Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] FWHM smoothing for surface based
by Douglas N Greve 20 Jul '12

20 Jul '12

Yea, that is pretty smooth to start with. How did you choose to smooth by (an additional) 15mm? How are your results if you don't do anymore smoothing? doug On 07/20/2012 11:22 AM, jm wrote: > On 07/18/2012 11:14 AM, Douglas N Greve wrote: >> I think that the LGI is a very smooth measure, so even if you only >> smoothed by 15mm, there is a lot of smoothness in the unsmoothed data. >> This is what fwhm.dat is picking up. What happens if you do not smooth >> the data? What fwhm do you get? >> doug > > if I not smooth lgi data I get fwhm=13.2 into fwhm.dat > >> >> On 07/18/2012 08:02 AM, jm wrote: >>> Dear Freesurfer Team: >>> >>> I would like some information on FWHM.dat folder glmdir and its >>> relationship with mri_glmfit-sim. >>> It happens that when I use mri_glmfit-sim with --cache-in can't find >>> the data for fwhm 51 - which is logical because they exist only to >>> 1..30, but my data were smoothed previously for fwhm 15 (pial_lgi). >>> That interpretation would take this outcome? Something could go wrong >>> when he observed these differences between the smoothing of my data >>> and the reported in fwhm.dat >>> >>> thanks in advance >>> >>> >>> >>> _______________________________________________ >>> 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

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freesurfer issue
by David Eugene Klein 20 Jul '12

20 Jul '12

Hello, I'm using freesurfer edit in the tkmedit format and running into issues. I'm editing them in quest server. I type the following command: tkmedit <subjid> brainmask.mgz -aux wm.mgz -surfs where <subjid> is the subject. The subject loads but I get the following error message, and the red and yellow lines that are supposed to appear do not: > >>>> > > Error: Loading volume wm.mgz > > Couldn't read the anatomical volume. > Tkmedit couldn't read the volume you specified. > > This could be because the image format wasn't recognized, > or it couldn't find the proper header, > or the file (s) were unreadable, > or it was the wrong size. > > >>>>>> I have run recon-all so I don't think that's the problem. If someone could help me figure this out it would be greatly appreciated. Thank you. David Klein

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covariation analysis
by Ivanka Savic Berglund 20 Jul '12

20 Jul '12

We are trying to evaluate the covariation pattern in cortical thickness from a selected cortical ROI along the entire brain cortex. However, the output received gives only positive values. Is this inherent in the program, or could it be a matter of the input command? Sincerely I Savic

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Longitudinal analysis question
by Kairys, Anson 20 Jul '12

20 Jul '12

Hello FS experts, I am running a group up subjects pre/post treatment. When trying to do group analysis, after converting data with the mri_slope command, when I made the long table into a cross table, I noticed in qdec it averaged my "time" variable and only supplies a mean and there is no longer separate timepoints for subjects, just one value per subject. Do I need to define time as something more descriptive than 0 (tp1) and 1 (tp2)? I am so close to analyzing these data, just need a little help with the group analysis Thanks Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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slice-by-slice predictors
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Is it possible to have slice-by-slice predictors in Freesurfer, and if so, how? Thanks, Caspar

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stats
by Oertel, Viola 19 Jul '12

19 Jul '12

Dear Doug, I have a question: when I create the stats tables, there are two tables: lh.aparc.a2005s.thickness.stats and lh.aparc.thickness.stats which one is the right one if I want to get the thickness values of the significant clusters from the main effect (pat. / controls)? Thanks and best regards, Viola

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retroicor
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar

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hippo_subfields questions
by Gabriel Gonzalez Escamilla 19 Jul '12

19 Jul '12

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Automated sub-region segmentation - Amygdala
by Marc Rudolph 18 Jul '12

18 Jul '12

Good afternoon, I am new to freesurfer - is it possible to auto-segment the Amygdala into sub-regions? Thank you for your time, Marc

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mni152.register.dat
by Garikoitz Lerma Usabiaga 18 Jul '12

18 Jul '12

Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have the same problem when I convert it to surface: cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov ../../ROI2/ROI45.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI45.mgh \ --reshape - Is this a correct way of using it? Should I get proper results or I am missing anything? and, - Does it make sense creating a new fsaverage using the /spm8/canonical/avg152T1.nii, then applying the ROI which is already in 152 space, and referring the cortical thickness of all the subjects to this "new fsaverage"? (the functional analysis is being carried in SPM as well). Many thanks for your answers, Gari

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