Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

2 1

subcortical gray matter segmentation
by asaf achiron 21 Oct '09

21 Oct '09

when conducting a subcortical gray matter segmentation, the volume of the cerebral cortex is also measured . how this is performed? is it also based upon the probabilistic atlas ? thank you Asaf

2 1

{Disarmed} Re: mgz file is tilted
by Jay Ives 20 Oct '09

20 Oct '09

2 1

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