Re: [Freesurfer] tkregister2 problems

Hi Doug, On Feb 19, 2010, at 7:16 AM, Douglas N Greve wrote: > Hmmm, da stimmt etwas nicht. Ganz genau, das ist was faul im Staate Daenemark... :) > I cannot replicate this. How was the original f.nii created? Can you send me > f.nii? The f.nii is in the filedrop (https://www.

Re: [Freesurfer] ICV Error fs 4.3.1

also note that if the subjects were processed by a prior version, then when re-run with v4.X, talairach.xfm will not get overwritten, as it is assuming it was edited. so you should check of talairach.xfm and talairach.auto.xfm are the same, and if not either re-run with -clean-tal, or just copy ta

Re: [Freesurfer] ICV Error fs 4.3.1

Can you check the talairach.xfm and the talairach_with_skull.lta to make sure that they are different across subject? Jeff Sadino wrote: > Hi Doug, > > Thanks for the quick reply. It just seems like an error that all 149 > subjects would line up exactly with the talairach transform (that > wou

Re: [Freesurfer] ICV Error fs 4.3.1

Hi Doug, Thanks for the quick reply. It just seems like an error that all 149 subjects would line up exactly with the talairach transform (that would give a determinant of 1.00?). The following commands I used from my script were: recon-all -sd /scratch/data431 -s 040002_S04 -autorecon1 *cod

Re: [Freesurfer] ICV Error fs 4.3.1

The ICV is *estimated* from the talairach transform. Did you happen to run recon-all with -notalairach? You can check that the talairach transforms are all different. doug Jeff Sadino wrote: > Hello, > I reconed 149 subjects using freesurfer 4.3.1 automatically using our > cluster. When I did

[Freesurfer] ICV Error fs 4.3.1

Hello, I reconed 149 subjects using freesurfer 4.3.1 automatically using our cluster. When I did asegstats2table, all 149 subjects had the exact same icv: # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.00, mm^3 Running mri_segstats manually, here is the beginning of the output:

Re: [Freesurfer] mris_expand problem

how about the thickness files? Is there space left on the disk?On Fri, 19 Feb 2010, Gregory Dierksen wrote: > > Yes, I can view both the left and right white matter surfaces in tksurfer. > > Sorry for the delay, and thanks for your help. > > Greg > > On Thu, 18 Feb 2010, Douglas N Greve wrote: >

[Freesurfer] Question.

Dear experts, When I tested my FreeSurfer, and when I input the command of *"tksurfer bert lh inflated*", only a bit part of the brain surface could be seen. Also, I often failed to drag the tksurfer window. What is the possible problem? Thank you very much. -- Best regards, Jijun Wang, MD & PhD

Re: [Freesurfer] mris_expand problem

That should work, but I would recommend using recon-all -s subject -finalsurfs you can spec a hemi if it is only the rh doug Gregory Dierksen wrote: > > Ok, there's the problem. rh.thickness will not load as an overlay and > returns the Input/Output error message. > > So can I just run the co

Re: [Freesurfer] mris_expand problem

Ok, there's the problem. rh.thickness will not load as an overlay and returns the Input/Output error message. So can I just run the command mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs rh to re-generate the right hemisphere thickness file? On Fri, 19 Feb 2010, Douglas N Greve wrote

Re: [Freesurfer] mris_expand problem

Sorry, it looks like it is the thickness file, not the white surface, it is having problems with. Can you load the thickness as an overlay? Gregory Dierksen wrote: > > Yes, I can view both the left and right white matter surfaces in > tksurfer. > > Sorry for the delay, and thanks for your help.

