Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Trouble running TRACULA on tutorial data
by Philip Lindner 24 Sep '14

24 Sep '14

Hi Freesurfers, I am having some trouble running TRACULA on the tutorial data that I downloaded from the site ("diffusion_recons" and "diffusion_tutorial" sets). The first step, trac-all -prep, finnishes without error (at least it claims so), yet when I try and run the second step, trac-all -bedp, it complains about "/diffusion_tutorial/elmo.2012/dmri/data not found" and exits. The file referred to, /diffusion_tutorial/elmo.2012/dmri/data.nii.gz, seems to be a symbolic link. Does anyone have any suggestions? TRACULA appears to be the perfect tool for my research questions so I would much appreciate any feedback that would help solve this problem. Cheers, Philip Karolinska institutet, Sweden

2 1

DWI questions
by Gabriel Gonzalez Escamilla 24 Sep '14

24 Sep '14

2 1

tracula -prep fails at mri_convert
by Peggy Skelly 24 Sep '14

24 Sep '14

Hi, I'm processing 3T data with 60 direction vectors and 2 images with b-val = 0. Trac-all -prep has been failing at the command: > mri_convert --frame 0 31 <my_subj>/dmri/dwi.nii.gz <my_subj>/dmri/lowb.nii.gz > mri_convert: extra argument ("<my_subj>/dmri/lowb.nii.gz") > type mri_convert -u for usage Since --frame seems to only want one value, but we have 2 images with low b values. Has anyone encountered this problem before? Peggy

2 1

bbregister with T2 in trac-preproc
by Barbara Kreilkamp 24 Sep '14

24 Sep '14

Dear Freesurfers, I would like to alter the trac-preproc to include an EPI to T2 registration (diffeomorphic) as I do not have a field map, is there a way of doing this? I saw that bbregister actually only uses 6 doF. Thank you very much, Barbara

2 1

trac-all
by BigBen2293＠web.de 24 Sep '14

24 Sep '14

2 1

trac-all: saving tensor in dtifit
by Barbara Kreilkamp 24 Sep '14

24 Sep '14

Dear all, I would like to make amendments to the FSL dtifit call during trac-preproc. In which way can I edit the call in trac-preproc? # LS tensor estimation set cmd = dtifit set cmd = ($cmd -k $dwidir/dwi.nii.gz) set cmd = ($cmd -m $brainmask) set cmd = ($cmd -r $dwidir/bvecs) set cmd = ($cmd -b $dwidir/bvals) set cmd = ($cmd -o $dwidir/dtifit) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $fs_time $cmd |& tee -a $LF if ($status) goto error_exit endif The background is that I would like to save the tensor file for being able to correct the tensor to be positive-definite (not possible within FSL). Then I would have to map the scalar outputs of the tensor fit (originating from the new corrected, positive-definite tensor) to the MNI template after that (would it be sufficient then to re-run step 1.7 in trac-all)? Thanks a lot Barbara

2 1

Scatter plot from mri_glmfit analyses
by Celine Louapre 24 Sep '14

24 Sep '14

Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: > Hi > > I am trying to calculate correlation coefficient using freesurfer GLM > for associations between volumes and IQ. I found this ealier answar, > but the matlab script but the link appear to be dead. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html > > Best regards > > Knut J > > > > > _______________________________________________ > 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 gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Map both hemisphere to lh of fsaverage_sym
by ting xu 24 Sep '14

24 Sep '14

Dear FreeSurfers, I have data has been recon-all analyzed. I would like to compare the symmetry of function/structure property between LH and RH, such as cortical thickness. I already know that the vertices in the left hemisphere are not correspond to vertices in the right hemisphere. I would like to know the exactly symmetric vertex for both hemisphere. Thus the question is, how can I register both hemisphere to one hemisphere of fsaverage_sym, then compare them? I followed the instruction: xhemireg --s sub001 surfreg --s sub001--t fsaverage_sym --lh surfreg --s sub001/xhemi --t fsaverage_sym --lh --xhemi then here is the error: MRISread(/data/sub001/xhemi/xhemi/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file /data/sub001/xhemi/xhemi/surf/lh.sphere No such file or directory Thank you in advance for any suggestion! Regards, Ting

2 1

longitudinal analysis and linear mixed effects models
by Emma Thompson 24 Sep '14

24 Sep '14

Hi FS, I want to conduct a within-subjects longitudinal analysis, I thought I would be able to run a LME model in QDEC but this doesn't seem to be the case at all, is this correct? It seems I have to do everything using Matlab (big sigh). https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels I have already preprocessed the data: 1) cross for all time points, 2) base, and then 3) long according to the awesome tutorial provided by FS. I have only one group, a patient population that was scanned prior to (bseline) and at various time points (3 time points post) following treatment. Would you agree that the best analytical approach for me would be the LME model, especially since I have a few subjects with a couple of missing post-treatment time points? Is there any way you would recommend another approach using QDEC? Lastly, I have done everything in FS version 5.1, I'm considering upgrading to 5.3, since my freeview software seems to be out of date. It also seems that the Matlab tools I need to run LME are only available in FS version 5.2. At this point a little concerned since I'm hoping I didn't waste a bunch of time just realizing all this now, would upgrading to 5.3 negatively impact all the work I've done thus far using version 5.1? Thanks for the help!!

3 2

Volume to surface coordinates
by Michael WOODMAN 24 Sep '14

24 Sep '14

Hello freesurfers, I would like to identify, in surface/vertex coordinates, certain points in a volume. Is there a straightforward way to obtain relevant transform? Thank you, Marmaduke Woodman

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Freesurfer September 2014