[Freesurfer] Multiple comparison question

Hi, We extracted volume measures from 7 ROIs in 2 groups and compared a) Mean of each ROI volume between group, and compared independently such as i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 and

Re: [Freesurfer] Multiple comparison question

t; > All the best, > > Anderson > > > On 2 February 2017 at 12:09, neuroimage analyst < > neuroimage.anal...@gmail.com> wrote: > >> Thanks, Anderson. If there are several other measures such as volume, >> thickness, FA, can I then put them in a single csv file an

Re: [Freesurfer] Multiple comparison question

erson M. Winkler" <wink...@fmrib.ox.ac.uk> wrote: Hi VM, Please see below: On 1 February 2017 at 02:38, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > We extracted volume measures from 7 ROIs in 2 groups and compared > a) Mean of each ROI

[Freesurfer] Cortical thickness to volume

Hi, Freesurfer Users. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the

[Freesurfer] Cortical thickness to AAL template

Hello, freesurfer users. Reposting the previous question again here. I would appreciate any response. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my

[Freesurfer] Fdr correction using command line

Hi, I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ? Thanks Regards MV ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Fdr correction using command line

nks Regards MV On Fri, Oct 7, 2016 at 1:11 PM, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > I was wondering if there is a way to perform fdr correction using command > line in freesurfer without using matlab as mri_glmfit-sim only does > bonferroni ? &

Re: [Freesurfer] Question about mri_glmfit-sim

te > that if your cluster p-value is much less than .05, then you're probably in > good shape. > > On 10/24/16 9:49 PM, neuroimage analyst wrote: > > Hi FreeSurfer experts, > > I am currently performing some cortical thickness comparisons in my group > of subjects and

Re: [Freesurfer] Fdr correction using command line

.harvard.edu > wrote: > try this binary > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr > > > > On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > > > Hi, > > > > I was wondering if there is a way to perform fdr correction using >

[Freesurfer] Question about mri_glmfit-sim

Hi FreeSurfer experts, I am currently performing some cortical thickness comparisons in my group of subjects and using mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces found some clusters that have significantly different cortical thickness values, Given Eklund et al

Re: [Freesurfer] Fdr correction using command line

t; positive indicates A>B. The F.mgh is the map of F values which are > unsigned. The gamma.mgh file will have the contrast values themselves > including sign. The sig.mgh will be the -log10(p) signed by the sign of > gamma.mgh at that vertex > > > On 10/12/2016 02:23 PM, neuroimage

[Freesurfer] Multiple comparison correction on subcortical volume

Hi, I extracted thalamic, caudate, and putamen volume (left hemisphere), and cingulate thickness (right hemisphere) from freesurfer's parcellation. Then I compare these volumes and thickness across two groups using R and found significant differences in these measurements. Do I have to correct

[Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage

Hi, I am attaching this message again and I wI'll appreciate if somebody could kindly comment on the approach. Thanks Regards -VM -- Forwarded message -- From: "neuroimage analyst" <neuroimage.anal...@gmail.com> Date: Dec 18, 2016 2:22 PM Subject: Register

[Freesurfer] Registering ASL-CBF maps to fsaverage

Hi, all. I want to register CBF maps derived using pCASL to freesurfer's surface and derive CBF values in the same regions where I report my cortical thickness, and volumes. Hence, I did the following: 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold

Re: [Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage

Thank you! Regards --VM On Wed, Dec 21, 2016 at 10:41 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > > On 12/21/2016 01:02 PM, neuroimage analyst wrote: > > Hi, Doug. > > > > Thank you for your response. > > > > _Step 1: _I think what

Re: [Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage

, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Sorry for the delay > > On 12/21/16 12:15 AM, neuroimage analyst wrote: > > Hi, > > I am attaching this message again and I wI'll appreciate if somebody could > kindly comment on the approach. > > Thanks > >

[Freesurfer] cortical label mask fro mri_glmfit

Hi, I am just curious whether the mask.mgh file returned in glmdir folder created from lh.cortex.label? If so, how can I create my own surface mask from the label file? (mri_label2vol and mri_vol2surf ?) Second: How can I compare the subcortical volumes between the 2 groups using glm tools in

Re: [Freesurfer] cortical label mask fro mri_glmfit

other. Am i right? thanks regards VM On Thu, Dec 22, 2016 at 11:32 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > > On 12/22/2016 01:33 PM, neuroimage analyst wrote: > > Hi, > > > > I am just curious whether the mask.mgh file returned in glmdir folder

Re: [Freesurfer] cortical label mask fro mri_glmfit

Also, there my be some differences in the definition of the medial > wall across subjects. This does not change with contrast. > > > On 12/22/2016 02:40 PM, neuroimage analyst wrote: > > Thanks, Doug for that quick response! > > > > Does mask.mgh varies between differe

[Freesurfer] Longitudinal freesurfer

Hi, We are currently doing longitudinal FreeSurfer analysis on subjects some of whom are scanned over a period of 6 years. There were 2 groups. One was the control group and the other was mTBI group. The hypothesis was the control group would have a fairly stable cortical and sub-cortical volume

[Freesurfer] Cuda 8, Centos 7, FreeSurfer 6

Hello. We recently installed Centos 7 with cuda 8 and tried to build the FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so. Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing to share the binaries with us or share their steps with us? We will

Re: [Freesurfer] CNR of each surface

surf/?h.w-g.pct.mgh, which you can average > over each parcellation. Not sure where you would get the noise term from. > > On 4/3/19 5:23 PM, neuroimage analyst wrote: > > > > External Email - Use Caution > > > > I apologize, Dr. Fischl, that I wasnt clear.

Re: [Freesurfer] CNR of each surface

u mean by CNR of a surface? > On Wed, 3 Apr 2019, neuroimage analyst wrote: > > > > > External Email - Use Caution > > > > Hi, > > We were interested in measuring CNR of each of the 68 surfaces in > Desikan-Killany atlas and compare > > between t

[Freesurfer] CNR of each surface

External Email - Use Caution Hi, We were interested in measuring CNR of each of the 68 surfaces in Desikan-Killany atlas and compare between the groups to verify if our results are being biased by CNRs in the group? I came across mri_cnr and mris_ms_surface_cnr binaries in the

Re: [Freesurfer] CNR of each surface

gt; gray/white CNR = 2.196, gray/csf CNR = 0.851 > > rh CNR = 1.523 > > total CNR = 1.540 > > > > > > cheers > > Bruce > > > > On Wed, 3 Apr 2019, neuroimage analyst wrote: > > > >> > >> External Email - Use Cauti

[Freesurfer] Postdoctoral position

External Email - Use Caution Hi. We are looking for a postdoc to work with us on multimodal MRI and machine learning to predict Parkinson's disease dementia. An ideal candidate should be well versed and understand multi-shell diffusion MRI analysis and processing and have an