Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

lGI value aberrantly high
by Prapti Gautam 22 Oct '09

22 Oct '09

Dear freesurfers, I have a problem running localGI in one subject. I previously got an error message that said that one of the vertex value was aberrantly high. The mris euler number on the subject was fine - but I relaunched the recon-all -autorecon2 -autorecon3 for the hemisphere in question and tried re-running the localGI command since this has been previously suggested as a fix to the problem. However, I get the same message (aberrantly high lGI value) even after re-running autorecon2 and autorecon3. Is there anything else I can try to complete lGI successfully? Thanks for your help, Prapti

3 3

How to flip a surface model?
by Jürgen Hänggi 22 Oct '09

22 Oct '09

Dear FS experts We investigated patients with unilateral pain. For some patients, the pain was on the left side, for others it was on the right side. We would like to do a group analysis on cortical thickness maps vertex-wisely but we do not know whether it is possible to flip a surface model (e.g. the left cortical thickness map) so that we can pool patients with pain on the left with the patients who have pain on the right. Is there an easy way to do this? Thanks in advance 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. ----------------------------------------------------------------------------

3 2

Mri_label2vol memory error
by Alex Fornito 22 Oct '09

22 Oct '09

Hi all, I've tried running mri_label2vol on a few different computers now and keep encountering the same memory error. Can anyone provide suggestions as to how to get around this problem? I've included the output from a run using linux on a dual 3.05 GHz Xeon with 8GB ram below. Thanks for your help, Alex mri_label2vol --annot 1002593/label/fsavg_lh_500_compact.aparc.annot --identity --temp 1002593/mri/orig.mgz --subject 1002593 --hemi lh --o output.nii Number of labels: 0 Annot File: 1002593/label/fsavg_lh_500_compact.aparc.annot Template Volume: 1002593/mri/orig.mgz Outut Volume: output.nii Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: 1002593 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.25.2.3 2009/06/09 16:22:30 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.white nvertices = 143248 Reading thickness /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.thickness Loading annotations from 1002593/label/fsavg_lh_500_compact.aparc.annot reading colortable from annotation file... colortable with 596 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2 005.txt) annotidmax = 595 Allocating Hit Volume (1392508928) voxels MRIalloc(256, 256, 256): could not allocate 131072 bytes for 22406th slice Cannot allocate memory

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About Difference
by zhenxt03 21 Oct '09

21 Oct '09

Hello Experts, I want to know if there is any differece between thickness results computed in different Operate Systems or with different machines? Thanks Xiantong Zhen

1 0

How to smooth functional retinotopic data on the gray matter surface?
by Andreas Schindler 21 Oct '09

21 Oct '09

Hello I am analysing my phase encoded retinotopic data with FS-FAST. Meanwhile everything is running fine. However I still haven't figured out how I can find out what colours of tksurfer's overlay colourmap correspond to which phase. Further I was wondering if it is possible to calculate an automatic fieldsign map (combining polar and eccen data) with paint-sess without having an occipital flat map. I am grateful for any kind of hint :-) Many thanks best wishes Andreas

2 1

2009年10月21日 23:07:55 自动保存草稿
by zhenxt03 21 Oct '09

21 Oct '09

Hello experts, Can you please detail the difference between the current version of Freesurfer and the previous ones ? Does it compute the thickness more precisely than before? Thanks in advance, Regards Xiantong Zhen

2 1

Tal 2 MNI
by Gabriel Go.Es. 21 Oct '09

21 Oct '09

Hello i have a question i want to convert an MRI subject (brainmask.mgz in talairach apace) and a mask of subcortical structure of the same subject, from freesurfer to MNI colins space to work with SPM5, how can i make it? and in fact i need to make this transformation to a set of subjects. any help will be so appreciated Best Regards Gabriel _________________________________________________________________ Convierte las fotos que más te gustan en tu nuevo fondo de escritorio para el ordenador. Es fácil y además gratis http://wallpapers.msn.com/es-es

3 2

About corrected t-statistics and p-values
by jorge luis 21 Oct '09

21 Oct '09

Hello freesurfer experts I would like to know how to get in freesurfer corrected p-values and t-statistics for the FDR analysis and corrected t-statistics for the clusters in the cluster size inference by permutation testing. In advance thank you very much Jorge Luis

3 2

Hippocampus
by Kelly Silva 21 Oct '09

21 Oct '09

Hello, I would like to know which structures (or elements) were included into the hippocampus (aseg.stats) when this volumen was created. Thanks in advance, Kelly ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 1

running motion correction
by Ahmed, F, Me <fahmed＠sun.ac.za> 21 Oct '09

21 Oct '09

Hello, I'm currently converting my dicom images into the mgz format and I was wondering, I only have one acquisition per subject, therefore do I have to run the motion correction step before running autorecon1? Or can I just go straight into running autorecon1? From the tutorial, I'd imagine I must run the motion correction step as it says that autorecon1 uses the output from the motion correction step, so I'm just a little confused. Thank you, Fatima

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