Re: [Freesurfer] mri_convert - returns different image size

Thank you very much! It works now! Best regards, Veronica -Original Message- From: Sindhuja Tirumalai Govindarajan [mailto:sindh...@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 19:29 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns

Re: [Freesurfer] longitudinal data check problem

Would it be possible to send us the norm.mgz file and one of the surface file that causes crash? Thanks, Ruopeng On 4/25/12 6:22 AM, Charlotte Bernard wrote: Dear Freesurfer users, I try to visualize my longitudinal data for one subject whit the command line given in the freesurfer website:

[Freesurfer] About GroupAnalysis

Dear All, I am learning GroupAnalysis and I have some problem about the vector that embodies the hypothesis we want to test(such as:0 0 0.5 0.5).I just want to know how each number of the vector involve in the calculating process of mri_glmfit.That is, I want to acquire some materials of how

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - Does it die at that point or does it keep running? If it's the latter it doesn't look wrong. For your first problem you should make sure that your path includes the bin/ directory under the FSL distribution. a.y On Wed, 25 Apr 2012, Viviana Siless wrote: Hi Anastasia, I ran:

Re: [Freesurfer] bbregister for fmri FEAT data

And the functional is test.nii.gz? If so, can you upload vol0001.nii.gz, register-test.dat, test.nii.gz, and orig.mgz to our file drop? doug On 04/25/2012 07:49 AM, Erlend Hodneland wrote: > Both the fmri data registered to orig is mismatched, and also the original > raw fmri data are mismatc

Re: [Freesurfer] Parcellation Colorscale

sure. I advise bugging Ziad! Bruce On Wed, 25 Apr 2012, Baum, Sarah H wrote: > Yes, everything is good in tksurfer, but something after > @SUMA_Make_Spec_FS is causing an issue. Thanks for the help! > > > > > > On 4/24/12 3:23 PM, "Bruce Fischl" wrote: > >> Hi Sarah >> >> if it is correct, you'l

Re: [Freesurfer] Parcellation Colorscale

Yes, everything is good in tksurfer, but something after @SUMA_Make_Spec_FS is causing an issue. Thanks for the help! On 4/24/12 3:23 PM, "Bruce Fischl" wrote: >Hi Sarah > >if it is correct, you'll probably need to bug Ziad and the SUMA guys >about why the colors are wrong. If you are resamp

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

If you all have a fixed binary for a Mac Pro running Mac OS 10.6.8 that you would be able to forward me, I would greatly appreciate it. Thanks, Andrew From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2012 8:56 AM To: Alexandre Gra

Re: [Freesurfer] Fwd: Load Brodmann surface area into inflated surface

Hi Bruce, I'm using freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0. I will also be using FS 5.1 paralelly. Thank you very much!! Andreia Citando Bruce Fischl : > Hi Andreia > > I just modified label_area to allow the specification of a threshold > (with -t ) and a surface (with -s ), and

Re: [Freesurfer] labels export

sorry, I don't know what obj format is either Bruce On Wed, 25 Apr 2012, Gabriel Gonzalez Escamilla wrote: And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels? Regards, Gabriel El 24/04/12, Bruc

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

thanks Alex. If anyone needs a fix before the next release let us know what hardware/software version you are running and we'll send you a binary cheers Bruce On Wed, 25 Apr 2012, Alexandre Gramfort wrote: > hi all, > > @bruce : I've just given a try your own binaries in > > ~fischl/dev/frees

Re: [Freesurfer] Fwd: Load Brodmann surface area into inflated surface

Hi Andreia I just modified label_area to allow the specification of a threshold (with -t ) and a surface (with -s ), and to use white by default. If you let us know what hardware/software platform you are running on we can send you an updated binary cheers Bruce On Mon, 23 Apr 2012, _andre...

Re: [Freesurfer] bbregister for fmri FEAT data

Both the fmri data registered to orig is mismatched, and also the original raw fmri data are mismatched with orig, see the link here showing our raw data (fmri, orig and 152MNI) shown in fslview http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a It is orig.nii converted from orig.mgz that

Re: [Freesurfer] trakula segmentation fault

Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri and got the following output: subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage But before it to

[Freesurfer] longitudinal data check problem

Dear Freesurfer users, I try to visualize my longitudinal data for one subject whit the command line given in the freesurfer website: freeview -v 00049_T1/mri/norm.mgz -f 00049_T1/surf/lh.pial:edgecolor=red 00049_T1/surf/rh.pial:edgecolor=red 00049_T1/surf/lh.white:edgecolor=blue 00049_T1/surf

Re: [Freesurfer] labels export

Well I'mactually looking for something like convert the segmented structures, i.e. hippocampus, thalamus or putmen to an object or ROI file.Regards,GabrielEl 25/04/12, Gabriel Gonzalez Escamilla escribió:And what about exporting as obj format, I have found a function to transform surfaces to obj,

Re: [Freesurfer] labels export

And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels?Regards,GabrielEl 24/04/12, Bruce Fischl escribió:they are just ascii files so it should be easy enough to do yourselfOn Tue, 24 Apr 2012, Gabriel G

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

hi all, @bruce : I've just given a try your own binaries in ~fischl/dev/freesurfer/bin/ and it worked fine. It looks like a bug has been fixed since the last stable release. Alex On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich wrote: > Sadly, I haven't been able to determine the problem ye