Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Tracula stats COR-.info does not exist
by Simon Jones 15 Dec '15

15 Dec '15

Dear Tracula developers, I posted a problem with tracula when I ran trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message Loading output reference volume from /home/spj24/app/freesurfer/subjects/cvs_avg35 corRead(): can't open file /home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35 There is no file called COR-.info in the directory /home/spj24/app/freesurfer/subjects/cvs_avg35/ I have now changed the lines in the configuration file set doregcvs = 1 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # #set cvstemp = donald set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects to set doregcvs = 1 set cvstemp = cvs_avg35/mri/brainmask.mgz set cvstempdir = $FREESURFER_HOME/subjects i.e. explicitly pointing to an image in the cvs_avg35 directory and the stats seem to complete without error. Is that the right thing to do? Thanks for your help, Simon

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Tracula with multi-shell data?
by Henrik Sjöström 15 Dec '15

15 Dec '15

Hi! I have some questions regarding Tracula and multi-shell DWI. -Is it possible to activate the multi-shell model within bedpostx when running it through tracula? -does anyone have experience on running multi-shell data through Tracula (2 or 3 crossing fibers)? We are planning an experiment and discussing protocols consisting of around 32 directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions on this with regard to Tracula processing. Thanks! Henrik Sjöström

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Tracula Tracts density
by John Anderson 15 Dec '15

15 Dec '15

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TRACULA visualisation differences
by Worker, Amanda 15 Dec '15

15 Dec '15

Hi all, I'm just visualising tracts that have been processed using TRACULA and I'm noticing some differences that seem slightly odd. For example, when I load the ILF for one subject, the pathway looks huge and takes up a very large portion of the brain. However, when I load the same tract along with all of the other tracts it looks like a well segmented region. I have checked my registration with the T1 and it looks good, so I'm not sure why there is a difference. Looking at the stats for this tract volumes range from 300-600 approx. This is a patient vs control study so I would expect some differences in volume, but this seems like a big difference from the example given on the wiki which is around 160. But the average MD and FA seem reasonable and consistent at around 0.0008 and 0.4. This is the same for many of the subjects - would you base your quality control on the visualisation of the single tracts or all of the tracts loaded together. Is there an obvious difference/ why would they load differently? I have attached some screenshots so that you can see what I mean. Thanks in advance. Amanda

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Question about running recon-all with deface
by Mishra, Virendra 15 Dec '15

15 Dec '15

Hi, I will appreciate if somebody could reply to my message that was posted earlier. I copy-paste the message here again. We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0 on CentOS. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all -i original_T1 -deface 4) Step 4: recon-all -i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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recon-all base error
by salvatoreandrea.92＠libero.it 15 Dec '15

15 Dec '15

Hi Freesurfer experts! I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error: Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation Cannot allocate memory Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/LinuxI tried with a more powerful pc but I encountered the same problem. Following further information: SUBJECT template_base DATE ven 11 dic 2015, 08.17.47, CET USER salvatore HOST salvatore-HP-630-Notebook-PC PROCESSOR x86_64 OS Linux Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/salvatore/freesurfer/bin/recon-all PWD /home/salvatore/freesurfer/subjects/template_base/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh

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Re: [Freesurfer] mri_label2vol --fill-ribbon argument
by Arnaud Boré 14 Dec '15

14 Dec '15

Dear Freesurfer's experts, I wanted to add this picture so you can understand better what I mean by "The ribbon is not well filled". Is there a way to fill the ribbon completely ? [image: Images intégrées 1] Thank you in advance for your help. PS: If needed here is a link to the picture https://www.dropbox.com/s/wmeez9ajfuvni9r/label2vol_ribbon_not_filled_corre… Arnaud

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Freesurfer 6 - matlab crash
by Scott Quadrelli 14 Dec '15

14 Dec '15

Hi, I’m running freesurfer 6 on a cluster. I am having issues with the matlab crashing during the hippocampal segmentation. I am allocating 10gb for each job, however that hasn’t fixed the problem. Sometime the segmentation works fine, however many segmentations fail due to matlab crash. I have attached two example crash reports one with ‘segmentation violation’ the other common one is ‘Abort signal detection’. What else should we be looking at to fix the problem ? Cheers, Scott

1 0

Graph theory analysis in R
by Watson, Christopher 14 Dec '15

14 Dec '15

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the release of an R package I created, called "brainGraph", for performing graph theory analyses of brain MRI data. You can use it for cortical thickness, volume, surface area, or LGI. It can also be used for tractography data (I have code that works with the outputs of FSL's "probtrackx2"), and it should work for resting-state fMRI as well. It is very heavily dependent on the fantastic R package "igraph" (see http://igraph.org/redirect.html) I created a GUI for quick and easy data exploration, but it isn't quite as polished as others out there (e.g., BrainNet Viewer). For usage, please see the User Guide I put together (direct PDF link: https://www.dropbox.com/s/j831n3q9muyz1go/brainGraph_UserGuide.pdf?dl=0 ). You will find some code for getting your data into R, and I have documented many analysis steps and include multiple figures. I hope this is intuitive for both veteran and novice R users. Additionally, there are System Requirements, Installation instructions, and links for help learning R. Some features that should be of interest include: * bootstrapping & permutation testing * random graph generation, small-worldness, and global/local/nodal efficiency * rich-club calculations * robustness ("targeted attack" or "random failure") & vulnerability: PDF of figure (PNG: https://www.dropbox.com/s/k14gdg1lomhh4l2/failPlot-1.pdf?dl=0) * Plotting GUI - full GUI (PNG): https://www.dropbox.com/s/e0hdng7flrxsgd2/brainGraph_GUI.png?dl=0 * Plotting GUI - union of vertex neighborhoods (PNG): https://www.dropbox.com/s/aag5cn1p1z9xzxr/brainGraph_GUI_neighborhoods.png?… * Plotting GUI - community (module) plots (PNG): https://www.dropbox.com/s/8zzpd5j268qstmg/brainGraph_GUI_communities.png?dl… You can install it directly in R by typing: install.packages('brainGraph') My Github page for the package (https://github.com/cwatson/brainGraph) contains the development version, and you can install that by typing: devtools::install_github('cwatson/brainGraph') Please see the NEWS.md file (https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for updates made since the CRAN submission. To work properly on Windows, you may need to install the devel version. This is still a work-in-progress, so I am very happy to receive bug reports, feature requests, general coding help questions, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-help Chris Watson

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excessive topological defect
by Elisabetta del Re 14 Dec '15

14 Dec '15

Dear FreeSurfer team, we are running FreeSurfer on 1.5T cases. For a few of them we get error messages that I am attaching. Mostly the message error relates to excessive topological defect. Any suggestions you can give to us? Thank you, regards, Elisabetta -- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre(a)hms.harvard.edu

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