Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

error message
by Ahmed, F, Me <fahmed＠sun.ac.za> 22 Jun '09

22 Jun '09

Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command: "recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message: [fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009 Please can you advise me on what the problem is and how to correct it? Thank you. Fatima

5 12

Problem "curvature file 'lh.area.mid' has wrong number"
by Grimm, Oliver 22 Jun '09

22 Jun '09

Hi! I'm trying some first steps with freesurfer and got the error mris_calc: curvature file 'lh.area.mid' has wrong magic number after I started recon-all all for some nifti MPRage files. I'm running freesurfer on openSUSE 11.1. What does this error mean, what can be done? Bye, Oliver Grimm Central Institute for Mental Health Research Group Imaging in Psychiatry J5 D-68159 Mannheim Germany oliver.grimm(a)zi-mannheim.de

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[Fwd: con and sig]
by adrzezga＠nmr.mgh.harvard.edu 21 Jun '09

21 Jun '09

Dear freesurfers I know this has been discussed before, but I could not figure out a satisfying answer from the precedent discussion: Could someone advise me (in a comprehensive step by step approach :-)) how to read out freesurfer-designed labels with mri_anatomical_stats on a series of images, which have been transformed into fsaverage surface space and are NOT located in the usual freesurfer directory structure ? Thanks a lot ! Alex

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longitudinal stream command line arguments
by Dabbs (Kevin) 19 Jun '09

19 Jun '09

The command line arguments for creating the base subject in Freesurfer Ver. 4.4 longitudinal stream do not agree between the Wiki and recon-all --help. On the Wiki support page, 2. create the base template and process it cross sectionally: recon-all -base <baseid> -tp <tp1id> -tp <tp2id> ... -all >From recon-all --help 2) create base subject and cross-sectionally process: recon-all -base longbase -base-tp tp1 -base-tp tp2 -all Is the correct argument "-tp" or is it "-base-tp" Thanks for the software and support, Kevin

3 2

mc-z, the same CWP for all clusters?
by Nasim Maleki 18 Jun '09

18 Jun '09

Hi all, I did the correction for multiple comparisons using mc-z with 10000 iterations (sign=abs, Threshold=1.3). Now for all the clusters (30 clusters) on one of the hemispheres I find the same CWP (0.00140), CWPLow (0.00090) and CWPHi(0.00190) for all of them. For the other hemisphere however there is only one cluster with CWP of 0.01940 and all the other clusters (34 clusters) again have the same values for CWP (0.67740) , CWPLow(0.67140) and CWPHi (0.68340). Is this normal?!! I have 2 groups with 10 subjects in each group. I was thinking maybe I should just increase the number of iterations... I appreciate your comments on this. Thanks, Nasim

1 0

[Fwd: fsaverage to average7]
by Yigal Agam 18 Jun '09

18 Jun '09

Hi all, Is there a way to convert results that I have on fsaverage to average7? I need to do that to be compatible with some average7 results that go into the same paper. When I use mri_surf2surf, activation is displaced. Any advice would be appreciated. This is what I've done: mri_surf2surf --srcsubject fsaverage --trgsubject average7 --sval [fsaverage file]--hemi lh --tval [average7 file] Thanks, Yigal

2 1

Qdec
by free_surfer＠virgilio.it 18 Jun '09

18 Jun '09

Dear Freesurfer users, We are experiencing a problem using Qdec (FS version 4.2.0; Qdec 1.0) for group data analysis. Indeed, the qdec display [after creating the qdec.table.dat and the <factor>.levels files] doesn't visualize properly (as in the tutorial) the Data Table View and other window-options that should allow us to select "Generate Stats Data Table" and proceed with the group analysis. Any suggestion would be greatly appreciated. Many Thanks in advance for your help, Antonio Gallo, MD, PhD Department of Neuroscience Second University of Naples Ph: +39-081-5665090

2 1

talairach_afd error
by Pål Gunnar Larsson 18 Jun '09

18 Jun '09

I have one volume that stops with error in tailarach_adf. The volume was axial rotatet some 20 degrees, but that was manually corrected. Recon-all still stops with the same error. The nu.mgz looks OK. What is the problem? I have attached the last part of the output. I am using Freesurfer Centos 4.3.1 on Ubuntu 8.10 Regards Pål

2 1

Error in Analyze
by Toh Hock Wong 18 Jun '09

18 Jun '09

Hi Douglas, Thank you for your quick reply. I have tried again with two discrete and continuos factors. The same error of mri glmfit --y still appears towards the end. I have attached a more detailed version of the error for your reference. Any suggestion will be much appreciated. Cheers! Toh Wong

1 0

Co-vary
by Jeff Sadino 18 Jun '09

18 Jun '09

Hello Freesurfers, My apologies for this very basic question more about statistics than freesurfer, but I have not found an answer anywhere on the wikis, or the web (maybe it is too basic :-) ) I am interested in age-related effects of hiv and I wanted to covary for age and education in mri_glmfit. For example, if my fsgd file is: class control class hiv variables age ed input subj1 control 40 13 input subj2 hiv 35 12 ... ... and I use dods, is my contrast matrix the place where I would tell it to covary? Something like: 0 0 -1 1 1 1 1 1 (y-int) (age slope) (covary for age) (covary for ed) As always, thank you for your help, Jeff _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori…

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Freesurfer June 2009