Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

problems with qdec
by Paula Diniz 23 Jul '09

23 Jul '09

Hello I`m problems with the levels files. The error is : Loading data table /Users/paula/Freesurfer_ELT_primeiro_trabalho/qdec/qdec.table.dat... Number of columns: 5 fsid column: 1 Number of factors: 4 Number of subjects: 52 Reading discrete factor levels from config file /Users/paula/Freesurfer_ELT_primeiro_trabalho/qdec/gender.levels 'Female', done ERROR: 0xbfffa334 is invalid. Must have at least two levels. Error loading the data table. where is the problem? What I have to do? Thanks -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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Cluster correction for multiple comparisons using mri_glmfit-sim
by Devdutta W 23 Jul '09

23 Jul '09

Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness). As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki. Can anybody shed some light on this? Why this discrepancy between the two? Thank you, Devdutta

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declaring spherical ROIs centered at common Talairach coord.
by Stephen Towler 23 Jul '09

23 Jul '09

We want to extract a spherical ROI of cortical thickness values centered at the same Talairach coordinate for each brain in a study. Any suggestions? In the 2007 archives there is an instructive thread about declaring spherical ROIs on a volume, but I'm not clear about how we would place the initial point at the same Talairach coordinate in every participant. Thanks, Stephen

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Customised color bar in tksurfer
by 류철형 23 Jul '09

23 Jul '09

Dear all 1. I would like to display average thickness on surface model in tksurfer. The basic color bar included the tksurfer seems to be insufficient for displaying thickness difference (e.g. red to yellow etc.). I'd like to use rainbow color table in displaying the thickness result. How can I make this in tksurfer? or Should I use another utility for displaying purpose (e.g. surfstat)? 2. The y.mgh file contains thickness data of all subjects, I guess. Then, when the y.mgh file is imported and overlayed on the surface in tksurfer, does the displayed color represent the average thickness in y.mgh file subjects? Best Wishes >From Lyoo

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WM bug fix
by Tricia Merkley 23 Jul '09

23 Jul '09

Hi, I tried to use the white matter bug fix using v4.4.0 for data that was originally run using v4.0.4. I then noticed that the IntraCranialVol measure in wmparc.stats and aseg.stats for one of the subjects was -2083.23 (after rerunning recon-all -segstats -wmparc). Is this due to the new way of calculating TIV (as of v4.3.0)? Should I revert back to using the values prior to the bug fix? Here is the bugr info if needed: FREESURFER_HOME: /fslhome/mendy22/freesurfer4.4.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-53.1.14.el5 x86_64 cmd line executed: recon-all -s <subject_id> -segstats -wmparc Thanks so much, Tricia Merkley

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recon-all exited with errors
by sameer kumar 22 Jul '09

22 Jul '09

hi all, I ran recon-all on a case, and it exited with errors, and the error message looks like this: ERROR: Talairach QA check failed! z-score = -6 <= -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. will there be a difference in the results if i use that flag to skip the test? Thanks, Regards, Sameer

2 1

left right nifti
by Narly A Golestani 22 Jul '09

22 Jul '09

Hello everyone, I would like to know if there are left-right orientation issues when converting images from nifti format to the mgz format. I suspect not as nifti, unlike analyze, contains the left-right information in the file itself. But I would like to make sure that there are not issues such as the ones reported with going through analyze, such those reported here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09329.html thanks in advance! best wishes, Narly.

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Estimated total incranial volume
by Flavio Seixas 22 Jul '09

22 Jul '09

Dear All, In addition to eTIV based on Tailarach transform matrix (see Buckner et al. paper), is there other estimated total intracranial volume method, for example, using the BET2 (brain extraction tool)? Thank you in advance, Flavio

2 1

Colortable
by Eylem Kirlangic 22 Jul '09

22 Jul '09

Hi, Is there any way to extend the colortable in freesurfer? Cheers, Eylem ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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floating area with significant difference in qdec
by Rosa Steimke 22 Jul '09

22 Jul '09

dear freesurfer experts! I am trying to make a ROI of an area the showed significant difference in qdec. to do so i am drawing around the area per hand, but it doesnt look very precies. is there also a function that will float the whole area which is coloured? thanks in advance! rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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