Re: [Freesurfer] freesurfer's template for sphere registration

Hi Bruce, Thanks for your reply. I'm not clear about two points you mentioned. ->To represent a folded surface we either (1) map to an individual subject, or (2) use a volume transform such as tal and the vertex correspondence from the sphere.reg to find the average coordinate of a vertex. This

[Freesurfer] Customised color bar in tksurfer

Dear all 1. I would like to display average thickness on surface model in tksurfer. The basic color bar included the tksurfer seems to be insufficient for displaying thickness difference (e.g. red to yellow etc.). I'd like to use rainbow color table in displaying the thickness result. How can I

Re: [Freesurfer] qdec question

Dear freesurfers, I have a few additional questions regarding qdec. 1. Is it possible to specify in qdec so that the results of the analyses run are saved in a separate destination than the SUBJECTS_DIR? 2. I have read in the qdec tutorial that it is possible to select up to 4 variables to re

Re: [Freesurfer] recon-all exited with errors

Hi Sameer, I don't think it'll affect your results, but before you rerun recon-all with -notal-check flag, check the registration in tkregister2 and make sure it's correct. Sita. On Wed, 22 Jul 2009, sameer kumar wrote: > hi all, > I ran recon-all on a case, and it exited with errors, and

[Freesurfer] recon-all exited with errors

hi all, I ran recon-all on a case, and it exited with errors, and the error message looks like this: ERROR: Talairach QA check failed! z-score = -6 <= -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check

Re: [Freesurfer] Cluster correction for multiple comparisons using mri_glmfit-sim

Here is the command line I am using. the same one was used both times; only the glmdir was different. mri_glmfit-sim \ --glmdir /data/zonda1/freesurfer_subjects/qdec/rh.area \ --sim mc-z 5000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite On Wed, Jul 22, 2009 at 12:43 PM, Douglas N Greve wro

Re: [Freesurfer] Cluster correction for multiple comparisons using mri_glmfit-sim

What are your command lines? In general, it's a good idea to send this each time, even if you're not sure it's useful. doug Devdutta W wrote: > Hi, > I just ran the mri_glmfit-sim command on our data and there were a > couple of things I did not understand. > We had previously ran the same com

Re: [Freesurfer] left right nifti

No, there are not, just make sure that the nifti itself is accurate. Garbage in, garbage out. doug Narly A Golestani wrote: > Hello everyone, > > I would like to know if there are left-right orientation issues when > converting images from nifti format to the mgz format. I suspect not as > nift

[Freesurfer] left right nifti

Hello everyone, I would like to know if there are left-right orientation issues when converting images from nifti format to the mgz format. I suspect not as nifti, unlike analyze, contains the left-right information in the file itself. But I would like to make sure that there are not issues suc

Re: [Freesurfer] Estimated total incranial volume

We don't have one. doug Flavio Seixas wrote: > Dear All, > > In addition to eTIV based on Tailarach transform matrix (see Buckner > et al. paper), is there other estimated total intracranial volume > method, for example, using the BET2 (brain extraction tool)? > > Thank you in advance, > Flavio

Re: [Freesurfer] Colortable

it's just a text file, so sure. If you want it integrated into tksurfer/tkmedit we'll need to compile it in as well. cheers, Bruce On Wed, 22 Jul 2009, Eylem Kirlangic wrote: > Hi, > > Is there any way to extend the colortable in freesurfer? > > Cheers, > Eylem > > > ---

[Freesurfer] Colortable

Hi, Is there any way to extend the colortable in freesurfer? Cheers, Eylem Forschungszentrum Juelich

[Freesurfer] Cluster correction for multiple comparisons using mri_glmfit-sim

Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to b

Re: [Freesurfer] continue from a specific stage of autorecon2

It would be: recon-all -s YOUR_SUBJ -make all --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/7/22 Gonzalo Rojas

[Freesurfer] continue from a specific stage of autorecon2

Dear Pedro Paulo: I need to continue the freesurfer professing from a specific stage of autorecon2 (careginv; stage 4 of autorecon2 in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4).. Which is the command line to do it ?... Sincerely, Gonzalo Rojas Costa ___

[Freesurfer] declaring spherical ROIs centered at common Talairach coord.

We want to extract a spherical ROI of cortical thickness values centered at the same Talairach coordinate for each brain in a study. Any suggestions? In the 2007 archives there is an instructive thread about declaring spherical ROIs on a volume, but I'm not clear about how we would place t

[Freesurfer] floating area with significant difference in qdec

dear freesurfer experts! I am trying to make a ROI of an area the showed significant difference in qdec. to do so i am drawing around the area per hand, but it doesnt look very precies. is there also a function that will float the whole area which is coloured? thanks in advance! rosa -- GRAT

[Freesurfer] skull-scalp volume extraction

Hi all, I have to implement a Difference element method on a volume extracted from a mri. Using freesurfer I am able to extract the volume file for the brain (ie. $h.ribbon), but I need also the volume files for the skull and for the skin. I have seen that the flag -surf exits in the watershed