Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

qdec analyses
by Jose Soares 22 Jun '09

22 Jun '09

Hi all, I am a little bit confused about the qdec display. I have some simple questions about two groups A and B: 1- In the question, does the average thickness differ between A and B? How this average is calculated? By the difference between the A average and B average (avgA-avgB) ? The negative values (normally in blue) mean that the thickness (average of B) B is higher than A? 2- I want to analyze lh parahippocampal thickness. What is the difference between insert the values manually in the qdec.table.dat file (like the tutorial) or import ( in subjects - stats data import) the lh_parahippocampal_thickness from aparc? 3- In the question, does the thickness--lh_parahippocampal_thickness correlation differ between A and B? what for instance a positive value mean on display? I only expected results in the parahippocampal area... Thaks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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how to segment hippocampus using freesurfer
by Wenlu Yang 22 Jun '09

22 Jun '09

Hi all, I want to use freesurfer to segment hippocampus from MR images, but I don't know how to do it because I am a newcomer here. could you give me some advices? thanks. wyang

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Mris_thickness_diff and FS4.4
by Jürgen Hänggi 22 Jun '09

22 Jun '09

Dear FS experts I run the following command with longitudinal data from FS4.4, but I am not sure whether I specified the files properly (_base files?) and used the right transform (tp1_to_tp2.lta?), because files and transforms changed in FS4.4. mris_thickness_diff -xform tp2.long.tp2_base/mri/transforms/tp1_to_tp2.lta \ -src_type curv \ -out tp2.long.tp2_base/surf/lh.thickness_diff \ -nsmooth 30 \ -abs -S tp2.long.tp2_base \ -L tp2.long.tp2_base/surf/lh_thickness_diff.log \ tp1.long.tp1_base/surf/lh.white \ tp1.long.tp1_base/surf/lh.thickness \ tp2.long.tp2_base/surf/lh.white \ tp2.long.tp2_base/surf/lh.thickness Thanks in advance for clarification Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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R: Re: [Freesurfer] Qdec
by free_surfer＠virgilio.it 22 Jun '09

22 Jun '09

Hi Allison, I send you the snapshot of qdec. Thanks, Antonio Antonio, Can you describe what qdec is showing that's wrong or send a screenshot of it? Thanks, Allison -- On Thu, 18 Jun 2009, free_surfer(a)virgilio.it wrote: > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >

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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

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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

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[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

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