[Freesurfer] FDR clustr-level Correction

Hi Freesurfer experts I am doing FS-nonlinear volume based FC analysis with cluster-level correction. 1. Could you please point me which command can do the FDR cluster-level Correction? 2. If i do correction using MonteCalo cluster-based correction. Is it right like the following command

Re: [Freesurfer] Freeview

Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To:

Re: [Freesurfer] F test results

Dear experts, I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a F test on the cortical thickness but the output doesn't make sense as it covered the whole brain (please see attached). I used the following commands: mris_preproc --fsgd 3gps_IQ.fsgd --cache-in

Re: [Freesurfer] Freeview

Page up / down is moving the current slice up and down but it not flipping between the slices ?! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:21 PM To:

[Freesurfer] Freeview

Hi Freesurfers, I can't change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the

[Freesurfer] surface lines in manual edits

Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was

Re: [Freesurfer] Freeview

Got it! Thanks Iglesias -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:38 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re:

[Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim

Hello Freesurfer's experts, I used the group analysis clusterwise correction with glmfit-sim and I found that Annot field in Cluster Summary Table don't always fit well with the corresponding region on ?h.aparc.a2009s.annot file. How is determined precisely each localization of each cluster in

Re: [Freesurfer] Freeview

Weird! The up and down arrows should move the current slice up and down, whereas page up/down should change the slice... You can also click on the other views to change the current slice. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal

Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

You can run this command to incorporate the T2 image: recon-all -i /path/to/MEMPRAGE -T2 /path/to/T2 -T2pial -s subject_name -all After completing, this will produce ?h.pial which use the T2 image, and ?h.woT2.pial which are the same pial surfaces as recon-all without T2 input. Best, Lee On

Re: [Freesurfer] Trakula

Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote:

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error:

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Hi Prya, that is because MriCron is not that great at overlaying images that are in the same physical space but not in the same voxel space. You have two options here: 1. Use FreeSurfer's Freeview rather than MriCron to visualize the output. FreeView will correctly overlay the segmentation. 2.

Re: [Freesurfer] visualizing paths stats by voxel

Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that

[Freesurfer] cross and long in qdec

Hi, If I have a set of subjects from a study collected at time 0 (T0) and a subset of these subjects that also have data collected at time 1 (T1), can I run qdec on the T0 subject's with no T1 together with the longs of the subject's at T0 that have a T1? Thanks, P

[Freesurfer] nu_correct flag for memprage

Hi, For memprage data collected on a 3T scanner could you please let me know what nu_correct flag should be used for recon-all? Should we use -nuintensitycor-3T? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu