Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

color coding for parcellations/regions of interest
by Lars M. Rimol 03 Jun '07

03 Jun '07

Hi, I have combined the Desikan parcellations into regions of interest, which I would like to visualize. So I need to create an ad hoc color coding scheme. In order to visualize the ROIs I would load a file equivalent to the ?h.aparca2005s.annot file, which would show the same color for those parcellations that belong to one and the same ROI. Which file contains those color definitions, or in other words which file do I need to modify in order to be able do that? Tank you! -- yours, LMR

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tkmedit scripting
by Sebastian Moeller 02 Jun '07

02 Jun '07

Hi List, getting into scripting of freesurfer I wonder whether it is possible to script false discovery rate for overlays in tkmedit. There seems to be Overlay_SetThresholdUsingFDR, but it is not really documented. So, here my question: what is the invocation to use FDR to select the thresholds for overlay 1, without any masking? thanks & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_vol2surf question
by Morgan Hough 01 Jun '07

01 Jun '07

Hi there, I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time. Cheers, -Morgan mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24

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spm_hrf mkanalysis-sess question
by Avram Holmes 01 Jun '07

01 Jun '07

All, I am interested in comparing a gamma fit analysis with the spm_hrf method. Unfortunately I am unable to use the '-autostimdur' or the '-TER' flags in with the SPM mode. When I do use these flags I get the following error... 'ERROR: paradigm is ill-conditioned (6.06514e+13). Check your paradigm file for file for periodicity's or for some event types that all ways follow other event types (or itself). Saving Xfinal to /Raid/shared/exp/CONCON/fMRI/functional/c01/Flanker/Flanker_SPM2/h0.sumxtx.mat It could also be due to the fact that the TER does not equal the TR. SubTR estimation only works when the event schedule has been optimized with SubTR estimation in mind.' Thanks for your time, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

fmri correlation map
by Cameron Ellis 01 Jun '07

01 Jun '07

Does anyone have an answer to this question? Hello, I am looking for a way to perform voxel-wise, within-subject correlations of two activation maps (in talairach space). The two existing maps reflect encoding and retrieval runs of a memory task. The idea would be to generate a correlation map across all subjects, to identify clusters where there was a positive or negative correlation between encoding and retrieval activation. I've seen this done with SPM but not Freesurfer. Any suggestions? (Perhaps this would involve glmfit?) Many thanks, Josh

2 1

Masking group data using mri_volcluster
by Dan Dillon 01 Jun '07

01 Jun '07

Dear FreeSurfers, I've run some fixed and random effects analyses in Talairach space and would like to constrain the output of mri_volcluster to areas within the brain (e.g., not the eyeballs). How do I create a brainmask that is the same dimensions as the input volume I pass to mri_volcluster? Without a mask, I'm currently getting stats on extra-brain voxels that I do not want, and I can't use the Talairach brainmask.mgz file b/c it doesn't match my input volume. Any help would be appreciated. Dan Dillon PS. The command I'm currently running, sans mask, is as follows: mri_volcluster --in LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/Rcue_v_Ncue/sig --in_type bfloat --reg LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/register.dat --thmin 3 --minsizevox 12

2 1

Next Release
by Michael Harms 31 May '07

31 May '07

Hello, There have been several mentions on this list of the intent to release a new FS version later this summer. As an aid to those trying to decide whether it is worthwhile to wait for the next version to start an analysis of a new group of subjects, I thought it would be helpful to know the following: 1) Can anyone comment on the target month, and how likely that target will "stick"? 2) At what stage of the processing would you have to begin reprocessing the data in order for the results to completely reflect v3.1? -- the very beginning? Somewhere in the middle of autorecon2? [I see from http://surfer.nmr.mgh.harvard.edu/fswiki/NextReleaseNotes? action=highlight&value=next+release that there is going to be a corrected aseg in v3.1. So, am I correct in assuming that everything following the creation of the aseg.mgz would have to be reprocessed?] thanks, Mike H.

2 1

Freesurfer mri_surf2surf-smoothing error
by Susanne Mueller 31 May '07

31 May '07

Hi, I am relatively new to freesurfer and trying to do my first group analysis. Following the web tutorial -although with my own data set- I was able to do the pre-processing incl. mris_preproc which created the desired output without any error message. However, when I try to perform the next step, i.e. smoothing the data, I get the following error message mri_surf2surf --hemi lh --s average --sval lh.ADvsContr ols.thickness.mgh --fwhm 10 --tval lh.ADvsControls.thickness.10.mgh srcsubject = average srcval = lh.ADvsControls.thickness.mgh srctype = trgsubject = average trgval = lh.ADvsControls.thickness.10.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 Reading source surface reg /cind/00/FAD/subjects/average/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject reading group avg surface area 922 cm^2 from file Segmentation fault I also tried to run the smoothing as a part of the mris_preproc with the same result. I am using the v3.0.5 version of freesurfer. Any help to figure out what I am doing wrong or what else is going on would be greatly appreciated. Susanne

2 1

tksurfer time course window
by Elaine Leung 30 May '07

30 May '07

Hello Freesurfer, Is there a way to adjust or set the y-axis of the time course window in tksurfer? Thanks in advance, Elaine

2 1

white matter surface leakage
by Paul Aparicio 29 May '07

29 May '07

Dear List, I am having a problem with mri_normalize. The problem is that after normalization the white matter areas in my volume have expanded and leaked into area that should be grey matter, is there a way to place control points for grey matter? Thanks paul

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