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30088 discussions

Avg.Thickness in a cluster
by Antonella Kis 18 Aug '11

18 Aug '11

Dear Doug, I just checked my results for the average thickness from each subject generated in the csdbase.y.ocn.dat file in different clusters (e.g. I have 5 clusters for p<0.05). For cluster #1 - posteriorcingulate, the average thickness for subject 1 is different from the average thickness value in the same region-posteriorcingulate, in the lh.aparc.stats for the same subject. I thought it should be the same. Why they are different? Is this right? MANY THANKS! Antonella

1 0

Trac paths error - bedpost files not found
by Moiyadi, Ammar 18 Aug '11

18 Aug '11

Hi Freesurfers - I am encountering an error in trac-all -paths where it cannot find the mean_dsamples.nii.gz file in my dmri.bedpostX directory since it was not created during the bedpost step. Because I ran the original bedpost (not the Seychelles version) I was wondering if this output file was specific to the other version. I have a feeling bedpost is not getting through its entire process but I don't receive any error messages as feedback - once it reaches 47 slices processed it starts queing the post processing stage and then the program ends. Is it possible that the post processing stage has not completed and as a result the required files are not being created? Currently I have the following files in my bedpost output directory: dyads1.nii.gz dyads2.nii.gz mean_th1samples.nii.gz mean_th2samples.nii.gz mean_f1samples.nii.gz mean_f2samples.nii.gz mean_ph1samples.nii.gz mean_ph2samples.nii.gz merged_th1samples.nii.gz merged_th2samples.nii.gz merged_f1samples.nii.gz merged_f2samples.nii.gz merged_ph1samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz It appears I am missing both the mean_dsample and dyads_dispersion files. Any ideas why these files haven't been created and when they should have been created during bedpost? Thanks for your help, Ammar Moiyadi

2 3

update v5.1 and trac-all command
by Carolina Valencia 18 Aug '11

18 Aug '11

Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command? Thanks, Best regards Carolina

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aseg.stats and wmparc.stats in FreeSurfer 5.1
by Tali Swisher 18 Aug '11

18 Aug '11

Hi all, In the aseg.stats and wmparc.stats output files in *version 4.2.0*, there were four volumes named: Left-Cerebral-White-Matter Left-Cerebral-Cortex Right-Cerebral-White-Matter Right-Cerebral-Cortex Does anyone happen to know what the corresponding volumes are in *version 5.1*? They don't appear in the same place or under the same name anywhere, hence the confusion. Thanks! Tali -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

2 1

Error while loading qdec project file
by Tetiana Dadakova 18 Aug '11

18 Aug '11

Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, Tanja.

2 7

pial surface documentation
by Jeff Eriksen 17 Aug '11

17 Aug '11

Where may I find the documentation explaining the content and format of the pial and gray-white surface files? Thanks, -Jeff

3 2

17 Aug '11

Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody know how to do that? Thanks! Francesca

2 5

FMRI Asymmetry Analyses
by Andy Mayer 17 Aug '11

17 Aug '11

Hello- Trying this post again. I would like to directly compare asymmetries in FMRI activation in surface space based on the Greve et al poster presented at HBM this year. We would like to register each subject’s T1 data to the contralateral hemisphere of fsaverage and made templates of the contra (?h.con.sphere.reg ) and ipsilateral (?h.sphere.reg ) registrations. Is the following correct for the cross hemisphere registration? Thanks mris_register -reverse -curv surf/rh.sphere {$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif surf/rh.CON.sphere.reg

2 1

outline of a label as an overlay
by Ritobrato Datta 17 Aug '11

17 Aug '11

Hello All, Is there a way to save the outline of a label as an overlay (say .mgh file) ? Please let me know. Thanks Ri

2 1

voxel assignment error in V1
by Ritobrato Datta 17 Aug '11

17 Aug '11

Hello All, We have processed retinotopy data and piped the phase maps into freesurfer stream. As can be seen on the attached reconstructed image, there are patches of cortex (some reds) within the calcarine sulcus that are wrongly assigned to the upper bank. Any ideas on how to correct for these mis-identified patches in FreeSurfer ? I have already checked using tkregister the registration of the functional data to the freesurfer anatomy and that looks fine. Please let me know Thanks Ri

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