[Freesurfer] question about visualization of negative activation

shown however it is in Red-Orange-Yellow color scale. How can I get this negative activation to be represented by Dark and Light Blue color scale. Thanks in advance for the help! Balaji Goparaju ___ Freesurfer mailing list Freesurfer

[Freesurfer] preproc-sess : Problem with spatial smoothing and brain masking

HI, I ran the preproc-sess command, but in the output for spatial smoothing, the fmcsm5 file is not created. It says [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -upda

[Freesurfer] Preproc-sess: Spatial smoothing and brain masking

Hi, I used the command preproc-sess -s LD-functional -fwhm 5 However, the command does not seem create the fmcsm5.nii file. The process completes motion correction successfully, but it does not complete the spatial smoothing and brain masking. I get a "Motion correction SUCCESSFULLY completed" me

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking

ok, Here is the output: I am still getting the same output. [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm ---

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking

Ok, here is the terminal output as an attachment On Mon, Jul 21, 2008 at 12:44 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > Can you send the terminal output? The ls results are not informative. > > doug > > > Balaji Goparaju wrote: > > ok, Here is the output: I am

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking

after executing the command you suggested, /Users/balajigoparaju/Desktop/subjectdata contains some files which are enclosed as an attachment On Mon, Jul 21, 2008 at 12:55 PM, Balaji Goparaju <[EMAIL PROTECTED]> wrote: > Ok, here is the terminal output as an attachment > > > On

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking

Hi, I copied the new version of the programs mktemplate-sess surfsmooth-sess stc-sess mkbrainmask-sess mc-sess When i try to run preproc-sess -s LD-functional -fwhm 5 again, I get the following error, -- preproc-sess logfile is log/prep

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking

Hi, Thank you for the help. I saved it as a plain text. and it did not give me that error again. However, even after I saved the new version of the mkbrainmask-sess, i get the same error. Tue Jul 22 14:32:30 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd

[Freesurfer] Compute individual statistics (selxavg3)

Hi Doug and all, There is another problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR:

[Freesurfer] Preproc: Brainmasking

Hi Doug and all, I used the new version of mkbrainmask-sess. It looks like the file is getting created but it cannot find fslmaths for avmaths. Is this error something to do with the freesurfer software itself, or is there anything I can do about it? Thu Jul 24 09:15:51 EDT 2008 /Users/balajigop

[Freesurfer] First Level analysis

Hi Doug and all, There is a problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR: loadin

[Freesurfer] Compute individual Statistics

Hi Doug, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional --

[Freesurfer] Compute First Level Analysis

Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional --

[Freesurfer] Compute First level Analysis

Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional --

[Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

terchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations. What is the best way to achieve the resampling? Any guidance is really appreciated! Regards, Balaji Goparaju ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

.dat file from Freesurfer 5.1 and keep the rest of the analysis the same as before? Thank you once again for this help! Regards, Balaji Goparaju On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve wrote: > To go from mni152 to the MNI305 2mm space, use > > mri_vol2vol --mov mni305.2

Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

Thank you for the help! On Tue, Jun 14, 2011 at 9:10 PM, Douglas Greve wrote: > ** > You should be able to use the reg and mni305.2mm.nii.gz in 4.5 > doug > > > On 6/14/11 12:25 PM, Balaji Goparaju wrote: > > Thanks for the response! I seem to be getting better results