Freesurfer

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19 participants
30088 discussions

cortical thickness in freesurfer 3.02 vs 4.5
by Rune X 22 Aug '11

22 Aug '11

Hi, We are concerned about differences of cortical thickness when we process the same scans in freesurfer 4.5 and 3.02. We have attached an excel spreadsheet of the differences in thickness between 4.5 and 3.02 using the mean thickness of parcellations of both versions in both hemispheres. The difference in the paracellations vary from 3-11% between the versions. Are these findings reliable and explainable in choosing freesurfer 4.5 as our final version. Any comment are greatly appreciated, Thanks! Rune

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pial and WM missing after reunning skullstrip
by Julia Hill 22 Aug '11

22 Aug '11

Hi Bruce I am new to freesurfer and im having a few issues with a number of my scans. The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas. When i review the scans afterwards, the pial and WM surfaces haven't included the original missing sections of the scans. How do i go back and include these missing sections? I have attached a screenshots. Thank you kindly Julia Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268

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recon-all error messages
by Catherine Wan 19 Aug '11

19 Aug '11

Dear List, I've been encountering a series of error messages when I did recon-all on a number of subjects, using Freesurfer v5.1 Below are the error messages for 3 different subjects (all with lesions). I tried them using both dicom and nifti, and on various computers, but the same messages appeared. Any advice would be much appreciated. Many thanks! Catherine *SUBJECT 1* Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 15 iterations marking ambiguous vertices... 188852 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /mnt/nfs/hippo1/freesurfer5/freesurfer/subjects/Aphasia_MIT/DMAR_pre1_nii/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.1436 (-5.0718) -vertex loglikelihood: -8.7336 (-4.3668) -normal dot loglikelihood: -3.6140 (-3.6140) -quad curv loglikelihood: -7.5212 (-3.7606) Total Loglikelihood : -30.0124 CORRECTING DEFECT 0 (vertices=98583, convex hull=1425) Excessive topologic defect encountered: could not allocate 1019599903 edges for retessellation Cannot allocate memory *SUBJECT 2* mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.9 mm, total surface area = 58524 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 060: RMS=0.039 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm Segmentation fault *SUBJECT 3 *(stuck on this step for > 48 hrs) CORRECTING DEFECT 0 (vertices=130, convex hull=179) After retessellation of defect 0, euler #=-30 (62919,184624,121675) : difference with theory (-51) = -21 CORRECTING DEFECT 1 (vertices=46, convex hull=64) After retessellation of defect 1, euler #=-29 (62936,184700,121735) : difference with theory (-50) = -21 CORRECTING DEFECT 2 (vertices=75, convex hull=105) After retessellation of defect 2, euler #=-28 (62974,184859,121857) : difference with theory (-49) = -21 CORRECTING DEFECT 3 (vertices=54486, convex hull=3968)

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bug report tracula stage 2
by Knut J Bjuland 19 Aug '11

19 Aug '11

Hi I have started to run tracula on my own data. However when I run the second stage I get this erros bedpostx_seychelles: line 260: /media/Elements/freesurfer/dti/1/dtsave/1/dmri.bedpostX/monitor: Permission denied. I have tried running is as root as well but it did not help. Is there anything I can do to bypass thiss error. I am using Fedora 15. Knut J

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qdec: Measure: area vs area.pial
by Tetiana Dadakova 19 Aug '11

19 Aug '11

Dear list, In qdec in "Measure" option I can choose either area or area.pial. What is the difference between them? Thank you, Tanja.

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Talairach error
by Ahmed, F, Me <fahmed＠sun.ac.za> 19 Aug '11

19 Aug '11

Hello Freesurfers, I got this error on my processing and wondered what the problem may be: Talairach Failure Detection Mon Aug 15 16:26:35 SAST 2011 /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/NN117/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 15 16:26:35 SAST 2011 Any help would be greatly appreciated! Kind regards, Fatima

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[BUG] mri_convert help inconsistency
by Chris Filo Gorgolewski 19 Aug '11

19 Aug '11

A tiny typo in mri_convert: filo@filo-Precision-M6500:~$ mri_convert | grep voxsize -vs, --voxsize <size_x> <size_y> <size_z> : specify the size (mm) - useful for upsampling or downsampling filo@filo-Precision-M6500:~$ mri_convert --voxsize mri_convert --voxsize mri_convert: unknown flag "--voxsize" type mri_convert -u for usage filo@filo-Precision-M6500:~$ mri_convert -voxsize mri_convert -voxsize mri_convert: argument -voxsize expects 3 floats; only 0 arguments after flag type mri_convert -u for usage filo@filo-Precision-M6500:~/workspace/nipype$ cat ~/opt/freesurfer/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Best, Chris

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skullstrip result after autorecon1
by Wei-Ta Chen 18 Aug '11

18 Aug '11

Hi I did autorecon1 on T1 structural brain images acquired by GE magnet. However, a small piece of skull with dura still remained on brainmask.mgz (around the occiput), even after adjustment of watershed threshold to 10. (Some brain would loss when threshold was lowered to 7 or 5). I wondered if I can use the brush to erase these pieces then click Save Volume from the File menu before continuing autorecon2 and autorecon 3? Do I have to do this? If I can use the brush to edit brainmask.mgz, do you recommend that instead of watershed adjustment because it is more intuitive and I don't have to find the optimal threshold value of watershed. Is there any difference between their effects? Thanks for your time and patience answering these. Best, Wei-Ta

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Re: [Freesurfer] FreeSurfer on AWS
by Pedro Paulo de Magalhães Oliveira Junior 18 Aug '11

18 Aug '11

I'll try to write a tutorial this weekend -- iOS 5 Em 18/08/2011, às 20:01, Nolan Nichols <bnniii(a)uw.edu> escreveu: Hi Pedro, I came across your post on the FreeSurfer mailing list and am trying to find the AMI you created ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html) I have tried a few times now to install FreeSurfer 5.1 on an AMI with EBS, but it is not working. Is there any chance you could help me out? Thanks! Nolan

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Problems Installing Freesurfer on an EC2 AMI
by Nolan Nichols 18 Aug '11

18 Aug '11

Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the "Testing your Freesurfer Installation" section. I am not trying to use any of the visualization tools, just "recon-all -s bert -autorecon1" and the mri_tools, like mri_convert. I get the following error when I run "recon-all -s bert -autorecon1" (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running "mri_info" to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan

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