[Freesurfer] LGI longitudinal data

Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point?    If so, please spe

Re: [Freesurfer] LGI longitudinal data

That command works.  Thanks so much, Martin! Best, Tricia From: Martin Reuter To: Tricia Merkley Cc: Freesurfer list Sent: Thursday, October 3, 2013 9:48 AM Subject: Re: [Freesurfer] LGI longitudinal data Hi Tricia, try recon-all -long subject001

[Freesurfer] LGI question

Hi, Would there need to be any special considerations when calculating lgi with microcephalic brains?  Could TIV ever affect the results and need to be accounted for?  (It doesn't seem like it should, but just wanted to verify.) Thanks, Tricia Me

[Freesurfer] WM bug fix

) Kernel info: Linux 2.6.18-53.1.14.el5 x86_64 cmd line executed:  recon-all -s -segstats -wmparc Thanks so much, Tricia Merkley ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] White Matter Regional Volumes

further? Thanks, Tricia Merkley --- On Tue, 5/27/08, Doug Greve <[EMAIL PROTECTED]> wrote: From: Doug Greve <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] White Matter Regional Volumes To: [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu Date: Tuesday, May 27, 2008, 9:17 AM T

[Freesurfer] Version 4.0.4

We ran several subjects using version 4.0.4 and now need to reinstall freesurfer to finish the processing.  Is there a  linux centos4, 32 bit version available somewhere? Thanks, Tricia Merkley ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Version 4.0.4

.0.5-full.tar.gz from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Nick On Tue, 2008-07-22 at 14:59 -0700, Tricia Merkley wrote: > We ran several subjects using version 4.0.4 and now need to reinstall > freesurfer to finish the processing. Is there a linux centos4

[Freesurfer] Siemens Trio 3T imaging parameters

Hi Freesurfers, Does anyone have a suggestion for an optimal scanner protocol for structural scans using Siemens Trio 3T? Thanks, Tricia Merkley ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Talairach xform problem

Hi Freesurfers, Is there a solution for fixing a bad talairach transform as shown in the attached figures?  Recon-all completed without error (with the -notal-check included, v4.5.0), and the output looks pretty good.  However I'm concerned that the 'IntraCranialVol' value will be off since it

Re: [Freesurfer] Talairach xform problem

Have you seen anything like this before?  Thanks, Tricia --- On Thu, 8/12/10, Bruce Fischl wrote: From: Bruce Fischl Subject: Re: [Freesurfer] Talairach xform problem To: "Tricia Merkley" Cc: freesurfer@nmr.mgh.harvard.edu Date: Thursday, August 12, 2010, 6:34 PM Hi Tricia, when

[Freesurfer] Small voxel size

., as compared to 1mm cubic voxels.  When would it be appropriate to use the '-cm' flag for mri_convert? Thanks, Tricia Merkley ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

Re: [Freesurfer] Small voxel size

e. Thanks, Tricia --- On Wed, 3/9/11, Bruce Fischl wrote: From: Bruce Fischl Subject: Re: [Freesurfer] Small voxel size To: "Tricia Merkley" Cc: "freesurfer@nmr.mgh.harvard.edu" Date: Wednesday, March 9, 2011, 5:01 PM What is the resolution of your other subjects? On M

Re: [Freesurfer] Small voxel size

, Tricia --- On Thu, 3/10/11, Bruce Fischl wrote: From: Bruce Fischl Subject: Re: [Freesurfer] Small voxel size To: "Tricia Merkley" Cc: "freesurfer@nmr.mgh.harvard.edu" Date: Thursday, March 10, 2011, 6:37 AM Hi Tricia, I don't think you can use that subject. It will

Re: [Freesurfer] Cerebellum segmentation, auto vs manual reference?

between analysis methods, whereas cerebellar WM volumes differed (likely due to differing boundary inclusion/exclusion criteria and challenges for image quantification due to the numerous folia of the cerebellum). Hope this helps. Tricia Merkley --- On Fri, 5/13/11, McLean John (NHS Greater

[Freesurfer] Hippocampal subfield segmentation

volumes in 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3.  Is that correct? Thanks, Tricia Merkley ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The