[Freesurfer] Volume to surface

Hello all FS users and experts,I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file,For this I'm using the next commands:First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.niiTo preserve  t

[Freesurfer] Volume to surface 2

I did forget to tell you that when I use the last command it always outputs the following error:ERROR: MRISread: cannot read surface data from file lh.aseg2raw.mgh! It gives me the same error when trying to load the surface into tksurfer, Is that I've made something wrong?Regards, Gabriel 

[Freesurfer] matrix error

Hello, I am analyzing cortical thickness in a patient and control group. I have two covariates: age and length of disease. I am using the model from: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V However, for the control group I put length of disease as 0 in my FSGD file. When I run the GLM

Re: [Freesurfer] Volume to surface

Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called "ascii

Re: [Freesurfer] matrix error

Hi Allie, the 5th column of your design matrix is all 0s, which causes the ill conditioning. I don't think this design fits into our standard framework. You can still analyze and test, we'll just have to figure out exactly what needs to be done. In the end, what is it that you want to test? Jus

Re: [Freesurfer] trac-all -path error

Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" isn't getting created, I think. This is after I ran bedpostx on its own, per your instructions from this thread. Here are the last few lines of output from trac-all -path: Loading BEDPOST parameter samples from /raid2/fmri8/c

[Freesurfer] inability to pick points

Hi, I'm just wondering if there is something that needs to be selected using tkmedit to get electrode coordinates. I usually don't have this issue, but right now i'm unable to move my cursor to a new location. Thanks so much, Mia ___ Freesurfer maili

[Freesurfer] problems with analysis after using fslmaths

Hi, I am trying to use fslmaths to filter my data before I plug it into a resting state analysis. However, once I obtain a pcc map, all correlation coefficients are <0.1, even the autocorrelation with the seed voxel. The data look fine when I open them in Matlab using MRIread; the correlations betw

Re: [Freesurfer] trac-all -path error

Hi Chris, The diff_slices folder is still there, which means that bedpostX probably did not finish processing. That folder usually gets deleted after bedpostX processing completes. It's strange that you have merged_ph2samples.nii.gz and not merged_ph1samples.nii.gz. Did you accidentally run bedpo

Re: [Freesurfer] trac-all -path error

Yes, I figured out that I had previously run "trac-all -bedp" and it created "data_slice_0002". I deleted this directory, and bedpostx finished, but now I get this error from "trac-all-path": Segmentation fault (core dumped) /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/

Re: [Freesurfer] problems with analysis after using fslmaths

Is this doing all of those seeds simultaneously or one seed at a time? On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote: > Hi, > I am trying to use fslmaths to filter my data before I plug it into a > resting state analysis. However, once I obtain a pcc map, all > correlation coefficients are

Re: [Freesurfer] inability to pick points

Make sure that the "Select Voxel Tool" is activated in the tool bar (or drop down tool menu). Sounds like you have the navigation button selected. doug On 05/07/2012 02:05 PM, Borzello, Mia wrote: > Hi, > > I'm just wondering if there is something that needs to be selected using > tkmedit to get

Re: [Freesurfer] matrix error

Hi Doug, Is there a different number I can substitute into the fifth column so the numbers are not all zeroes? Thank you, Allie On Mon, May 7, 2012 at 12:39 PM, Allie Rosen wrote: > Hi Doug, > > Thanks for the help. The fifth column is all zeroes because the covariate > - length of disease -

Re: [Freesurfer] inability to pick points

"Select voxels" is actually highlighted already (and "Navigation" isn't), but it's still not working. Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu]

Re: [Freesurfer] inability to pick points

is your input volume "conformed"? I think tkmedit disables some features if it is not On Mon, 7 May 2012, Borzello, Mia wrote: > "Select voxels" is actually highlighted already (and "Navigation" isn't), but > it's still not working. > Thanks, > m > > From

Re: [Freesurfer] problems with analysis after using fslmaths

Did you regenerate the seeds after filtering? On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote: > I have tried analyses with only one seed time course (either 1 voxel, > mean of a sphere of 1 voxel radius, or mean of a functionally defined > roi), as well as several seeds within the same desi

