[Freesurfer] ages of subjecs in buckner_data-raw_dicoms.tar.gz

Hi there, we are trying to determine small atrophy changes based on novel analytic approaches. At this point of our project MPRAGE sequences were adquired in a group of MCI patients (65-85 yrs.) but we do not have healthy controls of the same age interval. For this purpose, I decided to downl

Re: [Freesurfer] ages of subjecs in buckner_data-raw_dicoms.tar.gz

Hi Jose, you're better off getting the Oasis dataset from Dan Marcus and Randy Buckner. It's much bigger, well characterized and distributed on DVD. cheers, Bruce On Fri, 5 Jan 2007, Jose Luis Cantero wrote: Hi there, we are trying to determine small atrophy changes based on novel analytic

[Freesurfer] label

Hi All, When I ran mri_annotation2label --subject UNC_4 --hemi rh --labelbase ./labels/aparc-rh --table $FREESURFER_HOME/surface_labels.txt Some labels are always skipped such as 6,7... I also tried on tutorial data, the same thing happened. Any ideas? Is surface_labels.txt a complete label li

[Freesurfer] ca normalize

I have a subject that has gotten stuck on the CA Normalize step. I have tried running it several times and it always gets stuck in the same place, running away for days if I let it, using 99.9% of the CPU. We are running RH4-x86_64-R302. Is this something that has been observed / dealt with

[Freesurfer] Coloring problem after autorecon2

Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/colo

Re: [Freesurfer] ca normalize

Hi Don, I've never seen that happen. Can you send us the data? Bruce On Fri, 5 Jan 2007, Don Hagler wrote: I have a subject that has gotten stuck on the CA Normalize step. I have tried running it several times and it always gets stuck in the same place, running away for days if I let it, u

[Freesurfer] Freesurfer Installation Problem

I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the installation with the command "tkmedit bert orig.mgz": $ tkmedit bert orig.mgz Talairach transform /autofs/space/freesurfer/subjects/bert/

Re: [Freesurfer] Coloring problem after autorecon2

Hi Niels, This looks like what would happen to the aseg if it was run on a subject who was missing a cerebellum. Did you run the aseg before you manually fixed the cerebellum and not re-run it? If so, the aseg needs to be rerun (in fact, all of -autorecon2 does). Another thought is, how di

[Freesurfer] control points and white matter edits

Hi all, I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled

RE: [Freesurfer] problem with mris_anatomical_stats

Abdel, Indeed mris_fix_topology had the same bug as mris_anatomical_stats (when running on Slackware Linux). I've posted a fixed version of mris_fix_topology here: http://surfer.nmr.mgh.harvard.edu/pub/dist/ named: mris_fix_topology.gz mv this to your $FREESURFER_HOME/bin, then type: gu

RE: [Freesurfer] control points and white matter edits

Hi Paul, The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get. Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them i

[Freesurfer] FS-FAST: problem with extracting BOLD time courses with a tksurfer tcl script

Hi, I am trying to extract numerical values for BOLD time courses of (a large number of) ROIs. For this purpose I use a tksurfer tcl script. Everything works fine when I only have a small number (~6) of contrasts/stimulus categories (as defined in the paradigm files), but if I increase the number