[Freesurfer] q about disc space

Hello. How much space is required for running one recon-all? If I needed to work on several people's brains, say 4-5, how much memory am I likely to need? Thanks! -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

Re: [Freesurfer] mri_convert: dicom to mgh

1. the dicom standard is LPS (left-post-sup), we use RAS, so the xy components are negated. 2. Very slowly. Below are the rules that I used to compute the geometry use by mri_convert, including how to go from mosaics. doug Critical Parameters for a given series, and the rules Doug Greve (gr...@

[Freesurfer] Recon-All Talairach error

Hello, I am working on unpacking a subject scanned in Bay 8 on Thursday, 3/11/2010. I entered recon-all -autorecon-all -s FB0011090A and after unpacking for approximately 45 minutes, it reported: Wed Mar 17 12:52:07 EDT 2010 talairach_avi done # #...

Re: [Freesurfer] Recon-All Talairach error

Dave, Yep, if it looks okay, just run with -notal-check. Allison -- On Wed, 17 Mar 2010, Dave Brohawn wrote: > Hello, > > I am working on unpacking a subject scanned in Bay 8 on Thursday, 3/11/2010. > > I entered recon-all -autorecon-all -s FB0011090A > > and after unpacking for approximately 4

[Freesurfer] Averaging cortical thickness maps

Hi, I have a question regarding how to average cortical thickness maps. I have a dataset with 10 MR brain images and I've run recon-all on each of them. So I've got thickness maps ?h.thickness for each subject. I wonder whether freesurfer provides a tool that can average the cortical thickness ma

[Freesurfer] Replicating qdec analysis with more than 2 continuous variables

Hello Freesurfer folks, I hope this question is simple to answer: Is there any way to do a surface-based group analysis, a-la qdec, without the limitation of 2 continuous variables? My goal is to analyze a thickness relationship with continuous variable X, which I have so far analyzed controll

Re: [Freesurfer] Replicating qdec analysis with more than 2 continuous variables

you have a couple options: 1) assuming you are using 64b linux, you can download a new version of qdec which supports selecting 'nuisance' variables in the design. you can get it here: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/ copy qdec.bin to your $FREESURF

Re: [Freesurfer] Replicating qdec analysis with more than 2 continuous variables

Nick, Thank you so much. I'd love to try option 1, but I need centos 32bit if possible. This is great news thank you so much for the quick reply! Victor From: Nick Schmansky [ni...@nmr.mgh.harvard.edu] Sent: Wednesday, March 17, 2010 1:18 PM To: Laluz

Re: [Freesurfer] recon-all failture

Try running this: recon-all -skullstrip -no-wsgcaatlas -s If that goes through without error, you can finish processing your data by running: recon-all -autorecon2 -autorecon3 -s Allison -- On Wed, 17 Mar 2010, Gabriel Go.Es. wrote: I was trying to run a recon-all and I recibe an error

Re: [Freesurfer] Averaging cortical thickness maps

Hi Xiaojing, mris_average_curvature will do it, and I think Doug has some other tools that will as well. cheers, Bruce On Wed, 17 Mar 2010, Xiaojing Long wrote: > Hi, > > I have a question regarding how to average cortical thickness maps. > > I have a dataset with 10 MR brain images and I've ru

[Freesurfer] segmentation using freesurfer

Hi All, Is it possible to get only csf via using freesurfer to do segmentation? Best, Xiaoying ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is in

Re: [Freesurfer] segmentation using freesurfer

not sulcal CSF (which you really can't get from just a T1), but you can measure ventricular CSF On Wed, 17 Mar 2010, Xiaoying Tang wrote: > Hi All, > > Is it possible to get only csf via using freesurfer to do segmentation? > > Best, > Xiaoying > ___ >

Re: [Freesurfer] segmentation using freesurfer

Thanks a lot. Actually, I also didn't find the separated csf after segmentation. I am not sure whether I am on the right way. I just want to ensure. Best, Xiaoying - Original Message - From: Bruce Fischl Date: Wednesday, March 17, 2010 8:48 pm Subject: Re: [Freesurfer] segmentation usi

Re: [Freesurfer] segmentation using freesurfer

there are separate labels in the aseg.mgz for things like lateral and third ventricles. You should be able to find it in there, or in the aseg.stats file for summary measures like ventricular volume. cheers, Bruce On Wed, 17 Mar 2010, Xiaoying Tang wrote: > Thanks a lot. Actually, I also did

Re: [Freesurfer] q about disc space

Hi Janani, I think the current recons take between one third and one half gig/subject. cheers, Bruce On Wed, 17 Mar 2010, Janani Dhinakaran wrote: > Hello. > How much space is required for running one recon-all? If I needed to work on > several people's brains, say 4-5, how much memory am I lik