Re: [Freesurfer] skull striping error question

Even the Supratentorial volume ? Supratentorial volume includes some structures outside the surfaces ? Thanks Subha - Original Message - From: Bruce Fischl Sent: 10/23/13 01:13 PM To: Subhabrata Chaudhury Subject: Re: [Freesurfer] skull striping error question You should be fine if the

[Freesurfer] skull striping error question

Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will

[Freesurfer] volume of subcortical structure calculation

Hello Where can I get information on how freesurfer calculates volumes of subcortical structures ? Is there a paper which provides insights into this method ? Is it that for certain subcortical structures, it just counts the number of voxels and adds them up since the voxels are 1mm3 ? Thanks

[Freesurfer] 2D smoothing kernel and cluster size

Hi All, When we say FWHM 10, does that mean a circle with a radius of 10 mm ? Also I have some significant clusters from my analysis, will the area of the cluster be in mm2 ? How is the area of a significant cluster calculated ? I mean the math behind it. Is it mapping the cluster to the 1mm3 v

[Freesurfer] first level glm analysis on surface space

Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take eac

Re: [Freesurfer] combining masks in freesurfer ??

can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: > Hi All, > Is there a way to combine multiple binary volumetric masks into a > single binary volumetric mask in freesurfer ? >

[Freesurfer] combining masks in freesurfer ??

Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

[Freesurfer] volume and mean value of a custom made white matter ROI

Hello Everyone, Greetings. I am learning freesurfer tricks. I am stuck and have a question. I have run 10 subjects through freesurfer. I have made custom volume regions for arcuate fasciculus for 10 subjects. Now I want to get some measurements inside this region. How do I get the volume of

[Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface

Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you S

Re: [Freesurfer] question about glm setup

about glm setup Hi Subha, yes, you can. You will need to create a table in the format with QDEC expects. Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis doug On 5/4/13 11:31 AM, Subhabrata Chaudhury wrote: Hi, I am new to freesurfer. I have

[Freesurfer] question about glm setup

Hi, I am new to freesurfer. I have run reconall on 50 AD subjects. I have also run recon-all -qcache. So I have the following - 1) Whole brain thickness map for each AD subject 2) age of each subject 3) gender of each subject 4) clinical score of each subject I DO NOT have control subjects.