Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Eugenio, Thanks for the response. I just tried that and it still didn't work (same error message). Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 Current Stamp: freesurfer-Darwin-OSX-dev-20150826 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/f

Re: [Freesurfer] Parcellation stats

mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve wr

Re: [Freesurfer] GRF correction in mri_glmfit-sim

I am also very interested in these questions, but I do not find the response. Could anyone provide the answers? Thanks, Feng 发件人："Meiling Li" 发送时间：2015-09-22 22:09 主题：[Freesurfer] GRF correction in mri_glmfit-sim 收件人："freesurfer-help" 抄送： Dear FS experts I do GRF correction using mri_glmfit

[Freesurfer] R: import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results (conjunction maps) in FSL, opening them by fslview.Could you provide me any suggestion? Thank you very muchBest regards, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

[Freesurfer] import FS-FAST results in FSL

Hi list, I would like to import FS-FAST results (conjunction maps) in FSL, opening them by fslview.Could you provide me any suggestion? Thank you very muchBest regards, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Matthieu, use lme_mass_fit_vw and the y is a simple vector. I would mask the image before doing this and only pass the brain voxels (to increase speed and reduce comparisons). Best, Martin On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote: Hi Martin, I understand for the multiple compari

[Freesurfer] Question about the negative value of surface area

Dear Freesurfer experts, I read the raw area file and the area resampled to the fsaverage space and found several interesting things. raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area value is [-0.0471 6.2118] raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); %

Re: [Freesurfer] warping surface label to volume space

filedrop2 url at the end of this email On 9/29/15 10:34 AM, Jacobs H (NP) wrote: Sure, where should I upload it to? Thanks! Heidi From: Douglas Greve > Reply-To: Freesurfer support list > Date: Tuesday 29 September 2015 1

[Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

Dear Freesurfer experts, In the stats folder of subject in the SUBJECTS_DIR, I found the files of lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results belong to two different atlas? Because the values and brain regions are different in these two files. In these two file

Re: [Freesurfer] total grey matter volume

Many thanks, Michael! L From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Harms, Michael Sent: 29 September 2015 15:54 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total grey matter volume They are conveniently already pro

Re: [Freesurfer] total grey matter volume

They are conveniently already provided for you in the {lh,rh}.aparc.stats files.  And even more conveniently, if you run 'aparcstats2table', with --measure=thickness, the last column is the mean cortical thickness (for that hemisphere), and if you run with --measure=area, the last column is

[Freesurfer] Longitudinal_analysis_results

Dear Freesurfer Experts, I am trying to run a longitudinal analysis. I have done the first three steps of the analysis. Now, I am trying to visualize my results. However, I am having trouble doing the last step of the analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova ba

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Martin, I understand for the multiple comparisons problem. But if I consider a voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for estimation), how could I consider a correction for multiple comparisons in this univariate case ? Shouldn't I use the lme_mass_fit or lme_mass_fit_v

Re: [Freesurfer] warping surface label to volume space

Sure, where should I upload it to? Thanks! Heidi From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday 29 September 2015 16:28 To: "freesurfer@nmr.mgh.harvard.edu" mai

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Matthieu, yes, multiple comparisons are a problem for any mass univariate approach. You can use the FDR2 correction (in the lme matlab tools) which is less conservative than standard FDR. You can also work in specific ROI's and average there, to reduce the number of comparisons. Best, Mar

Re: [Freesurfer] Question about the volume conversion in freesurfer

Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer 收件人："freesurfer" 抄送： This is not an ea

Re: [Freesurfer] warping surface label to volume space

Can you upload the subject so I can look at it? On 9/29/15 9:05 AM, Jacobs H (NP) wrote: Hi Doug, The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong? Best Heidi Van: freesurfer-boun..

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

I would say that you can do that only if your data is continous (preferably close to normally distributed). Binary data or any non-continous data requires a different approach (eg. Generalized Estimating Equations). Best-Jorge De: Martin Reuter Para: Freesurfer support list Enviad

Re: [Freesurfer] qdec error

Try normalizing the continuous covariates (ie, subtract the mean and divide by the stddev) On 9/29/15 9:16 AM, Lim, Lena wrote: > Thanks, Amanda. Yep, I did that. It works alright if I removed IQ and used > only Age and Gender as covariates... > > > -Original Message- > From: freesurfer

Re: [Freesurfer] Sulc value of given Tal coordinates

when you load the fsaverage surface into freeview or tksurfer you will see some coordinates, those coordinates will be MNI305 coords. If you map the individual sulc or curv into fsaverage space and load is as an overlay, then you can see what the sulc/curv value is at a given coordinate. On 9/2

Re: [Freesurfer] problem fast_selxavg3b

oops, sorry, that did not make it into the distribution. You can get it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m thanks doug On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: > Dear members of the freesurfer mailing list, > > I'm using freesurfer-L

Re: [Freesurfer] qdec error

Thanks, Amanda. Yep, I did that. It works alright if I removed IQ and used only Age and Gender as covariates... -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Worker, Amanda Sent: 29 September 2015 14:11 To:

[Freesurfer] problem fast_selxavg3b

Dear members of the freesurfer mailing list, I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to analyse mri data with fs-fast. I did the preprocessing and used the function mkanalysis-sess and mkcontrast-sess without any problems. I tried to run the function selxavg3-sess

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Martin, Thank you for your answer. However, I would like to consider FA maps as a mass-univariate problem and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my voxels aren't independant, are they ? So, how to correct for multiple comparisons then ? Best regards, Matthieu 201

Re: [Freesurfer] qdec error

Hi Lena, Have you changed your Group.levels file to include the two groups you are currently looking at? If this doesn't match your qdec table it will not work. Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lim, Lena

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

You can also compare the results of your glmfit with the fsaverage cortex label to the one with the intersected label. If they look similar, I think it would be fine if you use the fsaverage cortex to avoid the holes. Still it may be good to investigate the cases that produce holes, maybe there

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Matthieu, if all your images are perfectly registered, you can do LME on a voxel-by-voxel basis, just as if you had hippocampal volume or any other ROI measure. Best, Martin On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote: Dear experts, I would like to know if it is possible to make a

[Freesurfer] Freesurfer methods and reviewer queries

Dear Freesurfer team, I have a manuscript under review which has used Freesurfer to compare cortical thickness differences between groups, controls and patients with a specific genetic mutation. There are robust, statistically significant group differences in biologically plausible regions. Howeve

Re: [Freesurfer] total grey matter volume

Thanks, Michael. How do I get the total thickness and total surface area values form Freesurfer/Qdec please? Thanks again, L From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Harms, Michael Sent: 29 September 2015 04:30 To: freesurfer@nmr.

Re: [Freesurfer] qdec error

Thanks, Doug. I used the qdec table attached. L -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 28 September 2015 21:54 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec er

[Freesurfer] LME toolbox for longitudinal FA volume maps ?

Dear experts, I would like to know if it is possible to make a longitudinal study with LME toolbox from volume FA maps registered in a common space ? I don't have T1 images so the recon-all process couldn't be processed. But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels for

Re: [Freesurfer] Sulc value of given Tal coordinates

Rudolph That's great, so as I understand I should be able to get the sulc value for a given vertex. Forgive my naivety, but how do I map the tal coordinates to the vertex mesh? Is there also a function for this? I'm very new to this! I just need the nearest vertex for a given tal coordinates (I