Re: [Freesurfer] Inflated.nofix has holes!!!

1. No, this is not a problem. The inflated.nofix is before the topology correction and will have 2. 10 hours is reasonable depending on your harward environment. 3. Visual inspection is best cheers Bruce defects. On Tue, 9 Jun 2015, Hassan bakhshi wrote: > Hi All, > I have 3 questions: > > 1

Re: [Freesurfer] Align functional to anatomical volume

fig2 I guess, but if that fails you should probably give us more details and Doug may be able to help you cheers Bruce On Tue, 9 Jun 2015, lucas hosse wrote: Dear Bruce, I have these two types of functional volumes (in fig1 and fig2). Which one do you suggest to use? Thank again. -

Re: [Freesurfer] Align functional to anatomical volume

Lucas, also remember to include all previous correspondence. I've already deleted the ones that had your command lines ... doug On 6/9/15 8:45 AM, Bruce Fischl wrote: fig2 I guess, but if that fails you should probably give us more details and Doug may be able to help you cheers Bruce On Tue,

Re: [Freesurfer] Timecourses In freesurfer

Hi Doug, I think I've realized what the problem is - my cespct file has only one frame How can I run mkanalysis-sess, mkcontrast-sess and selxavg3-sess in a way that produces the whole percent signal change time course? Thanks Jonathan ___ Freesurfer mail

[Freesurfer] License problem

Dear FS, I received my license e-mail for the upteenth time and converted the mail to license.txt in the $FREESURFER_HOME directory, but I stll get an error message: mri_convert /home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri/rawavg.mgz /home/rik88/GIfMI/Freesurfer/subjects/NMRD001/mri

Re: [Freesurfer] Inflated.nofix has holes!!!

About visual inspection!!! Which images should I check??? And how can I understand the defect in images? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

Re: [Freesurfer] Inflated.nofix has holes!!!

the defects are corrected and will be eliminated in the ?h.inflated, so don't worry about the ones you see in the inflated.nofix. In the end what you care about is making sure that the ?h.white surface follows the gray/white boundary and the ?h.pial surface follows the gray/csf boundary cheers

Re: [Freesurfer] License problem

Hello, Please refrain from sending the contents of the license file in the open to the freesurfer list. Unfortunately this is a known issue for all Opensuse platforms versions greater than 12.1 and there are two potential solutions. The first is to copy /lib64/libcrypt-2.14.1.so from an Opensu

Re: [Freesurfer] Inflated.nofix has holes!!!

Hi Hassan, You should probably start by working through the tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials This one covers that specific topic. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview hth d On Tue, Jun 9, 2015 at 12:32 PM, Hassan bakhshi wrote:

[Freesurfer] mirror labels across hemispheres

Hi, I am trying to map a label in the left hemisphere to the right hemisphere. To do so, I have registered the subject's native surfaces to the fsaverage_sym template using surfreg -s $subj -t fsaverage_sym -lh surfreg -s $subj -t fsaverage_sym -lh -xhemi What would be the best way to map the

[Freesurfer] errors after mri_matrix_multiply and tkregister2

Hello Freesurfer team I got a warning message when I checked tkregister2 after I did mni152.reg, mri_matrix_multiply command. I got warning messages and found that the axial image was suddenly showed up on coronal window view on tkregister2. The error messages as follow like this: [gencess:008

[Freesurfer] bad magic number

Hi, I'm getting a bad magic number error using mri_convert. I'm trying to convert a .nii file to a .mgz file. I've searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I've tried using the .nifti1 exte

Re: [Freesurfer] bad magic number

Hi Jennifer can MRIcro read it? Usually that means it is corrupted Bruce On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi,   I’m getting a bad magic number error using mri_convert. I’m trying to convert a .nii file to a .mgz file. I’ve searched all over and all I can find is th

Re: [Freesurfer] bad magic number

MRIcro opens it, and so does SPM 8. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, June 09, 2015 3:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] bad magic number Hi

Re: [Freesurfer] bad magic number

how was it created? On 06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote: > MRIcro opens it, and so does SPM 8. > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, June

Re: [Freesurfer] bad magic number

mricro -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 09, 2015 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad magic number how was it created? On 0

[Freesurfer] Versions compatibility

Hello, We are running on Mac OSX 10.6.8 X11 version 2.3.6 Reading the download page recommends Xquarts 2.7.5 for 10.7 How important is the X11 requirment? At this point (80 subjects freesurfed), is it recommended to update X11? I warned about not upgrading operating system between studies, c

Re: [Freesurfer] Versions compatibility

If you can open tkmedit then you do not need XQuartz. https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer If it doesnt open then you will most likely need it. Also, the X11 upgrade does not apply to the general rule against updating OS and/or freesurfer versions. -Zeke On 06/09/2015

Re: [Freesurfer] A few problems with freesurfer-Darwin-snowleopard-i686-dev-20150507

Carl, You can modify the other 'dev' recon-all that was working to include the fix. Find this line: if($UseNewTopoFix ) then which will be just above the line where orig_corrected is copied. Change it to this: if($UseNewTopoFix && -e ../surf/$hemi.orig_corrected ) then Nick On Sun, 2015-06-

[Freesurfer] selx3avg-sess and monkey data

Hi all, I’ve recently completed surface reconstruction of macaque brain using Sebastian Moeller’s pipeline (http://freesurfer.net/fswiki/MonkeyData) and now I’d like to analyse retinotopic data and display it on the surface. However, when I try running selx3avg-sess, I get this error: “ERROR: c

[Freesurfer] WM signal increase with adiposity and measure of cortical thickness

Dear FreeSurfer experts, Schwartz et al (Neuroimage 103, 2014, 192-201) have demonstrated that T1W WM signal increases with increased body adiposity, probably due to altered brain lipid composition. This would affect cortical thickness measurements in one of two ways: overestimating, in algorithms

Re: [Freesurfer] WM signal increase with adiposity and measure of cortical thickness

Hi Ricardo we do individual subject-level estimation of levels. And it could be a confound I guess, although we use intensity gradients to definite boundaries not absolute intensity levels, so we might be less prone to this problem. If it shifts the apparent boundary there isn't much we can do

[Freesurfer] darker user interface

Hello, Is there any way to have a black background / white font foreground for the user interface on Freeveiw? I am working in a dark reading room with others at times and the white user interface reflects on other screens. I noticed a dark mode for the command console on the preferences but i