Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Would adjusting watershed parameters change pial surface?
by Jake Freimer 02 Aug '06

02 Aug '06

I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake

2 1

aseg.stats
by Doug Greve 01 Aug '06

01 Aug '06

I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy. The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities). The values in the table (ie, volumes and intensities) should be exactly the same. This change only applies to dev (not to stable) and should be live on Tue. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

5 13

tkmedit problem
by Anthony Steven Dick 01 Aug '06

01 Aug '06

Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 ....and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: -------- freesurfer-Darwin-tiger-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR /Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR /Applications/freesurfer/mni/bin MINC_LIB_DIR /Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB /Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony

2 2

need a list of segmented subcorical regions and their intensity values...
by Shahabuddin Ansari 31 Jul '06

31 Jul '06

Hello, I have seen a list of 40 freesurfer-segmented subcortical objects with their respective intensity values somewhere in the documentation, but not able to locate it now. Could somebody help me please. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

mri_volcluster and neuroanatomical labels
by Paymon Hosseini 31 Jul '06

31 Jul '06

Hello, I was wondering if there is a Freesurfer command for getting neuroanatomical labels for the output clusters of mri_volcluster. thank you very much for your help, paymon

3 3

slice time correction?
by cameo＠nmr.mgh.harvard.edu 31 Jul '06

31 Jul '06

Hi all, I was wondering if fs-fast implements slice time correction at any point during processing? if so does it default to correction for either interleaved or linear acquisition and can this be modified? Thanks, Cameron

2 1

Help getting outer bits of brain
by Jake Freimer 31 Jul '06

31 Jul '06

I ran through autorecon1 and 2 for two subjects using the dicom images. One came out ok, but one is still missing some brain (as seen in the attached screen shots). I was wondering if there was a way to change the settings autorecon uses, because our scanner makes the inside so much brighter, or a way to batch convert rather than edit control points on all our subjects. Thanks -- -Jake

1 0

skullstrip
by dasoscia＠buffalo.edu 31 Jul '06

31 Jul '06

I keep getting this error when trying to skullstrip a scan... *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 53463 Find the largest 110-component... heap usage = 133076 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 46289 voxels first estimation of the COG coord: x=124 y=107 z=123 r=86 first estimation of the main basin volume: 2722274 voxels ******************************************* *********************************************** *********************************************** White matter intensity 4 is lower than CSF intensity 24. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************ Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 31 11:25:35 EDT 2006 Attached are some slices from my T1 images, numbered according to coronal slice number. I noted that they do look a little odd/different than previous scans. Suggestions? Thanks Dave

2 1

caudate/putamen values for mri_segstats
by Nguyen, Thang Q 28 Jul '06

28 Jul '06

Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang

3 5

Total Brain Volume
by Anil Roy 28 Jul '06

28 Jul '06

Hello All, Does freesurfer generate a file with total brain volume after the recon-all procedure? Where can this be accessed? Thanks, AR.

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer