[Freesurfer] (no subject)
I think this may have been something that other people have figured out, and I would be grateful to know how. In the past week if I try to run autorecon-2 it fails. Running each individual command that make up autorecon-2 it would seem that the error is with the final stage (-cortribbon). The message this generates reads as: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance avC06-1 mris_volmask.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory Linux jalapeno25.fmrib.ox.ac.uk 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS How can I get around this? Thanks, Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Autorecon1 and combining data from different sessions
I have two sets of images, one collected at timepoint 1 and one at timepoint 2, for each patient and control in an MS study. I am now trying to run autorecon1 on this data, at the same time attempting to form a combined model fit. I am using the following script: for subject in ***; do if [ ! -f $SUBJECTS_DIR/$subject-1/mri/brainmask.mgz ]; then fsl_sub -q short.q -a lx24-amd64 -l ../group_study/logs recon-all -i $subject/00/struct_noneck.nii.gz -i $subject/02/struct_noneck.nii.gz -subjid $subject-1 -autorecon1 -force The following error message is generated for the around half of the subjects, yet there seems to be nothing especially different between the ones that work and the ones that fail. error reading from file /Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img mri_average: MRIread(/Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img) failed Any ideas? Thanks, Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thickness repeatability
We have been following the protocol in Han's paper to test repeatability and the following questions cropped up: 1) how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?; 2) what was the reason for choosing this size? Thanks, D Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM volume estimation - image capture
Whilst estimating white matter volume using mris_wm_volume is it possible to save an image for inspection? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Feedback on Talairach QA and Q about segmentation in several atrophy
Using the -notal-check flag after recon-all to bypass Talairach allowed us to reclaim several images for inclusion in a study containing MS patients with severe atrophy. However, one image (which is nearly all ventricle!) is proving difficult to segment. The segmentation process parcels up bits of the ventricular space as thalamus and as caudate. Is there a way around this, or do images with very severe atrophy need to be excluded? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Linear registration of subject meshes with FLIRT
In the FreeSurfer reliability paper, you recommend linearly registering the subject's meshes to each other and point to the Jenkinson paper. How actually is this done with FLIRT? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mean FA values using wmparc
Once FA results are co-registered is there an easy way to use the wmparc.mgz to collect the mean FA values by region, or do we need to treat it like FMRI and make masks of each parcel and collect each mean separately? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FA registration problems
We are currently attempting to check the FA registration of each subject within an MS study group using the following command: tkregister2 --s fsaverage --surf white --reg /Volumes/Data/magnims/group_study/P??-??/dti_analysis/fa-tal.nii.reg --mov /Volumes/Data/magnims/group_study/P??-??/dti_analysis/fa-tal.nii However, this generates the following error message despite there being an orig.mgz in the fsaverage directory: ERROR: could not find orig as either mgz or COR Any ideas on what the problem might be? Thanks Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_ca_register
In addition to this we have several datasets here that have a couple of subjects failing with: Killed ERROR: mri_ca_register with non-zero status Linux jalapeno14 2.6.20-1.2320.fc5 #1 SMP Tue Jun 12 18:50:49 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux I see from the new 4.0.3 release notes that there is a fix for mri_ca_register for Darwin but all our errors have been on Linux. Could this be the same problem? D Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
