Re: [Freesurfer] Mri_concat: initial frame ok but noisy in output image

there's no real concatenation). Also, make sure that the bad subject in the mri_concat output is the same subject that you are looking at individually; you could be off by 1. doug Agnieszka Burzynska wrote: Dear experts, I used mri_concat to concatenate sig.mgh files from fixed-level

Re: [Freesurfer] DOF and smoothing in mri_glmfit

, Aga On 7/7/11 5:14 PM, Agnieszka Burzynska burzyn...@mpib-berlin.mpg.de wrote: Thank you! I think I will just try it out: now run it as it is but also run the 1st level with smoothing, as I need to add some contrasts anyway. Then I should also know the difference between volume and surface

[Freesurfer] ERROR: dimension inconsistency in source data

Hi, I am sorry to re-post this problem, but I cannot find the source of my problem: During sampling the feat data to fsaverage using for example: mris_preproc --target fsaverage --hemi lh --out 3runs/lh.cope1.mgh --iv run1.feat/stats/cope1.nii run1.feat/reg/freesurfer/anat2exf.register.dat

[Freesurfer] Mri_glmfit ERROR: dimension inconsistency in source data

Hi, During running fixed effects glm to combine runs, the analysis of all but one subject went fine. The log file contains this error message: mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval

[Freesurfer] Viewing a multi-frame image?

Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz

Re: [Freesurfer] Viewing a multi-frame image?

Dear Doug, Yes, it works, thank you so much! Cheers, Aga On 7/7/11 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Aga, try View-Configure-Overlay. The config window will have a time point entry at the top. doug Agnieszka Burzynska wrote: Dear all, I created a 3-frame image

[Freesurfer] DOF and smoothing in mri_glmfit

Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label

Re: [Freesurfer] DOF and smoothing in mri_glmfit

. At the group level, this is not such a big deal because you're either not using the varcope or you are using it as a weight. doug Agnieszka Burzynska wrote: Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I

Re: [Freesurfer] fMRI data from FSL into Freesurfer: is my workflow correct?

Dear Doug, Thank you again very much for your help. I am replying with a delay because I was travelling. Please see my questions comments below in the text: On 5/10/11 5:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Agnieszka Burzynska wrote: Dear Doug, Thank you a lot for your

Re: [Freesurfer] fMRI data from FSL into Freesurfer: is my workflow correct?

Dear Doug, Thank you a lot for your reply! Yes, I did use reg-feat2anat and registered example_func to the subject's anatomical. As far as I understand it, then the registration matrix can be used for a contrast of interest. That's great news that the software version will not be a problem. I

[Freesurfer] autorecon1 after Talairach correction: can I re-run other than with -notalairach?

Dear all, For one of my subjects I had to correct the Talairach step manually. My manual correction, however, may not be perfect. Is it possible to re-run autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the automatic registration? Thank you! Aga

[Freesurfer] average p-value from an ROI

Dear all, I have a follow-up question to the previous discussion (correction for behavioral varialbles in qdec Tue, 04 Aug 2009. Is there an option to extract the average p-value from a ROI? After a group analysis I specified ROIs at p 0.001 and extracted the mean cortical thickness, the peak

[Freesurfer] FSL and freesurfer: combine runs in volume or on surface?

Dear all, I am trying to figure out how to bring my fMRI data from FSL to the freesurfer surface. The way I understood it from the tutorial 3.0 Surface-based Group Functional Analysis( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) There are two possibilities of combining

Re: [Freesurfer] Label sizes, min ROI size

wrote: Try something like this mri_segstats --slabel fsaverage lh path/to/lh.yourlabel.label --sum lh.yourlabel.sum The 4th column of the summary file will have the Area in mm^2 doug Agnieszka Burzynska wrote: Dear experts, I have 2 questions: 1) I created labels for some ROIs

[Freesurfer] Label sizes, min ROI size

Dear experts, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage

[Freesurfer] Calculating ROI size from label, min ROI size

Dear all, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage surface).