[Freesurfer] Recon All on a 3 years old subject

ing at the structural images the contrast is quite good. Do you have any idea or suggestion on why I'm having these issues? Can you point out the exact points where I can look to find the error? I guess you'll need the entire recon-all, I can send it off if you wish. Thanks in advance, F

[Freesurfer] mri_ca_label killed process

(2): linear fit = 0.99 x + 0.0 (13532 voxels, overlap=0.871) Left_Cerebral_White_Matter (2): linear fit = 0.99 x + 0.0 (13532 voxels, peak = 104), gca=104.4 Killed francesco@francesco-F3JP:~$ I wasn't able to find any log file to find the cause. Anybody can help me with this? Thanks in

Re: [Freesurfer] Apply talairach.xfm to orig.mgz

Thanks, I'll try with tkregister2 as I want to just check talairach and not use it elsewhere. Still thanks for the help and quickness, Francesco Baldacchini 2014-04-01 14:18 GMT+02:00 Bruce Fischl : > Hi Francesco > > look at mri_vol2vol -help and search for talairach. It h

[Freesurfer] Apply talairach.xfm to orig.mgz

mmand do I have to use? I tried MRI_XFORM_TO_HEADER but it didn't work. Thanks everybody in advance and sorry if my question is too silly, but I'm a beginner. Francesco Baldacchini ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] reconstruction problem with pediatric images

inal release? I would be really glad to use it and make few tests with it on my patients. Thank you for the attention and for your time, Francesco Baldacchini 2014-03-21 16:12 GMT+01:00 Lilla Zollei : > Hi Francesco, > > Given that the recon pipeline is built on an adult atlas it is no

[Freesurfer] reconstruction problem with pediatric images

ether with T2 weighted images during recon-all? Another question is how important it is to use the mprage option in recon-all? Thanks, Francesco Baldacchini ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

[Freesurfer] register between structural and dwi

oc, and at which point of the process this is done. I'm doing this because I want to track down all the movements of the files used by Tracula. Thanks, Francesco Baldacchini ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

Re: [Freesurfer] Add new path to tracula

Ok, thanks. And if I want to add a new pathway which is the file I've to modify and where can I find it? Francesco Baldacchini 2014-03-04 17:28 GMT+01:00 Anastasia Yendiki : > > Hi Francesco - The pathways that tracula reconstructs are only the ones > included in its atlas

[Freesurfer] Add new path to tracula

Hi everybody, I'd like to know if it's possible and if yes how to add new paths to the tracula pathlist? Otherwise how can I add a new path after the entire trac-all process? Francesco Baldacchini ___ Freesurfer mailing list

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

into trac-all and the ones that get > created under dmri/.) > > Thanks, > a.y > > > On Tue, 11 Feb 2014, Francesco Baldacchini wrote: > > Hi again Anastasia, >> >> I tried also to convert my three row bvecs file in a three column one but >> I still go

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Hi again Anastasia, I tried also to convert my three row bvecs file in a three column one but I still got the same "bvecs and bvals don't have the same number of entries" error. I then tried also to change the dot to comma as the decimal separator but still nothing Francesco Bal

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

e: > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates > > This option was not available in the previous releases of tracula. > > Hope this helps, > a.y > > > On Mon, 20 Jan 2014, Francesco Baldacchini wrote: > > Hi, >> Sorry Anastasia, I'm seeing that my

[Freesurfer] bvecs and bvals don't have the same number of entries

nd bvecs in DTI folder are the one saved by trac-all in the dmri directory. I'm attaching also my configuration file "dmrirc.tutorial". Francesco Baldacchini dmrirc.tutorial Description: Binary data bvals Description: Binary data bvecs Description: Binary data bvals Description:

[Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki &

[Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries

Hi everybody, I'm trying to run the* trac all -prep *command but after some times I get this error "bvecs and bvals don't have the same number of entries". I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. What can

Re: [Freesurfer] trac-all -path Help needed

essing > steps before the inter-subject registration (see wiki page for how to turn > off steps). You also don't need to rerun bedpost. > > Hope this helps, > a.y > > > On Wed, 18 Dec 2013, Francesco Baldacchini wrote: > > Ciao Anastasia, >> Here is the log

[Freesurfer] trac-all -path Help needed

postx_mgh: line 439: 5294 Terminated ${subjdir}.bedpostX/monitor* In attachment I loaded my drirc.tutorial configuration file. Thanks, Francesco Baldacchini dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.