Re: [Freesurfer] Units of GI

Hi Bruce, As per this paper: https://elifesciences.org/articles/29285#abstract (Figure 1—figure supplement 4), Local GI is ratio of two quantities and as per this http://en.citizendium.org/wiki/Gyrification, GI is also ratio of two quantities. So both GI and LGI should be 'unitless' as per these

Re: [Freesurfer] Units of GI

Are you confusing GI with LGI? > On Dec 22, 2017, at 4:33 PM, Martin Juneja wrote: > > Hi, > > I came across several papers e.g. > http://www.sciencedirect.com/science/article/pii/S2213158215000856 where > gyrification index (GI) is indicated in 'mm'. > > By definition GI

[Freesurfer] Monte-Carlo f-test

Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for F-test? The doc says that it synthesizes a z map (I assume from a normal distribution) for computing the voxel-wise thresholds and cluster size distribution. Maybe I am wrong with my stats but I

[Freesurfer] Monte-Carlo correction and 3-groups comparison

Hello all, I am running a gyrification analysis between 3 groups. So I modeled my GLM like the one on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V I was wondering if it is correct to run a Monte-Carlo correction on the

[Freesurfer] Units of GI

Hi, I came across several papers e.g. http://www.sciencedirect.com/science/article/pii/S2213158215000856 where gyrification index (GI) is indicated in 'mm'. By definition GI is the ratio of two quantities: inner contour/outer contour (http://en.citizendium.org/wiki/Gyrification), therefore,

Re: [Freesurfer] the comand of 'segmentHA_T1_long.sh' is not found

Hi Gallen, segmentHA_T1_long.sh is only available in the freesurfer dev version. Also, if you’re getting the glibc license error while using the martinos freesurfer distribution, I will message you directly to sort this out. best, Andrew On Dec 22, 2017, at 3:11 PM, Gong, Liang

[Freesurfer] the comand of 'segmentHA_T1_long.sh' is not found

Hi, I just completed a longitudinal stream preprocessing job using Freesurfer5.3, and I want to further analysis on hippocampal subfields. I see the manual in the following link: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, Okay, I just updated the script at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface. Let me know if the issue continues. best, Andrew On Dec 22, 2017, at 9:25 AM, M del Mar Velasco >

[Freesurfer] OpenGL link errors

I posted this to the Freesurfer github site, but didn't exactly know if that was the most appropriate place. The Freesurfer build fails at this command: libtool: link: g++ -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mris_show mris_show.o

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, I am sorry for insisting, but I have found a new mistake in your new version of make_average_surface. rh.medial_wall.label contains 13733 vertex, it is a desired result. However, rh.cortex.label contains all 163842 vertex, i.e, it covers medial wall area too. That's why we still have the

[Freesurfer] "Normal MRI pictures"

 I would like to analyze clincial structural MRI exams with help of Freesurfer. Is it generally possible without applying special protocols or is it completely useless? Grateful for any hints Gernot ErnstKongsberg, Norway___ Freesurfer mailing list

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Lanbo, you could look at longitudinal changes of the left-right difference in volume per ROI. Or do you mean on the cortical thickness map (I have never done that, but probably works similarly, construct left -right registration, compute difference, then run the LME on that). Best,

Re: [Freesurfer] Longitudinal MRI but different scanner

Hi Shane, not really. You can of course run images through the stream. You will get measurements, but you will not know how much of that is caused by the scanner or by disease (or drug,etc). If you have 2 groups, you could model the scanner as a co-var, but there could be a group scanner