[Freesurfer] Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC

Postdoctoral Position in Neuroimaging – Quantitative Neuroimaging Laboratory (QNL), Cognitive Neuroscience Division, Columbia University, NYC *Job Summary:* QNL invites applications for a full-time postdoctoral position to conduct processing and analyzing of PET and MRI neuroimaging data, as

[Freesurfer] Curvilinear interaction with age

Dear FreeSurfer experts, I have a group variable (X) with two levels and I want to test if there is a curvilinear interaction with age (Z). Can this be tested in FreeSurfer? Specifically, the model would be Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error I want to test b5 while

Re: [Freesurfer] Curvilinear interaction with age

Hi Daniel, you can always specify your own design matrix X in mri_glmfit. So just create those columns, fit and test. Of course you need to make sure that the order of subjects in Y is identical with the one used in X. Cheers, Martin On 11/06/2015 06:14 PM, Yang, Daniel wrote: > Dear

[Freesurfer] Cortical thickness in the depth of a sulcus vs on top of a gyrus: Comparison

Dear FreeSurfer Developers, I have been wondering, if it is possible to compare cortical thickness in the depth of a sulcus with the the cortical thickness on top of the gyrus? I found the curvature maps in subjects' folders but I don't know how to proceed. I would be very thankful for every

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Dear Ruopeng, I tried different computers and on most of them it works when I test-delete a wm voxel and then save the wm.mgz. However, when I then go on to actually editing the wm.mgz Freeview crashes when I hit "save" as it's done on my computer. I've tried not using the button but going

Re: [Freesurfer] Surface-based registration

Hi Ray try doing: setenv DIAG 0x04040 then run it again and send me the output Bruce On Fri, 6 Nov 2015, Razlighi, Qolamreza R. wrote: Dear Bruce, Thank again for your kind help. I’m running version 5.1.0.  Below is the output of the command. I also ran it with parea=0 but almost no

[Freesurfer] 3T or nuintensitycor3t

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej

[Freesurfer] R: Re: R: Re: average z-score of each subject from a common cluster

I have run mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.masked. nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum summaryfile and I have obtained 9 columns and 5 rows. I'm confused on results. Where is the mean z-score for cache.th13.neg. sig.masked.nii.gz? #

[Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST

I hope that this information are fine fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim11.00 pixdim21.00 pixdim31.00 pixdim40.00

Re: [Freesurfer] Cortical thickness in the depth of a sulcus vs on top of a gyrus: Comparison

Hi Pawel I would use the sulc and pick say the top tenth as the crowns and the bottom tenth as the fundi. Easy to do in matlab cheers Bruce On Fri, 6 Nov 2015, Wrobel, Pawel wrote: > Dear FreeSurfer Developers, > > I have been wondering, if it is possible to compare cortical thickness in >

Re: [Freesurfer] 3T or nuintensitycor3t

Hi Kasper, The -3T flag uses a special 3T atlas for Talairach alignment, as well as enabling the 3T-specific NU intensity correction parameters that are turned on using the -nuintensitycor3t flag. The -nuintensitycor3t flag only changes the NU intensity correction parameters, without using

[Freesurfer] Problems with mri_nu_correct.mni

Hi, I have just installed FreeSurfer, and I have problems running recon-all. The error log says nothing, only "exited with ERRORS" after running the following line:                          mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 

Re: [Freesurfer] Surface-based registration

did you try setting dist to .01 or something very small? Note that we don't register individual surfaces to each other for a reason - the inverse variance weighting in the warp functional is critical to it being stable and accurate cheers Bruce On Fri, 6 Nov 2015, Razlighi, Qolamreza R.

[Freesurfer] MNI coordinates for regions in aparc+aseg.mgz file

Dear FS experts, I would like to know the MNI coordinates of my ROIs obtained from recon-all (aparc+aseg.mgz file). For example what for coordinates has number 10 (left thalamus)? Are the coordinates of each region listed somewhere? Many thanks for your help Best wishes André

[Freesurfer] Tracula Processing Question

Hello FreeSurfer experts, We have a large dataset that was processed in FreeSurfer v 5.1 and we would like to run tracula on the dataset. Should we use the v 5.1 version of tracula to process the data? Or would it be acceptable/possible to use the v 5.3 tracula (with the v 5.1 processed T1

Re: [Freesurfer] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1

Hi Bruce, 1) I was also concerned 3mm may be too thick but I will try a few subjects to see how it goes. 2) Hi Eugenio I wanted to see if you can give a bit of insight into the hippocampal issue. 3) Bruce, sorry for the confusion. I was referring to sqrt(T1w*B1 x T2w*B1) ~ B1 bias field

Re: [Freesurfer] mri_convert and large values

I've put a new linux version here that works on the dicom you sent me ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert On 11/05/2015 11:27 AM, McMains, Stephanie wrote: > We are finding a conversion problem with our latest multiband/SMS data > (Using a sequence from

Re: [Freesurfer] R: Re: R: Re: average z-score of each subject from a common cluster

under the "Mean" column On 11/06/2015 07:46 AM, std...@virgilio.it wrote: > I have run > mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.masked. > nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum > summaryfile > > and I have obtained 9 columns and 5 rows. > I'm