[Freesurfer] ANOVA in QDEC

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Is there any way to convert Freesurfer thickness files to SPM readable format? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi

[Freesurfer] Job opening: Biomedical Imaging Laboratory at Hospital Gregorio Marañon (Madrid, Spain)

Job available at the “Biomedical Imaging and Instrumentation Group (BiiG)http://image.hggm.es/index.php?lang=english”, Madrid. The “Biomedical Imaging and Instrumentation Group (BiiG)http://image.hggm.es/index.php?lang=english ”, is offering a position in system administration and programming

[Freesurfer] Longitudinal Freesurfer TRACULA quality control

Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per

Re: [Freesurfer] V1 Labels (fwd)

Hi again, I apologize for all of the emails, but I'm really trying to figure out what this labelling problem is. I've gone through all of my participants and for most of them, the talairach is fine and the voxel size is 1 x 1 x 1mm, so having a high resolution cannot be the problem, unless the

[Freesurfer] atlases labels coordinates

Dear all, I need the center coordinates of the anatomical labels from the desikan and destrieux atlases. I saw a similar post a while ago in which it was recommended the following: #1 Convert the annotation to a set of labels. This is for the Desikan atlas, but you can spec the destrieux

[Freesurfer] Normalization for brain/head size differences in a pediatric population

FreeSurfers, I have a couple of questions regarding normalization for brain/head size. We are trying to analyze a pediatric population with subjects between age 4 and 16 with variable brain (and head) sizes. We are mainly interested in measuring cortical thickness in these children, but not sure

Re: [Freesurfer] Longitudinal Freesurfer TRACULA quality control

Hi Vincent, for the surface based analysis (SBA) base and long runs need to be correct. You mainly need to do potential edits in the base. For a full description of potential manual edits (and where to make them) see: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits If you edit base,

[Freesurfer] LGI radius

Hi freesurfer experts is it possbile to change the radius for the LGI computation. ( it's normally set at 25 mm) we waned to try computing the LGI with a smaller radius. I looked the in the compute_lgi.m file, and it does not use radius, (even though radius is an input parameter for it) Thanks

Re: [Freesurfer] Longitudinal Freesurfer TRACULA quality control

Hi Vincent - I'll take on the tracula-related parts: 2. For tracula, the part of the recon-all output that matters is the aparc+aseg. The surfaces will play a role only the DWI-to-T1 registration (assuming you opt to use bbregister). 3. It's important to check your DWI data for obvious motion

Re: [Freesurfer] bvecs and bvals don't have the same number of entries

Hi Laura - Were these bval/bvec files created on windows or with excel by any chance? When you view them in unix (with the more command for example) you'll see an ^M character instead of every end-of-line. Can you try editing these files in a unix editor to fix that? Let me know if this

Re: [Freesurfer] LGI radius

Hi Jon, The fastest way is probably to change the radius value on row 40 in mris_compute_lgi. We originally intended to make an option for setting the radius, but I realize that we forgot it in the end. I'll see if we can change it for the next version, but in the mean time change the value