Re: [Freesurfer] mri_cvs_register error in step 2

The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview. Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register -

Re: [Freesurfer] Another -use-gpu experiment

On Fri, Apr 20, 2012 at 12:52 PM, Burns, Scott S wrote: > 2) Separately from the above experiment, I ran one gpu subject using 4 GTX > 480s and saw no significant time difference.  Is this to be expected, ie your > CUDA code doesn't scale across multiple GPUs? Just curious, certainly not a > d

Re: [Freesurfer] -clean

I have not done any manual interventions. I would like to re-run recon-all with different expert options in mri_normalize, and -skullstrip, and -mprage, and wanted be sure that my changes would be reflected in the downstream output. - On Fri, Apr 20, 2012 at 12:52 PM, Joshua Lee wrote: > If I

Re: [Freesurfer] improving automated cerebellar parcellation

probably in matlab On Fri, 20 Apr 2012, Anthony Dick wrote: Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line? Anthony On 4/20/12 3:53 PM, Bruce Fischl wrote: HI Anthony I would make sure to include an entire brain labeling i

Re: [Freesurfer] improving automated cerebellar parcellation

Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line? Anthony On 4/20/12 3:53 PM, Bruce Fischl wrote: > HI Anthony > > I would make sure to include an entire brain labeling in the training > set. You can do this by pasting your manu

Re: [Freesurfer] improving automated cerebellar parcellation

HI Anthony I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question. cheers Bruce On Fri, 20 Apr 2012, Anthony Dick wrote: Hello, I developed a new atlas for parcellating the cer

Re: [Freesurfer] -clean

Hi Josh if you specify a new directory that will certainly work. We try very hard to preserve any manual interventions you have taken so that is why -all doesn't start fresh - we don't want it to. cheers Bruce On Fri, 20 Apr 2012, Joshua Lee wrote: > If I were to want to re-run a recon-all

Re: [Freesurfer] mri_cvs_register error in step 2

Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then the

[Freesurfer] -clean

If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Do

[Freesurfer] mris_expand not working since upgrading to v.5.1.0

Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever sinc

[Freesurfer] Failure to download

Hi freesurfers, I tried to download the tutorial dataset for inspection of fs output, but receive this error message repeatedly, even with the -c flag: glia:shantanu[30] wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz --2012-04-20 15:27:05-- ftp://surfer.nmr.

Re: [Freesurfer] Brainmask.nii Reading

Hi Nooshin the function MRIread should load either the .nii or the .mgz in matlab. cheers Bruce On Fri, 20 Apr 2012, Nooshin Zadeh wrote: Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS.  For reading the data from "brainmask.mgz", I converted i

[Freesurfer] Brainmask.nii Reading

Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS. For reading the data from "brainmask.mgz", I converted it to "brainmask.nii". Can you please tell me how can I read the data from "brainmask.nii" is MATLAB? Do you know other way of reading the data fr

[Freesurfer] Another -use-gpu experiment

Freesurfers, I'd like to add my two about a recent experiment I ran with recon-all -use-gpu. (I'm using v5.1) I took 6 T1 scans, imported them into two subjects a piece (gpu_SUBJID, cpu_SUBJID) and ran 'recon-all -all -use-gpu' on the gpu_ subject and the normal 'recon-all -all' on the cpu su

[Freesurfer] long_qdec_table error

Martin, I'm getting the following error when running long_qdec_table: = [derin@otis ccnm_mprage_v4.5_long]$ long_qdec_table --qdec qdec/ccnm_prog_30_long_Th.qdec.table.dat --cross --out qdec/ccnm_prog_30_long_Th.cross.qdec.table.dat Parsing the qdec table: qdec/ccnm_prog_30_long_Th.qde

Re: [Freesurfer] WM modification

I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectly just b

Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

glad to hear it worked. it can be tricky getting the stream to work in a 'one size fits all' kind of way. n. On Thu, 2012-04-19 at 16:45 -0700, Joshua Lee wrote: > Nick, > Thank you. This recon-all script resolved my problems. I really > appreciate this post. > - > > Josh > > > > - > Joshua