Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

qdec-calculate the value of the slope
by asaf achiron 10 Jun '10

10 Jun '10

Hello Support, how can i calculate the value of the slope of a a plot when displaying the data for a particular vertex in qdec? thank you

1 0

Across Scanner Comparisons
by blazey＠artsci.wustl.edu 10 Jun '10

10 Jun '10

Hi All, Our group recently scanned subjects with two different scanners in order to determine how reliable FreeSurfer comparisons between the two scanners are. After putting each session through the regular cross-sectional Freesurfer pipeline, we noticed that there is much greater variability between the two scanners when we compare structures in the right hemisphere than in the left. Is there any FreeSurfer related reason for this? Also, we are currently running each subject through the longitudinal pipeline (i.e. Scanner 1 as TP1, Scanner 2 as TP2). Is there any reason to think that this will help reduce the variability seen between the two scanners? Thanks in advance for any help. - Tyler Blazey

2 1

advise on generating individual standard deviation map
by Michael Scheel 10 Jun '10

10 Jun '10

Dear FS experts, could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. Thanks, Michael

2 1

Registration of talairach and original space?
by Dickinson, Annelise (NIH/NIMH) [F] 10 Jun '10

10 Jun '10

Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

3 3

Calc stats on ROI in qdec
by Jeff Sadino 09 Jun '10

09 Jun '10

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff

1 0

Snowy background for T1 images
by Dave Brohawn 09 Jun '10

09 Jun '10

Hello, I keep seeing a snowy background for my T1 structural images. Here is my info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ cd /space/seymour/1/users/folate_subjects The command I entered and one of the subjects we are seeing this with - tkmedit-sess -s FB0011089A -a fmcsm5_functionals -c Cond1vFix Is this a problem? What can I do to fix this? Dave Brohawn

2 1

fsaverage aseg
by Michael Waskom 09 Jun '10

09 Jun '10

Hi all, How was the fsaverage aseg.mgz (in the 4.5 distribution, if it differs) created? I can't seem to find this information anywhere on the Freesurfer website. Thanks! Mike

2 1

Freesurfer to DTI space
by Tina Jeon 09 Jun '10

09 Jun '10

Hello all, I am using surface tracking in FSL to align my freesurfer surfaces to my diffusion data. I am wondering if it were possible to use the freesurfer2fa.mat registration file as the registration input for mri_label2vol. The freesurfer2fa.mat was generated using FLIRT in FSL by registering the freesurfer conformed structural space to diffusion space. Ultimately I want to align the gyri and sulci volumes to the diffusion images I have. Is this a viable solution? Thanks in advance, Tina Jeon

2 1

Question about getting fusiform stats
by Weisinger, Brian (NIH/OD) [E] 09 Jun '10

09 Jun '10

Hello I am trying to retrieve the fusiform volumes of a sample. I looked in the subject output files but didn't see any mention of the fusiform and when I searched the website so far all I could find involved fsl and functional data which mine is not. If it is possible to do could you please point me in the right direction to figure this out. Thank you for your help

3 2

prefrontal cortex values
by Ahmed, F, Me <fahmed＠sun.ac.za> 09 Jun '10

09 Jun '10

Hello, I require values (total volume) for the prefrontal cortex. I see labels for "G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are these correct to use? If so, could I add up the values for these to get one total volume for the PFC? Thank you, Fatima

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