Re: [Freesurfer] missing eTIV in asegstats2table

Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure EstimatedTotalIntraCranialVol in their aseg.stats file. The problem is that when I run asegstats2table, this variable is not exported to the created text file. I wonder if there is some way to extract eTIV for all

Re: [Freesurfer] Error running TRACULA

Dear Anastasia, using the command you told me I solved the problem with the bvecs file, however I get this error dmri_train(8994) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182):

Re: [Freesurfer] rh or lh?

Thanks! Got you. If only there can be a header/meta info/tag added into mgh -- that would be great. I believe it can help prevent errors and improve processing efficiency :) Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

Re: [Freesurfer] Error running TRACULA

Hi Lucia - Glad to hear the bvecs problem got solved. About the memory problem: Can you please click on the apple on the top left of your screen and go to About This Mac and give me the info on the little window that pops up? Thanks, a.y On Wed, 2 Oct 2013, Lucia Billeci wrote: Dear

Re: [Freesurfer] Problems with LME-Setup

Hi Jorge Thank you for your answer our question about CM. I worked so far and the results are in line with glm_fit as you predicted. If we would like to compare the groups (4th column in our qdec.table, with (responder = 1), (non-responder = 2) coded) the CM.C would be [0 0 1 0] ? We have

Re: [Freesurfer] Error running TRACULA

Thanks. And can you also check which freesurfer build you're using? Look for the line that says build-stamp towards the beginning of your trac-all.log file. On Wed, 2 Oct 2013, Lucia Billeci wrote: Hi Anastasia These are the information: Mac OS X 10.7.5 Processor    3.4 Ghz Intel Core i7

Re: [Freesurfer] Error running TRACULA

Hi Lucia - You are using an older version of tracula (from freesurfer 5.1 instead of 5.3). This version used to have memory issues in the mac build. There is an update of the 5.1 mac build that addresses the memory issue, but since you are just starting out, I *highly* recommend to use the

[Freesurfer] Fwd: Error running TRACULA

Thanks a lot Anastasia for your help. I will install the new version and run it on my data. Best wishes Lucia Inizio messaggio inoltrato: Da: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Error running TRACULA Data: 02 ottobre 2013 17:23:42 GMT+02:00 A: Lucia

Re: [Freesurfer] missing eTIV in asegstats2table

Hmm, when I run asegstats2table EstimatedTotalIntraCranialVol is the last column. What version are you using? doug On 10/02/2013 02:50 AM, Daniel Ferreira wrote: Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure EstimatedTotalIntraCranialVol in their

[Freesurfer] Why don't no-mask flag work?

Hi, I want to test activity outside the brain (around eyes/retina) but when I use -no-mask flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25

Re: [Freesurfer] Why don't no-mask flag work?

Does the same thing happen if you use the 2mm instead of the 1mm? On 10/02/2013 02:21 PM, SHAHIN NASR wrote: Hi, I want to test activity outside the brain (around eyes/retina) but when I use -no-mask flag in my mkanalysis-sess (to be able to see activity outside brain) as below:

[Freesurfer] Error when running mris_anatomical_stats on a label

Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t

Re: [Freesurfer] Why don't no-mask flag work?

I still receive the same error message (1mm is now 2mm in the message). outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 Error using MRIread (line 76) ERROR: cannot determine format of

[Freesurfer] Visualize cortical projections of fiber pathways using FreeSurfer

Hi, FreeSurfer experts I have a question regarding visualizing the cortical projections of a fiber bundle using FreeSurfer based on the data from a group of subjects. Since I am interested in seeing both the cortical projections on the surface and the trajectory of the fiber bundle derived

[Freesurfer] Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST OCTOBER 3rd, 2013)

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist.

[Freesurfer] Difference in GMV generated from qdec and mris_anatomical_stats

Dear FS experts, I was trying to find the gray matter volume of superior temporal gyrus (STG) for schizophrenia patients using freesurfer. I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec. From that, I got the volume for left hand lh_superiortemporal_volume,=11893. Out of