[Freesurfer] Problem with preproc-sess per-session and question about registration

Hi, I have two short questions concerning motion correction using preproc-sess and registration files 1) Running preproc-sess using per-session as e.g. like this preproc-sess -per-session -fwhm 0 -sliceorder siemens -surface vpID lhrh -s vpID -fsd bold -mni305 should result in a "fmc" output st

Re: [Freesurfer] fsaverage error - too many levels of symbolic links

Hi, Thank you for your suggestions Doug and Dan. Moving my subjects directory outside of the freesurfer tree and deleting the symbolic link and then recreating it as per the instructions at www.freesurfer.net/fswiki/FsAverage seem to have sorted the problem. Best wishes, Clare __

Re: [Freesurfer] Problem with covariates in design for surface based analysis

Charlotte, There is no difference, from a statistical perspective, of nuisance factors and covariates. The key questions are: (1) Do any of these covariates have a differential effect on thickness between groups? (2) Do you want to compare the actual group means or the covariate-adjusted group me

Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.

Thank you Allison, however, I checked the website and it is said that FreeSurfer transform the orig volume to the MNI305 atlas, so the spatial normalization in FreeSurfer is still done in volume space but not in surface space, right? Best, Xiangyu On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens

[Freesurfer] Question regarding sig.mgh

Dear All, 1)I would like to know what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the:  mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I

Re: [Freesurfer] mri_convert

Hi Jimmy, I think the problem, if you can call it that, is with fslview. Below is from our FAQ. See if that makes sense. doug Q. Why would the orientation of my scans look wrong after processing my DICOM files with 'mri_convert'? A: It can be misleading to check orien

Re: [Freesurfer] mri_convert

Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it wor

[Freesurfer] treatment of missing values in mri_glmfit

Hi, we´re running FS 5.1 and have a data set with a lot of missing values. There are different subsets of persons missing different values of interest, and we´re running analyses on concat files. mri_glmfit not qdec). Is there anyway we can run analyses w/ missings in the fsgd file? Best

[Freesurfer] REPOST: MNI coordinates

Hi, I am trying to find a way to get the segmentation/cortical label (to determine corresponding brain structures) in MNI space for a cluster for which I know the MNI coordinates. How can I do this? Many thanks. Antonella___ Freesurfer mailing list

Re: [Freesurfer] REPOST: MNI coordinates

You could register T1.mgz to MNI 1mm, invert the transformation and then map the cluster in MNI to Freesurfer space. Best, Martijn Verstuurd vanaf mijn iPhone Op 24 feb. 2012 om 22:19 heeft Antonella Kis het volgende geschreven: > > Hi, > > I am trying to find a way to get the segmentatio

Re: [Freesurfer] mri_convert

Oh, the problem may be in your label2vol cmd. Try this one mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/

Re: [Freesurfer] Frontal signal drop out

Dear Freesurfer Experts, Would it be easier to upload a typical example of the data I am trying to salvage, in order to get some hints on how I might proceed with this problem of loss of frontal signal drop off ? Thanks in advance. Mahinda On Thu, Feb 23, 2012 at 2:06 AM, Mahinda Yogarajah wro

Re: [Freesurfer] Frontal signal drop out

Hi Mahinda, I can take a look if you want to upload a dataset. Please find the instructions to upload in this wiki. http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Sita. On Sat, 25 Feb 2012, Mahinda Yogarajah wrote: Dear Freesurfer Experts, Would it be easier to upload

[Freesurfer] last index missing when using mri_label2vol

Hi, I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the final label from the color table file. I tried using the --thresh 1 option, but that didn't work either. i.e... mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o custom_lh.nii.gz --subject FREESURF

[Freesurfer] volume size

Hi - I would really like to use a volume size greater than 256^3. I know of all the options and reasons. what I want is a white matter surface than has fairly evenly spaced nodes that are in approximate match to the voxels they enclose. the reason is to seed, track and target using FSL surface

Re: [Freesurfer] volume size

sorry - re this: in principle, is freesurfer particularly sensitive to the orientation of the brain? It might fit in 256^3 if I rotated it. then I could rotate the surfaces back when I import to CARET. It was, actually, rather hard to get a good surface last time. it seemed that freesurfer needed