[Freesurfer] v5.1 control point mri_ca_normalize bug

Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the -nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize

Re: [Freesurfer] sequence advice for GE 750 & 8-channel coil

Hi Antonio, You can find information on recommended scanning protocols here: http://martinos.org/~andre/ These scans are designed to have good contrast between gray and white matter, so that results can be more easily processed in FreeSurfer. Although this page is mostly focused on Siemens scanne

Re: [Freesurfer] Visualizing individual ROI labels

Use mri_annotation2label to break the annotation up into labels, then use mris_label2annot to create a new annotation with just the labels you want. On 10/05/2014 09:17 AM, Bruce Fischl wrote: > Hi Elissa, > > you can load the labels into tksurfer or freeview and give them > whatever color you

[Freesurfer] Freesurfer troubleshooting for ageing data

Hello fellow Freesurfer user, I am currently working on an ageing data set (~60 subjects between 19 to 81 years old). I mainly want to use Freesurfer for two different things: 1. get a cortical and sub-cortical segmentation to use those regions for a connectivity analysis 2. use the WM/GM b

[Freesurfer] excluding labels from analysis

Hi all,I would like to exclude user-defined labels from the analysis. As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the new annotation file be inco

Re: [Freesurfer] Gyrification index vs cortical surface area

Hi Knut: Gryification and Surface Area are two completely different things. Surface Area, as measured by FreeSurfer, gives you the area of the surface (roughly length x breadth) of a given region of interest: e.g., Pars triangularis. It is measured in millimeter squared. Gyrfication index, by con

Re: [Freesurfer] Any ideas on how to automatically measure maximum thickness(diameter) of lesions?

Hi Sooyun what kind of acquisitons do you have? For just T1 we probably don't have anything. If you had a T2 or FLAIR we do have some tools, but they are not distributed/documented/tested/etc yet. sorry Bruce On Mon, 6 Oct 2014, 조수연 wrote: Hello, dear fellow Freesurfers. I was wond

Re: [Freesurfer] White matter and white matter lesions

Hi Leise the numbers come from our color lookup file that is in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Mon, 6 Oct 2014, Leise Borg wrote: > Hi Douglas > > Thanks for your answers. > I have two more questions: > 1) In which file(s) do I find the labels 151-255? > 2) What do th

[Freesurfer] Any ideas on how to automatically measure maximum thickness(diameter) of lesions?

Hello, dear fellow Freesurfers. I was wondering whether there was any way to automatically measure the longest or the maximum length(or thickness or diameter) of cortical lesions. By this I mean that if there were to say 3 distinctive lesions in the brain of the patient, each with 1mm, 2mm, 7mm

Re: [Freesurfer] Transform MNI-space segmentation into Subject-space

thank you much for your replay, but i am not sure how to use "spmregister" or "fslregister" for this purpose, becouse i want to get my MNI ROI's into the subject space, and i only have the transeformation from the subject space to the MNI space (instead of the inverse- from MNI space to the subject