Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Question about Longitudinal LME Modeling
by Karishma Smart 25 Sep '14

25 Sep '14

Dear Freesurfers, If I am planning to do a longitudinal analysis, I understand that the LME Model is probably the most appropriate choice. However, it says on the website that it is for univariate and mass-univariate analyses. I would need a longitudinal model that can handle *multivariate* statistics (a longitudinal study using multi-modal imaging + covariates). Can the LME model do this? If not, is there another way to do this in FreeSurfer? Thanks! Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015

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A question about spherical registration
by Reza Rajimehr 25 Sep '14

25 Sep '14

Hi, I have a question about spherical registration, and I couldn't find a relevant answer in the mailing list. I have two subjects S1 and S2 with corresponding functionals. I want to show the functionals of each subject on the surfaces of the third subject S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg files yet because these are monkey subjects and I did not want to register them to the buckner40.tif template. Since my goal is not group averaging, and it is just to map functionals to the same-subject anatomicals and then to the target-subject anatomicals, I was thinking of one of the following solutions: 1) Convert sphere of S3 to a template .tif file, then use mris_register to register spheres of S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Not sure if mris_make_template works for one subject though. 2) Make a template from "S1 and S2" through the procedure described at https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…. Then register S1, S2, and S3 to that template and generate sphere.reg for all the subjects. Which approach is recommended? BTW, I do not know of a monkey template that is based on the surfaces from a large group of monkeys. Thanks for any advice, Reza

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MNI Coordinates
by Venkataraman, Archana 25 Sep '14

25 Sep '14

Hi Freesurfer experts, I have a set of RAS coordinates in the Freesurfer fsaverage space. What is the easiest way to transform them to MNI152 space? Thanks. - Archana

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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

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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

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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

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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

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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

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