Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

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

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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

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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!!

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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

2 1

watershed problem
by Anastasia Klimovich-Smith 24 Sep '14

24 Sep '14

Hello, I have some unexpected results from the mne_watershed_bem script that uses Freesurfer mri_watershed program. For one of my subject's the inner scull surface ( xxxx_inner_scull_surface in bem/watershed/) partially excludes cerebellum (the left screen shot). All my other subjects have cerebellum included into the inner scull (right screen shot). As a consequence later stage scripts (mne_setup_forward_model and mne_do_forward_solution) produce similarly erroneous inner scull surface delineation. Did anyone experience this problem before, and if so, how would you advise to fix it? For this subject MRI MP RAGE sequence was acquired using the 12 channel coil, which, compared to the 32 channel one used for other subjects, produced images of worse quality. However, I have other subjects with 12 channel coil scans and their inner scull surfaces were separated normally (including the cerebellum). Thanks, Ana

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Re: [Freesurfer] Vertex wise analysis and area/pial area/volume interpretation
by Las Blawimo 24 Sep '14

24 Sep '14

Dear experts, I had a question concerning the output of the Monte Carlo Z-simulation (abs) in Qdec. When I run the analysis, Qdec prints out a table including the max vertex, p-values, and coordinates of significant clusters. However, when I hit the button 'Find clusters go to max', qdec provides a different max vertex as well as different coordinates. I was wondering what is the difference between the coordinates. Which output provides the coordinates of the maximum significant vertex? Thanks in advance. Kind regards, Las Blawimo # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 3.881 94038 3103.57 * 37.7 23.7 40.4* 0.00010 0.00000 0.00020 5981 caudalmiddlefrontal 2 3.187 66622 905.91 *19.3 35.7 36.9* 0.03260 0.03030 0.03490 1421 superiorfrontal Simulation complete. ============================================================ Generating cluster stats using min threshold of 1.3... Found 2 clusters Contrast: 'rh-Avg-thickness-SensTOTAV-Cor', 10fwhm, DOF: 185 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 4.0000 49 3103.57 * 39.1 -9.6 60.8* 5981 precentral 2 1.4868 43 905.91 *22.0 16.7 50.8* 1421 superiorfrontal

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Segfault Error
by Nikita Zhitkevich 24 Sep '14

24 Sep '14

Hi, I am currently running Freesurfer on Linux and while trying to test it out on the bert subject I received the error message: ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu. I searched high and low for the .xdebug_tkmedit file but could not find it, as it seems the system is not even creating this file. Do you have any suggestions on fixing this issue? Sincerely, Nikita Zhitkevich

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