Re: [Freesurfer] matrix error

The right way to do it is to remove the column entirely. You can't do this inside of the FSGD unless you use DOSS. You can use DOSS if there is no difference between the groups in the age slope. In fact, it is a good idea to run this test first. So, create an FSGD with just the age. Create a co

Re: [Freesurfer] problems with analysis after using fslmaths

What frequencies did you chose for the FSL bandpass filter? What is you mkanalysis-sess command? On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote: > yes > > 2012/5/7 Douglas N Greve > > > Did you regenerate the seeds after filtering? > > > On 05/07/20

Re: [Freesurfer] inability to pick points

I'm not sure what you mean by "conformed"? My input volume is that one that I coregistered if that's what you mean? From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 07, 2012 2:57 PM To: Borzello, Mia Cc: Douglas N Greve; freesurfer@nmr.mgh.

Re: [Freesurfer] inability to pick points

conformed means 1mm isotropic. What is your tkmedit cmd line? On 05/07/2012 03:04 PM, Borzello, Mia wrote: > I'm not sure what you mean by "conformed"? My input volume is that one that I > coregistered if that's what you mean? > > From: Bruce Fischl [fis..

Re: [Freesurfer] inability to pick points

tkmedit MGXX_SuferOutput_original norm.mgz lh.pial -aux ct.anat.mgz I named the folder with the extra "_original" because this person already had a SurferOuput folder. Could that be the problem? thanks. From: freesurfer-boun...@nmr.mgh.harvard.edu [frees

Re: [Freesurfer] trac-all -path error

So I'm assuming that you don't have any issues merged_ph* files anymore? As far as the error below is concerned, this is typically the last step in trac-paths, where it should merge all the 18 tracts to create a 4D tract volume for visualization. The input for this should be all the 18 posterior d

Re: [Freesurfer] matrix error

Hi, I tested for a difference between the groups on age slope using DODS and there was a difference. Does this mean I cannot re-run the model using DOSS? Please let me know if there is a way I can still test for the difference in thickness between groups. Thanks again, Allie On Mon, May 7, 201

Re: [Freesurfer] problems with analysis after using fslmaths

Hi Doug, I use the following command for fslmaths fslmaths fmc.nii -bptf 200 2 fmcfilt.nii where 200*(TR+2) is 400s, and 2*(TR=2)=4s. and for mkanalysis-sess -force -fsd bold -funcstem fmcfilt -analysis name -notask -tr 2 -runlistfile name -native -nskip 5 -mask brain -tpef name -taskreg name fo

Re: [Freesurfer] inability to pick points

is it 1mm isotropic, 256^3? Run mri_info on it On Mon, 7 May 2012, Borzello, Mia wrote: > I'm not sure what you mean by "conformed"? My input volume is that one that I > coregistered if that's what you mean? > > From: Bruce Fischl [fis...@nmr.mgh.harvard.

Re: [Freesurfer] problems with analysis after using fslmaths

The mkanalysis command looks ok. I don't know how to interpret those numbers for fslmaths. What are the cutoff frequencies? doug On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I use the following command for fslmaths > fslmaths fmc.nii -bptf 200 2 fmcfilt.nii > > where 200*(TR+

Re: [Freesurfer] problems with analysis after using fslmaths

the cutoff frequencies are 0.0025 Hz and 0.25 Hz. Caspar 2012/5/7 Douglas N Greve > The mkanalysis command looks ok. I don't know how to interpret those > numbers for fslmaths. What are the cutoff frequencies? > doug > > > On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote: > >> Hi Doug, >> I u

Re: [Freesurfer] problems with analysis after using fslmaths

Hi, is it possible that it is a data format problem? I tried forcing fslmaths to give float output using -odt float. This changed mostly the autocorrelations computed during selxavg, but not the pcc. Caspar 2012/5/7 Caspar M. Schwiedrzik > the cutoff frequencies are 0.0025 Hz and 0.25 Hz. > Cas

[Freesurfer] longitudinal study in counterbalance design

Hi all: We performed a thickness change study which related to the menstrual cycle. We scanned subjects during different menstrual phases in a counterbalance manner. Thus when we conduct a longitudinal analysis, we need to set time point according to the actual scanning order (i.e., 1st scan as Tp