[Freesurfer] FS-FAST using MRS voxel or .label as seed

96 Normal 0 14 false false false IT X-NONE X-NONE

Re: [Freesurfer] I: I: R: R: R: Re: To use a ROI.label as seed in FS-FAST

Why would the sig in MNI space overlap the native functional space? Please also look the file attached. This the sig.nii.gz (subcortical, MNI) overlapped on f.nii. Messaggio originale Da: std...@virgilio.it Data: 12-feb-2016 17.16 A:

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

Hmmm, I think I'm more confused. what do you mean by "mean thickness of ROI from longitudinal group comparison"? You are looking at how the thickness across cortex correlates with the mean thickness in your ROI? On 02/18/2016 05:50 PM, amirhossein manzouri wrote: > I just wanted to clarify a

Re: [Freesurfer] Entorhinal thickness

The ex vivo is probably more accurate since it was created by directly visualizing the relevant cytoarchitectur > On Feb 18, 2016, at 5:17 PM, Douglas N Greve > wrote: > > One (aparc) is derived from manual labels registered into the subject > space. The other is

Re: [Freesurfer] Statistical analyses with QDEC

Hi Cico, you can do some of this in qdec, but it might be easier to use the "command line" stream of mris_preproc, mri_surf2surf (to smooth), mri_glmfit, and mri_glmfit-sim (correct for multiple comparisons). The commandline us just much more flexible. You will set up and FSGD file that will

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

I just wanted to clarify a bit more to see if makes more sense now ? On Thursday, 18 February 2016, Douglas N Greve wrote: > Hi Amirhossein, I can't tell from below if you have a question or not > > On 02/18/2016 05:32 PM, amirhossein manzouri wrote: > >> Hi and

Re: [Freesurfer] Reading values from overlays with PETcoreg

If you are not doing PVC, then the easiest (and most accurate) will be to map the PET to the individual anatomical space, then use mri_segstats with aparc+aseg.mgz as the segmentation to compute the mean in each ROI. If you want to continue with your stream, you can use mri_segstats using

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

Hi and thanks, tp1 is before and tp2 after treatment, and the measurement is the mean thickness of ROI from longitudinal group comparison, so we basically want to see effect of treatment on cortico cortical correlation. On Thursday, 18 February 2016, Douglas N Greve

Re: [Freesurfer] Entorhinal thickness

One (aparc) is derived from manual labels registered into the subject space. The other is derived from an exvivo label. On 02/18/2016 10:23 AM, Mohamed Ali Bahri wrote: > Dear Freesurfer, > > The entorhinal has different volume and thickness in the > "?h_aparc.stats" &

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

It will be much easier if you subtract time point 1 from 2 then do a two-group t-test. See https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis On 02/18/2016 05:37 AM, María Díez Cirarda wrote: > Dear FS experts, > > I am trying to do a longitudinal analysis with a Repeated Measures > ANOVA

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

so you want to test whether the cross-sectional slope changes across time? That is unusual, but you can do it by specifying two classes in the FSGD file, one for each time point. Also specify a variable which is your measurement. Then create a contrast 0 0 1 -1. This will test whether the

Re: [Freesurfer] mris_diff documentation

There is not any more documentation. This is mainly a tool to help debug our software. If you just want to compute the difference between two images, you can use fscalc img1.mgh sub img2.mgh -o img1-img2.mgh doug On 02/18/2016 12:32 PM, Suchandra Thapa wrote: > Hi, > > I'm trying to use the

Re: [Freesurfer] 3D viewing ROIs by Freeview

Run it with --help to get more info on the color table On 02/18/2016 04:41 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > In my project, I need to have a view of several specific ROIs which > already specified after running re-con all based on Destrieux atlas. > In this purpose, I tried

Re: [Freesurfer] 3D viewing ROIs by Freeview

Hi Freesurfer experts, In my project, I need to have a view of several specific ROIs which already specified after running re-con all based on Destrieux atlas. In this purpose, I tried to run mris_label2annot command to create ROIs in annot format to be viewed in Tksurfer by overlaying on pial

Re: [Freesurfer] stable6

It is not a matter of "trusting" it so much as it will not represent an actual version of freesurfer. beta versions should not be used for production analysis. I would reprocess with a previous version. doug On 02/18/2016 02:45 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote: > > Hello all, >

[Freesurfer] stable6

Hello all, I have been slowly processing a longitudinal dataset off and on again since last August, sourcing /usr/local/freesurfer/nmr-stable6-env. Does this represent v.6.0-beta or v.6.0 in development? We were initially interested in applying the hippocampal subfield segmentation

