Freesurfer

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30086 discussions

Re: [Freesurfer] Error in creating stats using tracula
by Anastasia Yendiki 09 Sep '14

09 Sep '14

Hi Neeraj - The libnetcdf error you're getting probably means that you should install a different build of freesurfer (centos 4 instead of centos 6). Which one are you currently using? In the future please email the freesurfer list instead of me personally with questions about tracula. The purpose of the list is to get the messages archived so that people can search for questions that have been answered before in the archives. Thanks! a.y On Tue, 9 Sep 2014, Neeraj Upadhyay wrote: > Dear Anastasia Yendiki, > While analysing the DTI data with Tracula ,I stuck to a problem which is attached in the screen shot .Please guide me how to solve it because this is the > step to analyse the data group wise using voxelwise diffusion measures. > > hope for a positive reply soon. > With warm Regrads > -- > Neeraj upadhyay > PhD Fellow > Department of Neurology and Psychiatry > University of Rome La' Sapienza > Viale della Universita 30-00185,Rome,Italy > Guide: Professor Alfredo Berardelli > contact no:+393735282419 > >

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From bedpostX and recon-all to tracula
by Katherine Damme 09 Sep '14

09 Sep '14

Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they could share as an example? Thank you! Kate

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mri_glmfit problem
by Minjeong Wang 09 Sep '14

09 Sep '14

Dear all, i have some problem with mri_glmfit. The error message is "you must use '--surface subject hemi' with surface data" What do I do for solving this problem?? Help me.. :( M.J. --------------------------------- mri_glmfit \ --glmdir lh.cdr.glmdir \ --y lh.cdr.thickness.10.mgh \ --fsgd cdr.fsgd dods \ --C normal-CDR0.5.mtx \ --C normal-CDR1.mtx \ --C CDR0.5-CDR1.mtx \ --C group.effect.mtx \ --C normal+CDR0.5-vs-CDR1.mtx \ --surf fsaverage lh \ --cortex \? --glmdir lh.cdr.glmdir \ ? --y lh.cdr.thickness.10.mgh \ ? --fsgd cdr.fsgd dods \ ? --C normal-CDR0.5.mtx \ ? --C normal-CDR1.mtx \ gdfReadHeader: reading cdr.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --glmdir lh.cdr.glmdir --y lh.cdr.thickness.10.mgh --fsgd cdr.fsgd dods --C normal-CDR0.5.mtx --C normal-CDR1.mtx sysname Darwin hostname Youngui-Mac-Pro.local machine x86_64 user younghopark FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh logyflag 0 usedti 0 FSGD cdr.fsgd glmdir lh.cdr.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.cdr.glmdir Loading y from /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh ERROR: you must use '--surface subject hemi' with surface data [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C CDR0.5-CDR1.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C group.effect.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C normal+CDR0.5-vs-CDR1.mtx \ ? --surf fsaverage lh \ ? --cortex \ ? --C: Command not found.

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within individual multimodal correlation
by lorenzo pasquini 09 Sep '14

09 Sep '14

Dear Freesurfers, I am currently investigating the relationship between functional activation and cortical thickness at a within-subject vertex-based level. For this purpose I have mapped my activation on the vertex surface in the same subject. As you can see from the attached screenshot, I am able to visualize for the same vertex (e.g. coordinates vertex normal [0.97 -0.17 -0.14], curvature -0.190746) the value of the individual activation map (3.002379 on TkSurfer) and the individual cortical thickness value (2.61282 on FreeView). What I need, is for every vertex in my surface the activation value and the correspondent cortical thickness value to be able to compute a vertex-based individual correlation of both modalities. How ca I extract this information from my data? The activation map is saved in .w (paint format)... is it possible to extract such a matrix by saving my data in an other format? I have been trying read_annotation and other matlab commands as read_surf but could not access a matrix of vertex specific thickness/activation values. Is there a more elegant way to compute an individual correlation/general linear model in freesurfer (please note that the analysis in WITHIN a subject)? Or should I use softwares as SurfStat (http://www.math.mcgill.ca/keith/surfstat/)? Any help would be very appreciated, thanks, Lorenzo

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how to interpret a change in area of 0.004 mm² per year?
by Lars M. Rimol 09 Sep '14

09 Sep '14

Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: *intercept(random effect) + centered age + group + group x centered age + sex* I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this.... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Using fieldmap to correct EPI distortions
by Reza Rajimehr 09 Sep '14

09 Sep '14

Hi, I have a basic question, but the answer can be useful for others as well. I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So: My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan) My EPI data: fmc.nii.gz files in run folders Now I have three questions: 1) How can I unpack the fieldmap data? An example command ... 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful. 3) How will the undistorted volumes be used later on in the FS-FAST analysis stream? Your help would be very much appreciated. Thanks, Reza

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freesurfer commands from MATLAB
by Barbara Kreilkamp 09 Sep '14

09 Sep '14

Dear Freesurfers, Is there a way of calling freesurfer-scripts from within MATLAB? I know there are some setups needed to make MATLAB understand where it can find the commands (I have done this before with FSL). I am using bash, and when I type the Freesurfer commands in a terminal by hand, they work. So I am guessing it must have to do with setting up the environment: freesurf_path ='Applications/freesurfer'; setenv('FREESURFDIR',freesurf_path) setenv('FREESURFOUTPUTTYPE','NIFTI_GZ') curpath = getenv('PATH'); setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath)); Thanks a lot for any help, Barbara

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Re: [Freesurfer] QCACHE error
by Gayane Aghakhanyan 09 Sep '14

09 Sep '14

Dear list, I'm running longitudinal two stage model as is described in the tutorial here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel First, I've proceeded with longitudinal pipeline all my data, second, I've created longitudinal qdec table, and then, I've started to qcache my data, which after few seconds ends up with error: SUBJECT template_malfara fwhm 0 computing PC1 mris_calc -o /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh ./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div ./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh Saving result to '/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh' (type = MGH ) [ ok ] ERROR 1 : mris_calc compute percent change (pc1) problem? Please, could you give me a hint how I can overcome this error? -- Gayane Aghakhanyan, MD PhD candidate, Institute of Life Sciences Scuola Superiore Sant'Anna Piazza Martiri della Libertà Pisa 56127, Italy tel: +39 327 7013870 email: g.aghakhanyan(a)sssup.it

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Tracula reconstructed tracts quality
by Peggy Skelly 09 Sep '14

09 Sep '14

Hello Tracula experts, I was wondering if you could comment on the quality of the tracts reconstructed with our 1.5T data. These 2 files are from the same subject at 2 timepoints, processed in the longitudinal stream. Is much of the non-smooth look of the tracts due to the resolution of the dwi scans (1.8x1.8x4mm)? What could be the source of the diagonal lines/gaps in the tracts seen in tp1 when viewed from above? Thanks, Peggy

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hippocampal subfields: from posterior to binary masks
by Luigi Antelmi 09 Sep '14

09 Sep '14

Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages) that operates by summing up all the greyscale values <https://github.com/neurodebian/freesurfer/blob/master/GEMS/kvlQuantifyPoste…> (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. <http://www.ncbi.nlm.nih.gov/pubmed/19405131>, I can *"assign each voxel to the label with the highest posterior probability"*. Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find *t* such that: where *H* is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi.

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