Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

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.

2 1

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

2 1

[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

2 3

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

1 0

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

2 2

Avg.Thickness in a cluster
by Antonella Kis 18 Aug '11

18 Aug '11

Dear Doug, I just checked my results for the average thickness from each subject generated in the csdbase.y.ocn.dat file in different clusters (e.g. I have 5 clusters for p<0.05). For cluster #1 - posteriorcingulate, the average thickness for subject 1 is different from the average thickness value in the same region-posteriorcingulate, in the lh.aparc.stats for the same subject. I thought it should be the same. Why they are different? Is this right? MANY THANKS! Antonella

1 0

Trac paths error - bedpost files not found
by Moiyadi, Ammar 18 Aug '11

18 Aug '11

Hi Freesurfers - I am encountering an error in trac-all -paths where it cannot find the mean_dsamples.nii.gz file in my dmri.bedpostX directory since it was not created during the bedpost step. Because I ran the original bedpost (not the Seychelles version) I was wondering if this output file was specific to the other version. I have a feeling bedpost is not getting through its entire process but I don't receive any error messages as feedback - once it reaches 47 slices processed it starts queing the post processing stage and then the program ends. Is it possible that the post processing stage has not completed and as a result the required files are not being created? Currently I have the following files in my bedpost output directory: dyads1.nii.gz dyads2.nii.gz mean_th1samples.nii.gz mean_th2samples.nii.gz mean_f1samples.nii.gz mean_f2samples.nii.gz mean_ph1samples.nii.gz mean_ph2samples.nii.gz merged_th1samples.nii.gz merged_th2samples.nii.gz merged_f1samples.nii.gz merged_f2samples.nii.gz merged_ph1samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz It appears I am missing both the mean_dsample and dyads_dispersion files. Any ideas why these files haven't been created and when they should have been created during bedpost? Thanks for your help, Ammar Moiyadi

2 3

update v5.1 and trac-all command
by Carolina Valencia 18 Aug '11

18 Aug '11

Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command? Thanks, Best regards Carolina

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Freesurfer August 2011