Re: [Freesurfer] mris_expand problem

Yes, I can view both the left and right white matter surfaces in tksurfer. Sorry for the delay, and thanks for your help. Greg On Thu, 18 Feb 2010, Douglas N Greve wrote: > An Input/Output error often means that the disk is corrupted or possibly > full. Can you read the the lh.white with some

Re: [Freesurfer] mri_vol2surf resulting in different dimensions for two different images in the same space

You're better off loading in the surface annotation directly rather than dealing with aparc+aseg. To make surf2surf output the right dimensions, add --noreshape. doug Joonkoo Park wrote: > Dear Surfers, > > I (successfully) resampled a functional data on the surface map using > mri_vol2surf: >

Re: [Freesurfer] Error with ntrs using mc-sess

Thank you Doug, you were correct. I was using a faulty run. Gabriel On Wed, Feb 17, 2010 at 3:04 PM, Douglas N Greve wrote: > Look in that run to see how many TRs are in that run (mri_info f.nii). It > is possible that you unpacked an aborted run (or a run of some other type)? > > doug > > Ga

[Freesurfer] Local GI - euler number and compute_lgi

Hi all I am running recon-all ­localGI One subjects image is not getting processed and crashes repeatedly with message that there may be a topological defect in a particular vertex. It asks me to check euler number. The wiki indicates that this crash is a known issue and restrating _mris_compute_

Re: [Freesurfer] tksurfer colortable problem

That warning is always there (I'm going to go to remove it now). In general, we need to know at least the cmd line that you ran to be able to help you debug this type of thing. doug jen...@nmr.mgh.harvard.edu wrote: > Hi Guys, > > I'm running tksurfer on my laptop and when I try to load the

Re: [Freesurfer] tkregister2 problems

Hmmm, da stimmt etwas nicht. I cannot replicate this. How was the original f.nii created? Can you send me f.nii? doug Sebastian Moeller wrote: > Dear Freesurfer Experts, > > I am a happy user of freesurfer for a number of years now. And finally I > managed to switch over from v3.0.5 to 4.5.0. M

Re: [Freesurfer] Recon successful- ran for half a minute instead of 30 hours. Visualisation problems

what was your recon-all command line? On Fri, 19 Feb 2010, Janani Dhinakaran wrote: > tkmedit subjectname rawavg.mgz is the way to visualise the volume. The first > image. This is what happened. > > s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > tkmedit subj001

Re: [Freesurfer] Recon successful- ran for half a minute instead of 30 hours. Visualisation problems

does that file exist? Janani Dhinakaran wrote: > tkmedit subjectname rawavg.mgz is the way to visualise the volume. The > first image. This is what happened. > > s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > > tkmedit subj001 rawavg.mgz > ERROR: cannot find

Re: [Freesurfer] A basic question about visualising data

if 'jan' is your subject id your cmmdline needs to be: recon-all -s jan -i -all cheers Bruce On Fri, 19 Feb 2010, Janani Dhinakaran wrote: > Here are my attempts after exporting- > > s0964...@cric-0012:~$ export > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan > s

[Freesurfer] tksurfer colortable problem

Hi Guys, I'm running tksurfer on my laptop and when I try to load the .sulc surface it crashes and tells me WARNING: No colortable found! Everything else seems to work just fine but I need to visualize the sulci to complete my project. Any ideas? Thanks, Jon _

[Freesurfer] Recon successful- ran for half a minute instead of 30 hours. Visualisation problems

tkmedit subjectname rawavg.mgz is the way to visualise the volume. The first image. This is what happened. s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ tkmedit subj001 rawavg.mgz ERROR: cannot find /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.ad

Re: [Freesurfer] A basic question about visualising data

Here are my attempts after exporting- s0964...@cric-0012:~$ export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan s0964...@cric-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan s0964...@cric-0012:~$ echo $SUBJECTS

Re: [Freesurfer] A basic question about visualising data

Just a guess: if you are using a Mac, the path for the directory should be something like /Users/yourname/Desktop/ etc. instead of just /Desktop/ etc. hope this helps, roberto On Thu, Feb 18, 2010 at 10:15 PM, Douglas N Greve wrote: > The SUBJECTS_DIR is where you want the result of the freesur