[Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (LME) Models

Hi I am reposting a previous message about difficulty to install Bernal's Linear Mixed Effects Models. I am in doubt if I should log in as a guest (I assume so). Anyway I have tried this and I get a .dmg installation file that seems to be corrupted as it does not allow me to install. Any help wi

[Freesurfer] Question about the raw thickness range

Dear Freesurfer experts, I have two question about my freesurfer results. 1. I performed recon-all analyses on my data and found all the data's maximal value of cortical thickness is 5. Is there any standardization procedure in the recon-all that normalize the maximum value to 5? In addition,

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

Yes, it does. However, I am able to start Freeview whiteout any argument from matlab 2015b on Mac X 10.10.5. If I use this commandsystem('freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.white’); in matlab ferview crash, but I use this command system(‘freeview’) I am able to start

Re: [Freesurfer] Try to extract WM surface paceration to ASCII

sorry, I dont' think we have a binary for this, but it should be easy enough in matlab with read_annotation cheers Bruce On Wed, 16 Sep 2015, xtong wrote: > Hi Freesurfer experts, > > I would like to register my test subjects to fsaverage and extract WM > surface parcellation info into ascii fi

Re: [Freesurfer] Question about the raw thickness range

Hi Feng I'll answer 1. and leave 2 for someone else (Doug?). We have a hard limit on the max thickness of 5 but no lower bound other than 0 of course. This prevents large values due to surface inaccuracies. cheers Bruce On Wed, 16 Sep 2015, chenhf_uestc wrote: Dear Freesurfer experts,   I

[Freesurfer] glmf-fit with 8 categorical variables

Hello, I am trying to run glm-fit on a total of 36 subjects - there are 8 categorical variables (group, smoking, gender etc) and one continuous (age). I want to test group effect, regressing out all other variables. There are (correct me if I am mistaken) - 256 classes (2^8) - 256 *(1+1)=512 reg

Re: [Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (LME) Models

Please change the subject of your message to "Problem installing installing Freesurfer on Mac ". -Jorge De: pablo najt Para: "freesurfer@nmr.mgh.harvard.edu" Enviado: Miércoles 16 de septiembre de 2015 3:32 Asunto: [Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (L

[Freesurfer] cortical thickness of a volume-defined ROI

Dear Experts, I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm analysis following the instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) and got stuck at step 2. Please could you kindly assist? [spjwker@nanlnx2 FSL]0% cd $SUBJECTS_

[Freesurfer] How to handle the termination of recon-all after mris_remove_intersection

Hi, freesurfer developers. In some cases, I found that the recon-all script stops after running mris_remove_intersection. Here's an example of the recon-all.log in those cases: --- ..

Re: [Freesurfer] Question about the raw thickness range

For #2, that option won't do anything, but it probably needs to be there. On 9/16/15 8:28 AM, Bruce Fischl wrote: Hi Feng I'll answer 1. and leave 2 for someone else (Doug?). We have a hard limit on the max thickness of 5 but no lower bound other than 0 of course. This prevents large values d

Re: [Freesurfer] cortical thickness of a volume-defined ROI

you don't have write permission to that folder. Get write permission or put the reg file in a different place On 9/16/15 9:45 AM, Lim, Lena wrote: Dear Experts, I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm analysis following the instructions (https://surfer.n

Re: [Freesurfer] glmf-fit with 8 categorical variables

That is not going to work because you have way more regressors than you have data points. doug On 9/16/15 9:05 AM, Kallirroi Retzepi wrote: > Hello, > I am trying to run glm-fit on a total of 36 subjects - there are 8 > categorical variables (group, smoking, gender etc) and one continuous > (age)

[Freesurfer] Freesurfer/Qdec brain images

Dear Experts, I need some help regarding saving the brain images in Freesurfer/Qdec please: 1) Can I save the brain regions shown in Qdec group analysis as other files and view them in MRIcroN etc or does it only allow us to save the images as tiff files (inflated medial, inflated lateral, pia

Re: [Freesurfer] Freesurfer/Qdec brain images

Hi Lena, QDEC does not have that much functionality, so you may have to move to tksurfer or freeview. More answers below. On 9/16/15 10:05 AM, Lim, Lena wrote: Dear Experts, I need some help regarding saving the brain images in Freesurfer/Qdec please: 1) Can I save the brain regions shown

[Freesurfer] A mixed effect model approach: Qdec possible with three group study design?

