > I also used FS v5.1.0. Do I need to use another version or is there another > way to fix this? > > Laura > > ___

Re: [Freesurfer] Problems with ICV

Hi Bruce, Thanks for the quick response. I also used FS v5.1.0. Do I need to use another version or is there another way to fix this? Laura From: natalie.h...@gmail.com [natalie.h...@gmail.com] on behalf of Natalie Han [zh...@stanford.edu] Sent: 13 Augus

Re: [Freesurfer] mri_cnr

Hi, I was wondering if there is any documentation on mri_cnr, particularly how the noise is calculated. Thank you, Paul > > thanks Dr. B.that helped a lot > > - Original Message - > From: "Bruce Fischl" > To: "Kushal Kapse"