[Freesurfer] convert size

Hello FS experts, I would like to to convert binary images from size 256,256,256 voxels to size 256, 256, 256. Is there any FreeSurfer's module to make it? Thank you very much Andrea ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] Parcellation of cerebellum.

Dear freesurfer, I'm trying to perform parcellation on the cerebellum. After reading closely freesurfer wiki and the questions related to this topic on the mailing list, my understanding is that there is no way to perform fully automted cerebellar parcellation on structural mri with freesurfer. Co

Re: [Freesurfer] Parcellation of cerebellum.

Hi Charles that is true at the moment, although we are working on something that should be ready relatively soon. cheers Bruce On Mon, 10 Dec 2012, charles laidi wrote: Dear freesurfer,  I'm trying to perform parcellation on the cerebellum. After reading closely freesurfer wiki and the que

Re: [Freesurfer] convert size

Hi Andrea I think there is a typo in your email as your sizes are the same. If you have a volume you would like to reslice it like you can use the -rl option to do what you want. cheers Bruce On Mon, 10 Dec 2012, Andrea Tateo wrote:   Hello FS experts, I would like to to convert binary i

[Freesurfer] .licence problem

Hi, I am setting up freesurfer on a pc laptop for a colleague. I have installed Oracle VM virtual box, Neurodebian, and FreeSurfer. Freesurfer is now running, but when I try doing recon-all I get the error message: ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If

Re: [Freesurfer] .licence problem

Hi Eva is the file readable? Bruce On Mon, 10 Dec 2012, Eva Hilland wrote: Hi, I am setting up freesurfer on a  pc laptop  for a colleague. I have installed Oracle VM virtual box, Neurodebian, and  FreeSurfer. Freesurfer is now running, but when I try doing recon-all I get the error message:

Re: [Freesurfer] .licence problem

I have seen this a few times and always something was wrong, either a line of white space or so in the file / not enough truncated or some changes to the file name like license.txt or so. Hth, Denis --

Re: [Freesurfer] winkler surf data with qdec ?

Greg, one of the -qcache outputs is named 'fwhm0', which will be unsmoothed. you can also specify creation of just that file by adding '-fwhm 0' after the -qcache flag. Nick > Hi , > > I have winkler variety surface area data that is already smoothed and > converted to vertex wise data on my a

[Freesurfer] nuisance variable ICV

Hi Freesurfer Experts, Just to make it sure i have a question about correcting for cranial size. I compared two groups, 100 patients versus 50 Controls. I entered a discrete variable 'groups' (Patients: 1 and controls:2) in qdec. For cortical thickness difference between these groups, do i

Re: [Freesurfer] Detrending timeseries with yhat.mgh from mri_glmfit

Hi Chris, if you want the detrended time series, use --eres-save which will save a volume called eres.nii.gz doug On 12/09/2012 11:07 PM, Chris McNorgan wrote: > Hello, > > I have a question regarding the yhat.mgh file generated from some > resting-state functional data after running: > mri_glmf

Re: [Freesurfer] question retinotopic mapping

Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: > Dear Doug, > > I tried version 5 with the commands suggested on the webside and this is > working > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnaly

[Freesurfer] R: Re: convert size

Soory if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. thanks immensely Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 10-dic-201

Re: [Freesurfer] R: Re: convert size

do you want to increase the field of view and keep the same voxel size or keep the same field of view and reduce the voxel size? doug On 12/10/2012 12:27 PM, Andrea Tateo wrote: > Soory if I bother you again, > actually I would like to convert from 256,128,256 to 256,256,256 and > from 181,14

[Freesurfer] motion correction

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew ___

Re: [Freesurfer] abblocked documentation?

Hi Summer, there is some documentation in mkanalysis-sess -help. It's not very much documentation, so I just wrote a little bit more which I have included below. Let me know if you still have questions. doug -abblocked PeriodSec Design is AB-Blocked (ie, periodic, two condition). Specify the p

[Freesurfer] which step comes first

Hi, when reconstructing the brains including manual edits, does the step that incorporates control points "come before" the white matter edits? Ie so if I do both control points and white matter edits, will the white matter edits be take into account even if I just use -autorecon -cp , and not -wm

Re: [Freesurfer] nuisance variable ICV

Hi Stan, I don't think you have to correct thickness for head size or grey matter volume, but you should do so for subcortical volumes. Whether you use ICV or GM volume or brain volume depends on what you believe is happening and what hypotheses you want to test. Check out the paper by Randy B

Re: [Freesurfer] which step comes first

Hi Catherine, Using the -autorecon-cp will take care of both cp and wm edits. Be sure to run -autorecon3 afterwards if you are satisfied with the edits you made. -Louis On Mon, 10 Dec 2012, Catherine Bois wrote: > Hi, > > when reconstructing the brains including manual edits, does the step th

Re: [Freesurfer] nuisance variable ICV

In addition to the Buckner article, for other literature on the topic of adjusting for volumes you can see: O'Brien et al., Psychiatry Research: Neuroimaging 193:113-122 (2011) Sanfilipo et al., Neuroimage 22:1732-1743 (2004) I'll also mention that people sometimes use global global thickness as

Re: [Freesurfer] mri_glmfit-sim for interhemispheric comparison

Hi Shige, those are fine, but there is a warning here about performing the mri_surf2surf step. You need to make sure that you are doing this properly because it will run and complete even if you are not doing it properly:). to map the left hemi, run something like: mri_surf2surf --srcsubject su

Re: [Freesurfer] which step comes first

Hi Cathy yes, control points come first, so autorecon2-cp will do the wm stuff also cheers Bruce On Mon, 10 Dec 2012, Catherine Bois wrote: > Hi, > > when reconstructing the brains including manual edits, does the step that > incorporates control points "come before" the white matter edits? Ie

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Jorge, Thank you very much !! It worked !! I used the new versions: /lme_mass_F1; lms_mass_fit1 /and/lme_mass_fit_vw1/, which you sent me for the old Matlab. Additionally, I uploaded in Matlab - /lme_fit_init; lme_FSfit; lme_Gradient; vec; lme_E1/; /fs_write_fstats; fs_write_Y;/ it ended

Re: [Freesurfer] Fwd: Running Tracula: trac-preproc exited with ERRORS

Hello My trac- preproc has completed. However, I am confused about the status message. It says: #- trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 Does this mean it was completed

Re: [Freesurfer] Fwd: Running Tracula: trac-preproc exited with ERRORS

I'm guessing that this shows up in the scripts/trac-all.log of a particular subject? Then it applies to that subject. On Mon, 10 Dec 2012, s0675204 wrote: Hello My trac- preproc has completed. However, I am confused about the status message. It says: #-