Re: [Freesurfer] trac-all inquiry

Hi, just a though, would it be possible to skip the reconstruction of the right ILF, I mean to get the remaining tract statistics? that would be v/useful cheers ds On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi David - The screeenshots show that

[Freesurfer] R: Re: R: Re: R: Re: Linear regression

Dear Rujing, After recon-all and qcache, for correlation analysis, I have performed qdec by using a matrix that contains NPS test, 3 nuisance factors and one groups.For groups analysis I have applied mri_glmfit as described in the guide. Nothing in particular. Stefano Messaggio

[Freesurfer] FW: how do display a particular region for visucalization

From: tulu [mailto:t...@ms36.hinet.net] Sent: Wednesday, December 04, 2013 8:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: how do display a particular region for visucalization Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an

Re: [Freesurfer] trac-all inquiry

Of course, you can specify which tracts you want to reconstruct in the configuration file. Both the sample configuration file in $FREESURFER_HOME/dmrirc.example and the tracula tutorial have the info on how to do this. On Thu, 5 Dec 2013, David Soto wrote: Hi, just a though, would it be

Re: [Freesurfer] trac-all inquiry

ok thanks I did not realise! may I ask something else? 2 of my participants structural scan was distorted and could not be used by recon-all, so can not get the anatomical priors for tracula. It may sound a stupid questio, but is it possible(and worthy) to try to do some registration of the

Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts

Hi Zeke, thanks for the info. we had installed the 64 bit lion version of freesurfer. perhaps the trac-all was engaged from the wrong (older) directory. I am nuking the old versions. and will try it again Jon - Original Message - From: Z K zkauf...@nmr.mgh.harvard.edu To: Jon Wieser

[Freesurfer] Patch for -autorecon2

Dear FreeSurfer experts, Would it be possible to have the patch for this problem Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2 because ribbon.mgz is not present? Thank you very much in advance, Isabelle ___

Re: [Freesurfer] nuisance variable in qdec

you cannot do this in QDEC. In fact, it is a tricky analysis to do properly. For each group you will need an offset regressor and an age regressor, but only the patient group will have a burden regressor. This cannot be done with an FSGD file either. You will have to create your own design

[Freesurfer] nuisance variable in qdec

Dear Doug,   Thank you for your instantaneous response!   Correcting for disease burden was actually a reviewer comment.  We calculated mean cortical thickness estimates for regions that showed vertex-wise age-related cortical thickness differences between groups (using qdec) and then graphed

Re: [Freesurfer] nuisance variable in qdec

Yes, though I think it is the same as adding the Burden column. doug On 12/05/2013 02:04 PM, Cat Chong wrote: Dear Doug, Thank you for your instantaneous response! Correcting for disease burden was actually a reviewer comment. We calculated mean cortical thickness estimates for regions that

Re: [Freesurfer] Fwd: Problems with longitudinal analysis

Hi Knut There are a few confusing things in your question post. First, it seems that your attached images are depicting p-values. We usually use -log10(pvalue) format for visualization in tksurfer. The sig.mgh file saved by lme should be in that format. However we didn't use tksurfer to build

[Freesurfer] label to curv .mgh

hello, trying to convert a medial wall label to a curv format .mgh file running mris_convert --label lh.Medial_wall.label lh.white foo.mgh tried a few things but not getting there, what does it want ? thank You ___ Freesurfer mailing list

[Freesurfer] qdec analysis with 2 covariates

HI freesurfer experts I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec

Re: [Freesurfer] mri_convert Siemens .IMA error

Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs. Is there any additional

[Freesurfer] Freeview question

Hi Bruce et al, Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a brain in Freeview? thanks, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] possible pial surface editing

Hi Gen, I'm having the same problem right now with one participant where the pial matter border doesn't extend enough out to the edge of the cortex. Did you try adding control points as Ye suggested? If so, did it work? Thanks! Krista On Tue, Sep 24, 2013 at 11:52 AM, ye tian

Re: [Freesurfer] Freeview question

Hi Alan, You can use mri_binarize to pull it out of the aseg.mgz. FYI: Once loaded into freeview you can also generate an isosurface for the hippocampus label in the 3D view. -Louis On Thu, 5 Dec 2013, Alan Francis wrote: Hi Bruce et al, Is it possible to load just the Hippocampal

Re: [Freesurfer] trac-all inquiry

Sorry, trac-all requires freesurfer recons at the moment. On Thu, 5 Dec 2013, David Soto wrote: ok thanks I did not realise! may I ask something else? 2 of my participants structural scan was distorted and could not be used by recon-all, so can not get the anatomical priors for tracula. It

Re: [Freesurfer] Significance of value in sig.nii file under 'polar' directory

Thanks for your help Doug. That cleared things up. One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity? Cesar On Wed, Dec 4, 2013 at 1:03 PM, Douglas

Re: [Freesurfer] possible pial surface editing

Is this happening systematically? Eg, always on the left side? Or both sides? doug On 12/5/13 3:35 PM, krista kelly wrote: Hi Gen, I'm having the same problem right now with one participant where the pial matter border doesn't extend enough out to the edge of the cortex. Did you try

Re: [Freesurfer] Patch for -autorecon2

Sorry, I thought I had updated that link. Use this one and download the program for your OS ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ On 12/5/13 3:42 PM, Isabelle Deschamps, Miss wrote: I tried the link, but when I click on it, I get the following error ALERT 550

Re: [Freesurfer] mri_convert Siemens .IMA error

This may be a known problem. What version of FS are you using and what is your platform? doug On 12/5/13 3:26 PM, prasser wrote: Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm

[Freesurfer] refeventdur in mkanalysis-sess

Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. But I have two conditions with different durations that one lasts for

Re: [Freesurfer] R: Re: R: Re: R: Re: Linear regression

Dear Stefano, OK, I see. Thanks for your help. All the best. 2013-12-06 Rujing Zha 发件人：std...@virgilio.it 发送时间：2013-12-05 22:34 主题：R: Re: [Freesurfer] R: Re: R: Re: Linear regression 收件人：charujing123charujing...@163.com,freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Rujing, After