Freesurfer

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19 participants
30132 discussions

Incorrect white and pial surfaces
by Angel Wong 07 Oct '09

07 Oct '09

Dear Freesurfer experts I have encountered a problem of performing fully automated reconstruction of my T1 image. Attached please find the resulted image after the reconstruction. The white and pial surfaces do not follow the boundaries as specified by aseg.mgz segmentation. If I interpret correctly, the green line should lay on the boundaries between grey and white matters, and the red line should lay on the boundaries between CSF and grey matter. But that is not my case. The green and red lines seem following wrong boundaries, and it affected the later cortical parcellation stored in aparc+aseg.mgz file. How should I correct or make edit for my case? Is there anything going wrong in my procedure? For you information, I just have one T1 volume for each subject, and the version of my installed freesurfer is 4.3.0 The command-line I used is recon-all -i <directory that has the COR files> -s <subject_name> -sd <subjects_dir> -all Regards Angel

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Incorrect white and pial surfaces
by Angel Wong 07 Oct '09

07 Oct '09

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Please let me know whether the source code is open.
by Youngsang Cho 07 Oct '09

07 Oct '09

Dear all, I am a PH. D. student at KAIST in KOREA. I am researching cortical surface analysis. So I'd like to anaylize the source code, and it seems that the source code is open. However, I couldn't find any link or cvs ID in the freesurfer wiki. Please let me know whether the code is really open, and if it is open, how can I download it. Thank you very much. Youngsang Cho ========================================================================= Youngsang Cho Computer Graphics Lab, Computer Science Dept. KAIST, Gwahakro 335, GUSEONG-DONG, YUSEONG-GU, DAEJEON CITY, ROK, ZIP CODE 305-701 ▶ Tel.) : +82-42-350-3553 ▶ Fax.) : +82-42-350-2450 =========================================================================

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QA Cortex
by Jeff Sadino 06 Oct '09

06 Oct '09

Hello, I want to do a quality check of the cortex for 140 subjects, as far as making sure it is segmented correctly. What files are the best ones to load up to check this in fs 3? If I load the aseg.mgz file up in tkmedit and look at the cortical regions, there are some regions where there is no cortex at all. Would I make the edits on this file, or is there some other file that would be better to use. Thank you, Jeff Sadino

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mris_expand
by Don Hagler 06 Oct '09

06 Oct '09

Bruce recently wrote that you could run mris_expand like this: mris_expand -t lh.white 0.5 lh.graymid I found that didn't work, but this did: mris_expand -thickness lh.white 0.5 lh.graymid I am using version 4.4. By the way, is there a way to increase the resolution of the surfaces before creating final surfs? _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

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optseq2 help: DPSD and jitter
by Asaf Kaftory 06 Oct '09

06 Oct '09

Hello list, I'm new to optseq, and would like your help with the following issues: 1. What exactly does DPSD mean? and why does the TR has to be an integer of it? 2. My experiment design uses jitter - both ITI (i.e., between trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event? 3. Is it true that jitter in optseq is made by inserting "NULLS", and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right? hope to hear from you soon, Asaf.

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Re: [Freesurfer] tkregister2 questions
by Weisinger, Brian (NIH/OD) [E] 06 Oct '09

06 Oct '09

Would it be a problem to skip this step by using the -notal-check or would that mess the results up too much? On 10/6/09 2:03 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: That might be a problem as (I think) our target is made from 3T data, and the contrast might be different. Pratap, is your anatomical data from 1.5T? Weisinger, Brian (NIH/OD) [E] wrote: > These images are from a 1.5 scanner > > > On 10/6/09 12:24 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > It means that you don't have permission to write into that directory. > > The images look a little off. What kind of scanner are you using? > > doug > > Weisinger, Brian (NIH/OD) [E] wrote: > >> When I try to use tkregister2 I get this message, how do I go about changing not being able to save the changes I make. >> >> WARNING: cannot write to /Applications/freesurfer/subjects/00007/mri/transforms. >> You will not be able to save any edits. >> Hit Enter to continue: >> >> Also I just wanted to get your opinion about these images...It looks like I need to stretch them some so that the green part is in the white brain area. Would you agree? >> >> >> >> [cid:3337666238_142370727] >> >> >> >> >> [cid:3337666238_142392223] >> >> >> >> >> >> >> [cid:3337666238_142372460] >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > 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 > > > > > > -- 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

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tkmedit "save main volume as.." option...
by Gonzalo Rojas 06 Oct '09

06 Oct '09

Hi: I do all the steps of the "Manual Editing" process that appears in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but the "save main volume as.." option appears in gray (off)... Why ?... I thought it might be a access permission related issue, but it was not... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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How to use mris_register
by Xiaojing Long 06 Oct '09

06 Oct '09

Hi, all, I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use this command. Are the inputs often xx.sphere? I have two wm surfaces 'subj1.smoothwm' and 'subj2.smoothwm' and I want to align them. Can I use mris_register to do that? What information or parameterization are required by mris_register? Since when I run this command, I get errors saying that: "reading template parameterization from target.smoothwm HIPS unsupported No such file or directory" I don't understand what this error means. Could anyone help me? Thank you so much. Best, Xiaojing

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contrast matrix of 2 factors (2x4 groups)
by Stefan Brauns 06 Oct '09

06 Oct '09

Hi all, I am trying to examine the interaction of 2 factors (2 x 4 groups) and have difficulties to find the right contrast matrix for mri_glmfit. We have patients and controls at four different aquisition sites and want to know if the changes (i.e. thickness) between patients and controls are equal in every site. so we have 8 groups: patientssite1 patientssite2 patientssite3 patientssite4 controlssite1 controlssite2 controlssite3 controlssite4 the contrast for differences between patients and controls (T-Test) would be: 1/4 1/4 1/4 1/4 -1/4 -1/4 -1/4 -1/4 the contrast to investigate if the observed measured value is equal in all sites (F-Test) would be: 1/2 -1/2 0 0 1/2 -1/2 0 0 0 1/2 -1/2 0 0 1/2 -1/2 0 0 0 1/2 -1/2 0 0 1/2 -1/2 How would the contrast matrix look like if I want to test if there is an overall interaction between site and diagnosis, i.e. does the effect of diagnosis vary by site (F-Test)? Many thanks, Stefan -- Stefan Brauns

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