Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

qdec group analysis
by Cat Chong 18 Jun '12

18 Jun '12

Hello Freesurfers, I have created an ROI label for 80 subjects in qdec. My question is the following: Is there a command that will create a .stats file for all my subjects rather than using the below command on each person individually? mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b -f 4000/stats/rh.ento.stats 4000 rh best regards, Cat

2 1

Editing Putamen Segmentation
by Kristin Javaras 18 Jun '12

18 Jun '12

Dear all, For a number of my participants, Freesurfer's augmented segmentation of the putamen appears to include brain matter that isn't putamen (e.g., see attached images) - this persists across 5-6 slices, on average. I was wondering what people would recommend - should I edit the aseg? Thank you in advance for any advice, Kristin Javaras _______________________________ Kristin N. Javaras, DPhil Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Telephone : +1 (608) 890-1407

1 0

Correction for Multiple Comparisons - Sign Question
by mdkruepke＠uwalumni.com 18 Jun '12

18 Jun '12

Freesurfers- When choosing the simulation type does the ending have to match the sim sign? for instance i see examples with --sim mc-z 10000 3 mc-z.pos.3 --sim sign pos or --sim mc-z 10000 3 mc-z.neg.3 --sim sign neg I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3 mean? michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

2 1

Choosing a Scanning Sequence
by Sullivan, Patrick M. 18 Jun '12

18 Jun '12

Hello, We are working with previously acquired data, so unfortunately we are unable to use the MPRAGE sequence for the current data set. We would like to use T1 images to compute volumetric results. We are using a Philips 3T Achieva, and the sequences received by most participants are a T1-FFE (FLASH in Siemens terms or SPGR in GE terms) and a T1 TFE sequence (I believe this is TurboFLASH in Siemens terms, although I am not fully familiar with it). Are either of these scans appropriate for performing volumetric analysis of grey/white matter using FreeSurfer? Is either scan preferable to the other? Patrick Sullivan Research Assistant, Chapman Lab War Related Illness and Injury Study Center Veteran's Affairs Medical Center Washington, D.C. 20422 (202) 745-8000 (ext 7566)

1 0

Ridiculous story about Freesurfer
by Andrew Dumas 18 Jun '12

18 Jun '12

Did anyone else happen to see this ridiculous story on Gizmodo today? http://gizmodo.com/5919149/your-brain-scan-looks-different-on-mac-and-pc It cites the recent article "The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements" as its only source, and then goes on to completely misinterpret it. This sentence (if I had to pick one) is particularly troubling to me: "The finding is completely crazy, and casts doubt over the way many scans—such as CT and MRI—are analyzed in routine practice." Crazy, right? Enjoy... Andrew

1 0

mri_cnr
by Kushal Kapse 18 Jun '12

18 Jun '12

hi fellas, i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf.... the command gives following info as help: -bash-3.2$ mri_cnr usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ... -s <slope fname> <dist in> <dist out> <step in> <step out> i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname......it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command..... i checked on freesurfer mail archive, but no info since 2009 about any update on this command..... may someone please give an info if anyone ever used this command thanks kk

2 2

memory allocation error with mris_register for one subject
by Arno Klein 18 Jun '12

18 Jun '12

hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno

2 3

Cannot access "Apply" button in Configure Overlay Display dialog
by Vadim Axel 18 Jun '12

18 Jun '12

Dear developers/users, This is completely ridiculous known issue on a low resolution monitor :( Presumably, it was solved here: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer, but the file is inaccessible via ftp. Any other workaround? All I need is to change Min statistic threshold and hit apply button. Probably, something via command line? Unfortunately, there are no hot-keys and it is impossible to reach with a tab because the non-visible dialog elements presumable do not exist (tab goes to the top of the dialog after the last visible dialog element). I am using Ubuntu virtual box FS 5.1. Thanks a lot, Vadim

2 1

.license file
by Monica Giraldo 18 Jun '12

18 Jun '12

Hello, I created a file with this data, but when I'm going to save it as .license doesnt let me because a message appears and says that files starting with . are of the system and that i have to choose another name. What can I do? Thanks. Mónica Giraldo Chica PhD. Candidate Biomedicine Sherman Health Science Research Centre www.monicagiraldochica.com

3 2

Flipped and non-flipped data
by Schur, Remmelt R. 18 Jun '12

18 Jun '12

Dear Freesurfers, Grey matter volumes of the same structure seem to be measured differently depending on if FreeSurfer establishes it as in the left or in the right hemisphere. For example, if I take a look at the caudal anterior cingulate in the right hemisphere and I flip the image (creating a mirror image of the same hemisphere, which will then be treated by FreeSurfer as a left hemisphere), the same structure has a totally different grey matter volume (see attachment, on the right the original and on the left the flipped version). Does anybody know what's the logic behind this and what's the best way to avoid FreeSurfer creating asymmetry between left and right hemisphere (maybe averaging flipped and non-flipped data?) Thanks! Kind regards, Remmelt Schür IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

3 2

← Newer
1
...
6
7
8
9
10
11
12
...
20
Older →

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 June 2012