Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

FreeSurfer Labels for MNI template
by Ray Razlighi 25 Sep '14

25 Sep '14

Dear All, Is there any way I can get the Desikan-Killiany cortical and subcortical labels on MNI152 template. I know I can get a rough estimate using the linear transformation matrix "mni152.register.dat". I also find that the subject cvs_avg35 is non-linearly registered to MNI152 and given in the cvs_avg35_inMNI152 directory. But non of them are accurate enough for my purpose. I tried hopelessly to run the FreeSurfer on the MNI152 template itself and it failed. Any other suggestion is greatly appreciated. Best -- Ray Razlighi, Ph.D. Assistant Professor Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838

2 1

how to extract the individual cortical thickness or volume value of significant cluster after RFT correction
by wang kangcheng 24 Sep '14

24 Sep '14

Dear experts I have question regarding extracting the individual cortical volume value of significant cluster after RFT correction. I have 209 subjects in an analysis and G_pariet_inf-Angular showing significant correction with score of autism after RFT correction using command of mri_surfrft_jlbr in Matlab, how do I export individual subjects cortical volume values for significant regions ? In addition, I did not analyze it using QDEC and just use command following reference (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)Thank you and hope for responses. With best Regards,kangcheng Wang

2 3

Help on DTI pre-processing
by Gabriel Gonzalez Escamilla 24 Sep '14

24 Sep '14

2 1

Reporting of Significant Clusters
by Chris Wertz 24 Sep '14

24 Sep '14

Hi Freesurfers, I am curious about why in QDEC, when you correct for multiple comparisons and it spits out significant clusters with their cluster-wise p-values and annotations and then click on find clusters and go to max, it changes the annotation and coordinates of the previous output? I guess more importantly which cluster's annotation is more indicative of the centeroid of the significant cluster. For example after using the Monte Carlo Null-Z simulation I get a cluster that is labeled as the Pericalcarine and when I click on find clusters and go to max that same cluster is now deemed Precuneus? Thanks, Chris

1 0

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

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