[Freesurfer] TRACUAL eddy_correct Usage

External Email - Use Caution Hello, I notice that within TRACULA 6.0 that eddy_correct is used for the eddy current correction. This is an older tool as compared to eddy, is there a reason that eddy_correct is still used? Have you done cross comparisons between eddy_correct and

[Freesurfer] mri_convert

freesurfer 6 and 5.3.0 - HCP 2) Is there any way that I can download/install the newer version of mri_convert used for freesurfer 6 within 5.3.0 - HCP? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S

Re: [Freesurfer] Continuous co-variate by continuous co-variate interaction effects

Hi Doug, Yes thank you this was my contrast matrix, not my design matrix. I've taken your advice by multiplying the co-variates together. Thanks for the help! -Tim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Continuous co-variate by continuous co-variate interaction effects

is as follows: 0 0 1 1 0 0 0 0 0 0 1 1 Is this correct? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ Freesurfer

Re: [Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model

Doug, That did it! Thank you so much for your help! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Wed, Dec 21, 2016 at 12:47 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > your 10th colu

[Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model

qdec file, fsgd file, and design matrix. Any help would be extremely beneficial. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 0.000 1.000 0.000 0.000

[Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model

Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000

[Freesurfer] Trouble with Two Stage Longitudinal Analysis

lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry

[Freesurfer] Trouble with Two Stage Longitudinal Analysis

, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 1.000 0.000 0.000 0.000

[Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

lay/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota

Re: [Freesurfer] Cluster Color

It seems that this message has been ignored. I really do need an answer on this. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer

[Freesurfer] Longitudinal Stream on HCP Data

Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

I file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) -- Forwarded m

[Freesurfer] Longitudinal Stream on HCP Data

-archive.com/hcp-users@humanconnectome.org/msg03477.html. <http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html> Are there any workflows or development versions that I can download in order to perform something like this. Respectfully, -Tim Timothy Hendrickson Department of Psyc

Re: [Freesurfer] Two Stage Longitudinal Model

illCondMatrix_twoStage_years_10_31_16.txt. Additionally I've included my fsgd file for stage two and my qdec file for stage one. Any assistance would be extremely helpful, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) Normalized matrix

[Freesurfer] Two Stage Longitudinal Model

t" command and using that co-variate data to input into the FSGD file? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] mri_glmfit --pvr Assistance

that it must be done via command line with mri_glmfit and the --pvr flag. I am confused as to what sort of file I should input into the --pvr flag (do I run a separate analysis?, etc). Any advice would be extremely helpful. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry

[Freesurfer] Performing GLM within a Mask Specified by Another GLM

that the best thing to do is to set a mask representing the clusters from the first GLM and then run the second GLM on the mask. Is this a reasonable thing to do? What steps/commands would I perform in order to do something like this? Respectfully, -Tim Hendrickson Timothy Hendrickson Department

[Freesurfer] Design Matrix Creation

olumns 1-16 model the intercepts for all your classes >Columns 17-20 model the ages for your gender-x-diagnosis subclasses >Columns 21-24 model the ICV for your gender-x-diagnosis subclasses On 07/06/2016 02:04 PM, Timothy Hendrickson wrote: > Freesurfer Support, > > Thank you for

[Freesurfer] LGI Summary Statistics

like this for LGI? If I take the mean of all of the ROIs would that be equivalent to a hemispheric LGI measure? Thanks! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing

[Freesurfer] Design Matrix Creation

1 somewhere in columns 1-8 to indicate the class >(ie, site/dx) that the subject is in. On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > Hi Doug, > > Thank you for such a prompt response. Just to be clear you are > recommending that I manually create the matrix file right? > >

Re: [Freesurfer] Design Matrix Creation

like [0 0 0 0 0 0 0 0 1 -1] On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > Freesurfer Support, > > I'd like to create a design matrix for a group analysis outside of the > DODS and DOSS models. I understand that in order to do this the -X > flag must be used. However,

[Freesurfer] Design Matrix Creation

-- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] Cluster Color

I'm just following up on this e-mail. I have not heard anything yet. -Tim On Mon, May 9, 2016 at 3:16 PM, Timothy Hendrickson <hendr...@umn.edu> wrote: > Free Surfer Support, > > I have been using the command line version for group analysis since my > data set has too man