Re: [Freesurfer] mri_register memory error

Hi bruce, yes, mris_register solves the problem- i had to strugge a bit to see what works if i wanted to use a specific subject's {hemi}.sphere file for use in mri_glmfit. Thanks. shantanu On Fri, June 15, 2012 10:01 pm, Bruce Fischl wrote: > Hi Shantanu > What are you trying to register? I don't

Re: [Freesurfer] mri_register memory error

Hi Shantanu What are you trying to register? I don't ink mri_register is what you want. Possibly mris_register instead (note the "s")? Cheers Bruce On Jun 15, 2012, at 8:32 PM, "Shantanu Ghosh" wrote: > > Hi Freesurfer experts, > > I am receiving an error message while processing registra

Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]

Hi XJ - In your configuration file, you've set both doregflt and doregbbr to 0. You have to set one of them to 1, otherwise no intra-subject registration will be done and every step that relies on it will fail. a.y On Fri, 15 Jun 2012, XJ Kang wrote: > Hi Priti, > > I removed the NaNs in the

[Freesurfer] mri_register memory error

Hi Freesurfer experts, I am receiving an error message while processing registration to fsaverage using mri_register. Please tell me why it is happening and how to get this going. Here is the terminal output: glia:shantanu[219] mri_register /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recon

Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]

Hi Priti, I removed the NaNs in the 4D images and re-ran trac-all -prep. The warning message is gone (of course) but the error message of dlable/diff/White-Matter++.flt.nii.gz is still there since no "White-Matter++.flt.nii.gz" in the diff directory. Only one image in dlabel/diff/: lowb_brain

Re: [Freesurfer] precoloring - adjusted errors

It won't be so simple. If you can represent your filter as a matrix, then you can set the flac.TFmtx, but you'll need to do this in multiple places. You can do a search for TFmtx in the matlab code to see where On 06/15/2012 03:23 PM, Caspar M. Schwiedrzik wrote: > if i come up with the code for

Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]

Hi Priti, The 3D data are the averages of two or more sets of DWI data. All the DWIs were already perform the field map correction by "epidewarp.fsl", and they were also coregistered to T1 images in spm. So probably I don't need these two step. I may add the b0 inhomogenity correction. For the

Re: [Freesurfer] recon error- too many arguments?

bingo! thanks a lot! 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] Sent: Friday, June 15, 2012 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Free

Re: [Freesurfer] precoloring - adjusted errors

if i come up with the code for the newey white standard error, where in selxavg3-sess would i need to plug that in? caspar 2012/6/15 Douglas N Greve > I don't know anything about it. Looks interesting. > doug > > > On 06/15/2012 02:14 PM, Caspar M. Schwiedrzik wrote: > >> Hi Doug, >> if I filte

Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]

Hi XJ, I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out? When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0

Re: [Freesurfer] precoloring - adjusted errors

I don't know anything about it. Looks interesting. doug On 06/15/2012 02:14 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > if I filter, an alternative might be the Newey-West estimator > (http://en.wikipedia.org/wiki/Newey-West_estimator), I guess? > Caspar > > > 2012/6/15 Douglas N Greve

Re: [Freesurfer] precoloring - adjusted errors

Hi Doug, if I filter, an alternative might be the Newey-West estimator ( http://en.wikipedia.org/wiki/Newey-West_estimator), I guess? Caspar 2012/6/15 Douglas N Greve > Hi Caspar, it does not make sense to low pass filter and prewhiten. > Unfortunately, I don't have the precoloring implemented

Re: [Freesurfer] TRACULA dpath problem

Can you send us your configuration file (mytracula.conf) and log file (it should be under scripts/trac-all.log). I can take a look. Priti > Hi, > > I am trying to run the last step of TRACULA. I used the command line: > > % trac-all -path -c mytracula.conf > > Here is all the info I got on the sc

[Freesurfer] TRACULA dpath problem

Hi, I am trying to run the last step of TRACULA. I used the command line: % trac-all -path -c mytracula.conf Here is all the info I got on the screen: INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurf

Re: [Freesurfer] precoloring - adjusted errors

Hi Caspar, it does not make sense to low pass filter and prewhiten. Unfortunately, I don't have the precoloring implemented in FSFAST. doug On 06/15/2012 01:36 PM, Caspar M. Schwiedrzik wrote: > Hi! > I am processing a resting state data set, which I would like to low > pass filter to get rid of

[Freesurfer] precoloring - adjusted errors

Hi! I am processing a resting state data set, which I would like to low pass filter to get rid of some artifacts. The sample will be very small, so I won't run a RFX GLM, but an FFX GLM and/or single subject analyses. Since the low pass filter introduces high autocorrelations, it does not make sens

Re: [Freesurfer] recon error- too many arguments?

Hi Mia, I think the problem is that you have a space in the path to the dicom. Even though you put a backslash there, I think it is still causing the problem doug On 06/15/2012 01:13 PM, Borzello, Mia wrote: > Yes! I attached a screen shot. Thanks! > > >

Re: [Freesurfer] recon error- too many arguments?

Yes! I attached a screen shot. Thanks! From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, June 15, 2012 11:33 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon error- too many arguments? Hi Mia can you send

Re: [Freesurfer] recon error- too many arguments?

Hi Mia can you send us the actual command and screen output? thanks Bruce On Fri, 15 Jun 2012, Borzello, Mia wrote: > Hi, > > I'm trying to run a recon, but I keep getting the error: too many arguments > for the following command: > econ-all -autorecon1 -autorecon2 -autorecon3 -subject _Su

[Freesurfer] recon error- too many arguments?

Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M ___

Re: [Freesurfer] qdec

yes doug On 6/15/12 5:07 AM, Richter, Julia wrote: > Dear all, > > after comparing two groups in qdec and hitting the question "Does the average > thickness differ between group 1 and group 2?", do yellow areas mean that > group 1 has a thicker cortex in that area than group 2? > > Thanks, > > J

[Freesurfer] qdec

Dear all, after comparing two groups in qdec and hitting the question "Does the average thickness differ between group 1 and group 2?", do yellow areas mean that group 1 has a thicker cortex in that area than group 2? Thanks, Julia ___ Freesurfer ma