Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

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

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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.

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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

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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

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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

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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

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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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Re: [Freesurfer] tksurfer & rtview
by Michelle Umali 17 Aug '11

17 Aug '11

Hi Doug, Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data? The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings. I used 5mm smoothing. Thank you very much, Michelle Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > The activation looks pretty reasonable. As you point out, the angles > are a mess. How did you set the color scale for the angles? You should > leave it as a heat scale (if you're using tksurfer-sess). How much did > you smooth? > > doug > > Michelle Umali wrote: >> Hi Doug, >> Attached is a pic of the significance and angle maps for polar and eccen. >> >> What do you think? >> >> Thanks. >> Michelle >> >> Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >> >>> what does the activation look like? Does it look right? Can you send a pic? >>> doug >>> >>> Michelle Umali wrote: >>>> Hi Doug, >>>> The z-values are consistently near or greater than 4. It just >>>> seems that the >>>> visualization of the angles is somehow incorrect... >>>> >>>> Is there be anything else that I need to check? >>>> >>>> Thanks. >>>> Michelle >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ----- End forwarded message -----

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DOSS or DODS
by Tetiana Dadakova 17 Aug '11

17 Aug '11

Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja.

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preproc-sess registration problem
by raij＠nmr.mgh.harvard.edu 16 Aug '11

16 Aug '11

Hi Doug, We have an old EPI data set where automatic (preproc-sess) or bbregister with any init type give a bad result. Hence, we are attempting to use a manual register.dat file instead. However, we must be doing something wrong, because changing preproc-sess to use our manual register.dat (done a couple of years ago) seems to have no effect. I suspect our preproc-sess options as not set up correctly. Our goal is to present the results on fsaverage surface. Our preproc-sess command line is as follows: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat The whole analysis script is at /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh FS version = 5.1 machine = adapt (analysis running on cluster) setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ individual subject = avml07 surface analysis lhrh, results to be presented on fsaverage surface Total of 3 runs per analysis (each with different number of TRs) Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) FIR analysis Thank you for the advice in advance! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Freesurfer August 2011