Dear Jorge, I am testing 3 groups (HC, BD, relative) and want to apply your model. Now I am in doubt if I would be able to use qdec? Or if this instead will not be viable as I have 3 groups is not possible with qdec?ThanksPablo Date: Thu, 10 Sep 2015 13:44:36 + From: jbernal0...@yahoo.es

Re: [Freesurfer] A mixed effect model approach: Qdec possible with three group study design?

not possible with qdec On 09/16/2015 11:29 AM, pablo najt wrote: > > Dear Jorge, I am testing 3 groups (HC, BD, relative) and want to apply > your model. Now I am in doubt if I would be able to use qdec? Or if > this instead will not be viable as I have 3 groups is not possible > with qdec? > T

Re: [Freesurfer] glmf-fit with 8 categorical variables

please remember to cc the list, thanks. Also remember to include previous correspondence. 50 is still greater than 36 so that won't work. You can probably get away with 4, maybe 6. On 09/16/2015 11:53 AM, Retzepi, Kallirroi wrote: > So I should: > 1. keep in the FSGD file only the relevant cla

Re: [Freesurfer] subject specific ROI

Thanks！ On Tue, Sep 15, 2015 at 6:21 PM, Douglas N Greve wrote: > check out this page > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] How to handle the termination of recon-all after mris_remove_intersection

it seems that it stopped after a cp, not after the mris_remove_intersection call, no? On Wed, 16 Sep 2015, Nakyoung Kim wrote: Hi, freesurfer developers. In some cases, I found that the recon-all script stops after running mris_remove_intersection. Here's an example of the recon-all.log in

Re: [Freesurfer] hello freesurfer developer~

give it the .img as input, not the .hdr. Note that using analyze is not recommended though! It doesn't store direction cosines so you will never be sure that there is no left/right flip unless you have a fiducial marker like a vitamin E tablet cheers Bruce On Wed, 16 Sep 2015, A-reum Min wro

[Freesurfer] Tracula_weighted dti metrics values

Hi Anastasia, How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD values? I checked the command "dmri_pathstats" inside the file "trac-all.log" but I was unable to figure out how this weighting is working. Is it by multiplying the mean DTI metrics by the number of voxel?   I

[Freesurfer] Convert .xfm to .mat

Dear freesurfer experts, I want to concatenate *.xfm transformation from bbregister with *.mat from flirt. For that I need to convert .xfm to .mat. Any idea how can that be done? Thanks, Sneha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] Convert .xfm to .mat

note that bbregister does not output "xfm" files but either tkregister-style .dat files and .lta files. You can use lta_convert to convert to/from different formats. You can convert the .dat file to an lta (or output an lta directly), and convert the fsl to lta. Then use mri_concatenate_lta to

Re: [Freesurfer] Try to extract WM surface paceration to ASCII

Thanks. On 09/16/2015 08:26 AM, Bruce Fischl wrote: > sorry, I dont' think we have a binary for this, but it should be easy > enough in matlab with read_annotation > > cheers > Bruce > On Wed, 16 Sep 2015, xtong wrote: > >> Hi Freesurfer experts, >> >> I would like to register my test subjects to

[Freesurfer] slope_age.mtx unknown

Hi list,I'm performing one group and one covariate on resting state FAST analysis.Here, I'm reporting the error.ThanksBest regards, Stefano mri_glmfit --glmdir my-glm_age.wls --y y.mgh --nii.gz --fsgd file_age.fsgd --C intercept_age.mtx —-C slope_age.mtx gdfReadHeader: reading file_age.fsgd INFO:

[Freesurfer] Can MRIread function read .mgz file

Dear Freesurfer expert, How could I read the .mgz file into Matlab, the online manual FAQ stated Q. Can I load FreeSurfer output in Matlab? A: If you write it as .mgz format then load_mgh (or MRIread) will read it. In addition, in the MRIread function, it stated that % mri = MRIread(fstring,head