Re: [Freesurfer] Building from source -- autoconf error

> > is there a public clone of freesurfer on github? Sorry, their is no public freesurfer on github. But at the current moment (and forseeable future) the public repo is an exact mirro of the private repo. > > --disable-GUI-build -- wouldn't it disable then building all so necessary GUI >

Re: [Freesurfer] Error in surface-based interhemispheric registration

You should not be using 5.2. Use 5.3 instead, that will have fsaverage_sym On 02/18/2016 12:06 PM, Ilaria Mazzonetto wrote: > Hi Freesurfer experts, > I'm using freesurfer v5.2.0. > If I use surfreg --s $subject --t fsaverage_sym --lh, I have this > error: ERROR: cannot find

[Freesurfer] mris_make_surfaces dimensions error

Hello all, I am attempting to reshape the pial surfaces to fill the new boundaries in my edited ribbon.mgz file. I am using mris_make_surfaces with the -cover_seg flag but keep getting this error: ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. Any suggestions?

[Freesurfer] mris_diff documentation

Hi, I'm trying to use the mris_diff command to do some comparisons however I'm having trouble finding documentation aside from the help text that the command outputs. Is there a wiki page that documents the command or some other place with documentation? Suchandra Suchandra Thapa

[Freesurfer] Paired t-test for correlation analysis on two time points

Hi, We would like to run paired t-test on longitudinal within group data for correlation analysis of one measurement and cortical thickness, not cortical thickness comparison at the respective time point . I found the paired analysis and read that but in fact we need to see if correlation between

[Freesurfer] Error in surface-based interhemispheric registration

Hi Freesurfer experts, I'm using freesurfer v5.2.0. If I use surfreg --s $subject --t fsaverage_sym --lh, I have this error: ERROR: cannot find /home/T1/fsaverage_sym/lh.reg.template.tif. Does anyone know how can I fix this? Thanks a lot. Ilaria ___

Re: [Freesurfer] Building from source -- autoconf error

On Thu, 18 Feb 2016, Z K wrote: > I beleive the .travis.yml does work but it is still under active > development. is there a public clone of freesurfer on github? > The Ubuntu instructions in the linux developers page have been tested on a > clean install and should work >

Re: [Freesurfer] Building from source -- autoconf error

Hello, I beleive the .travis.yml does work but it is still under active development. The Ubuntu instructions in the linux developers page have been tested on a clean install and should work (https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page). However I have not yet

[Freesurfer] Entorhinal thickness

Dear Freesurfer, The entorhinal has different volume and thickness in the "?h_aparc.stats" & "?h.entorhinal_exvivo.stats" files. Could any one explain way and which one should be used? Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche,

Re: [Freesurfer] Building from source -- autoconf error

Hi Z K et al, What would be the recommended/tested debian/ubuntu release to approach the build with some guarantee of success? Is the .travis.yml "exercised" (failed to quickly find a sign of it on travis-ci.org)? I have tried on debian jessie to build stable5_branch-5622-gf3d0bcd of the

Re: [Freesurfer] pial edits in subject with severe atrophy

Hi Bruce, I exported the ribbon.mgz to itksnap and was able to edit the grey matter to include the atrophic frontal areas. I am wondering if there is a way to have these edits reflected in the pial surface? Thanks. Corinna On Wed, Feb 10, 2016 at 4:02 PM, Corinna Bauer

Re: [Freesurfer] Help - Surface extraction to Matlab

Hi Ittai We distribute m-files for reading and writing. Try read_surf.m Cheers Bruce > On Feb 18, 2016, at 4:02 AM, Ittai Shamir wrote: > > Hello, > > My name is Ittai and I am currently working on my M.Sc. in the department of > Neurobiology in Tel Aviv

Re: [Freesurfer] eTIV question and longitudinal issue

Hi all, I would be very grateful of any advice for the problem below with e-TIV. I have another problem with the longitudinal streaming (it is the first time I use it). I am running the .base and .long procedure in subjects with only one measure to include them in a mixed liner model analysis (as

[Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

Dear FS experts, I am trying to do a longitudinal analysis with a Repeated Measures ANOVA 2x2, with two groups (experimental and control group) and two times (pre and post treatment). First, I have followed the Longitudinal Processing Tutorial: 1) I have 2 acquisitions per subject so, I created

[Freesurfer] Help - Surface extraction to Matlab

Hello, My name is Ittai and I am currently working on my M.Sc. in the department of Neurobiology in Tel Aviv University. I am a new FreeSurfer user. My question regarding the software is- After successfully running my data (T1 image - MPRAGE) through FS, I would like to extract both cortical

[Freesurfer] infant data recon-all error

Dear Freesurfer experts, I'm involved in the infant research (less than 1 year of age). I tried running the recon-all command, however it fails and I got the error below at the end. Could anybody please let me know how to fix it? other error message please see attached file below. --- #@#