Re: [Freesurfer] recon-all autorecon2 error.

Mithra, Confirm that your skull-stripped volume (brainmask.mgz) shows just brain w/o skull, and that is has the cerebellum intact. You could also send me the brainmask.mgz and nu.mgz files, and i can have a look. If you want to do that, use the filedrop to upload those files to me: https://ww

[Freesurfer] recon-all autorecon2 error.

Hello, I ran autorecon1 this step worked fine. The transform obtained from this step looked good. When I run autorecon2, I get a segmentation fault error. Can anybody tell me whats wrong. Thanks a whole bunch. Error: Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST

Re: [Freesurfer] mris_anatomical_stats error

The problem is that this is being done an the average subject, which does not have a wm.mgz file. Should be easy to fix. Johannes, can you send your cmd line? doug Nick Schmansky wrote: Johannes, wm.mgz is produced in the -autorecon2 stage of recon-all. A handy table to consult i

Re: [Freesurfer] mri_convert options

Hi Derin, we keep the parameters around, but don't use them in the standard recon stream, so it shouldn't matter. cheers, Bruce On Tue, 31 Oct 2006, Derin Cobia wrote: Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7

Re: [Freesurfer] mris_anatomical_stats error

Johannes, wm.mgz is produced in the -autorecon2 stage of recon-all. A handy table to consult is: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable or http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm Nick On Tue, 2006-10-31 at 11:49 +, Johannes Kl

[Freesurfer] mri_convert options

Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz s1501p.img mri/orig/001.mgz It came to my attention today that the values we used for TI, TE, and TR are all actually in ms, and corresp

Re: [Freesurfer] automatic processing

Hi Nic, in part it depends on where in the brain you are interested. The biggest need for manual intervention in reprocessing is to remove dura. This is mostly a problem near entorhinal cortex where the tentorium is tangent to the pial surface, and extremely difficult to distinguish from gray

Re: [Freesurfer] ROI group analysis

Hi Doug, I tried using the registration file in the tal-rfx dir for this group and I received the following error: ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. Can I

Re: [Freesurfer] mris_anatomical_stats error

Hi Johannes, you can use "label_area", but note that the current version doesn't take into account the reduction in surface area of the average surface relative to all the individuals. We'll need to fix it and get you a new version. cheers, Bruce On Tue, 31 Oct 2006, Johannes Klein wrote:

[Freesurfer] mris_anatomical_stats error

Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir conta

[Freesurfer] automatic processing

Hi, I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big pict

[Freesurfer] Morphological measures

Dear Freesurfer users after running Freesurfer, I got 11 colums (without structure name) in the recon_all.log file with the different morphological indices: e.g. 208122451 3.056 0.740 0.125 0.0242 0.6 15 0.179 G_cingulate-Isthmus but actually there should be only 9 col