Re: [Freesurfer] recon-all for multiple subjects

Dear All, This worked for me... for x in SZ1 SZ2 SZ3 do recon-all -i $x.nii -s $x -all -hippo-subfileds done Thanks for your valuable inputs... From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Watson, Christopher christopher.wat...@childrens.harvard.edu

[Freesurfer] Missing pial surface right hemisphere for multiple subjects

Dear FS, I just started reanalyzing my data using FS5.3 (based on your feedback) after experiencing problems in the 5.0 version. Here however, I'm having a new problem: the pial surface of a number of subjects is missing only for the right hemisphere, while the white matter surface looks

Re: [Freesurfer] how does norm.mgz affect the behavior of mri_pretess?

Hi David there are situations in which mri_pretess can elimate pathological configurations by removing/adding any one of a set of voxels. In those cases the norm is used to decide among them (e.g. to remove the one that appears least like WM or to add the one that appears most like WM)

Re: [Freesurfer] how does norm.mgz affect the behavior of mri_pretess?

Thanks, Bruce! -David On Tue, Sep 10, 2013 at 5:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi David there are situations in which mri_pretess can elimate pathological configurations by removing/adding any one of a set of voxels. In those cases the norm is used to decide among

[Freesurfer] controlling for age in qdec

raw_age.fsgd Description: Binary data Dear Freesufer experts. I am trying to run attached fsgd file in qdec or in GLM-fit. I just want to do a group comparison in which I compare cortical thickness between groups controlling for age. when I run the analysis with age as a raw score - the

Re: [Freesurfer] controlling for age in qdec

Hi Olof, did mri_glmfit actually run with the FSGD file? The format is not correct. How did you convert your age variable to z? In particular, how did you demean them? Did you compute the mean on a group basis or for all subjects? What was your mri_glmfit command line? doug On 9/10/13

Re: [Freesurfer] convert .mgh to .label?

Gotcha, so you mean run mri_concat --conjunct on the original .mgh files first, and then use mri_surfcluster to extract labels from the finalized .mgh. By the way, mri_annotation2label works like a charm! -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT

Re: [Freesurfer] statistically truncate negative values

Hi Maya, you could create 3 separatestacks with isxconcat-sess (A, B, A-B), then create the mask you want with mri_binarize, something like mri_binarize --i A.nii --min 0.1 --mask B.nii --mask-thresh 0.1 --o A-and-B.nii Then use this as the --mask input to mri_glmfit. You should also

Re: [Freesurfer] z-scores age

When QDEC runs, it creates a y.fsgd file. Can you send me the y.fsgd for each design? doug On 09/10/2013 04:13 PM, olof lindberg wrote: Dear Douglas, no I did not run in GLM-fit - I run in qdec The conversion into z-scores was done in a statistical program (statistica) and was

Re: [Freesurfer] TALx coordinates

It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am

[Freesurfer] TALx coordinates

Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the

Re: [Freesurfer] TALx coordinates

Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N

Re: [Freesurfer] [martinos-tech]

Hi Suzanne, I'll cc the FS list so others can benefit ... On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote: Hi Doug, I have two follow-up questions to enhance my own understanding of Freesurfer. I know that MC simulations take into account the smoothness of the data. I noticed that the

Re: [Freesurfer] Number of independent vertices and Bonferroni correction

You can compute a vertexwise correction using gaussian random fields (instead of using clusters). This is done with mri_glmfit-sim, thought I don't think that many people use it. doug On 09/09/2013 09:11 AM, Bruce Fischl wrote: Hi Damien Doug can correct me if I'm wrong, but I don't think

Re: [Freesurfer] Editing WM

Hi Francesco, Could you maybe send a snapshot of the brainmask and wm volumes where you are seeing this? If you deleted any voxels on the wm mask then they should be a value of 1. You might want to look at the ?h.orig.nofix surfaces to see if that area in question looks better (or at least

Re: [Freesurfer] V1 label

How did you do the transfer? What was your cmd line? doug On 09/10/2013 05:31 PM, krista kelly wrote: Hello, I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the

Re: [Freesurfer] TALx coordinates

Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]';

[Freesurfer] statistically truncate negative values

Hi All, I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I

[Freesurfer] talairach transforms

after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12 Terminal window display was as shown bellow Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: