Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

broken X extension library
by Bart Boets 30 Nov '14

30 Nov '14

Hello, I have been running recon-all and trac-all analyses through remote access on the openmind.mit.edu cluster (from a windows7 i7 laptop using MobaXterm). The following software was set available: module add openmind/fsl/5.0.7 module add openmind/freesurfer/5.3.0 module add openmind/git module add netcdf/gcc/64/4.3.1.1 module add cuda55/toolkit/5.5.22 export LD_LIBRARY_PATH=/om/user/satra/projects/SAD/scripts/lib/:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/om/user/ksitek/HCP/scripts/lib/:/cm/shared/apps/cuda55/toolkit/5.5.22/lib64:/cm/shared/apps/cuda55/toolkit/5.5.22/lib:/cm/shared/apps/cuda65/toolkit/6.5.14/lib64:$LD_LIBRARY_PATH I guess all analyses went fine, but when I try to inspect output data by using freeview I encounter the following problem: I can open Freeview but when it tries to open a brain volume, the software always crashes and gives this error message: boets_env[20:08][2.53][26%]bboets@openmind:dmri$ freeview -v dtifit_FA.nii.gz & [1] 7594 boets_env[20:09][2.58][26%]bboets@openmind:dmri$ X Error: BadRequest (invalid request code or no such operation) 1 Extension: 146 (Uknown extension) Minor opcode: 187 (Unknown request) Resource id: 0x8000c3 [xcb] Too much data requested from _XRead [xcb] This is most likely caused by a broken X extension library [xcb] Aborting, sorry about that. freeview.bin: xcb_io.c:735: _XRead: Assertion `!xcb_xlib_too_much_data_requested' failed. Abort freeview -v dtifit_FA.nii.gz [1]+ Exit 134 freeview -v dtifit_FA.nii.gz I logged in into the server using ssh. The problem is identical while using ssh –X or ssh –Y. (likewise if I try to visualize images through mricron on the server it works extremely slowly and unreliably ...) Do you have any advice on how to handle this? I did not find any solutions in the archive? Thanks! Bart Bart Boets, PhD Postdoctoral fellow of the Research Foundation - Flanders Child and Adolescent Psychiatry – KU Leuven, Belgium Visiting Researcher at the Gabrieli Lab / Mc Govern Institute for Brain Research Department of Brain and Cognitive Sciences - Massachusetts Institute of Technology 43 Vassar Street, 46-5115-B, Cambridge, MA 02139, USA tel: +1 617-324-6365 fax: +1 617-324-5311 Email: bart.boets(a)ppw.kuleuven.be<https://owa.groupware.kuleuven.be/owa/bart.boets@ppw.kuleuven.be> or bboets(a)mit.edu<https://owa.groupware.kuleuven.be/owa/bboets@mit.edu> https://perswww.kuleuven.be/~u0032380/

1 0

convert mgh file to nifti
by angela.favaro＠unipd.it 30 Nov '14

30 Nov '14

Dear all, I found some interesting findings about gyrification and I would like to test any related problem in structural connectivity. My idea was to use the area where I found significant lower gyrification in my sample to perform probabilistic tracking with FSL. My question is: is there any way to label the area of significant difference (or I have to manually draw it) and to transform it in a nifti format? Angela

3 8

Fwd:
by elahe' yargholi 29 Nov '14

29 Nov '14

Dear Freesurfer experts, I used 'recon-all' command ('recon-all -i path/EYT1.mgz -s EYrecon -all) in freesurfer 4.5 and after 8 hours of process, I received the an error and it stoped. The error says it can not find files in surf folder... recon-all.log is attached. I use virtual machine 10- Ubuntu 12.04 - freesurfer 4.5. I do appreciate your attention. BR, Elahe'

2 1

DICE coefficient computing inconsistency
by Luigi Antelmi 28 Nov '14

28 Nov '14

Dear member of the list, I've compared the output of mri_compute_seg_overlap (FS 5.1.0 and 5.3.0) against an home-made script to calculate the DICE coefficients between two asg.mgz files. The results ranges from being perfectly equal (e.g. label 58) up to an error at the second decimal place (e.g. label 42), which is not acceptable. Where do you think is the origin of these inconsistencies? Here's the complete result of the test: freesurfer VS python script label 2 = 0.975814 label 2 = 0.975759 label 41 = 0.980171 label 41 = 0.980135 label 3 = 0.980298 label 3 = 0.961283 label 42 = 0.983296 label 42 = 0.965541 label 4 = 0.979572 label 4 = 0.979572 label 43 = 0.975789 label 43 = 0.975789 label 17 = 0.950502 label 17 = 0.942725 label 53 = 0.953055 label 53 = 0.945481 label 10 = 0.983729 label 10 = 0.983117 label 49 = 0.988228 label 49 = 0.987909 label 11 = 0.97027 label 11 = 0.970270 label 50 = 0.952635 label 50 = 0.952635 label 12 = 0.974187 label 12 = 0.974187 label 51 = 0.976775 label 51 = 0.976775 label 13 = 0.972107 label 13 = 0.972107 label 52 = 0.981569 label 52 = 0.981568 label 18 = 0.921979 label 18 = 0.920228 label 54 = 0.95705 label 54 = 0.950452 label 26 = 0.887918 label 26 = 0.887918 label 58 = 0.9501 label 58 = 0.950100 label 14 = 0.973062 label 14 = 0.971466 label 15 = 0.963786 label 15 = 0.960308 label 5 = 0.897959 label 5 = 0.897959 label 44 = 0.926717 label 44 = 0.924583 The core of the home-made python script is: import numpy as np import nibabel as nib # usage: DICE('pathToAseg1.mgz','pathToAseg1.mgz',label) def DICE(dataPathX,dataPathY,label=1): # X and Y must be binary images # or specify label to be used (e.g LeftHippocampus=17) imageX = nib.load(dataPathX) imageY = nib.load(dataPathY) X = (imageX.get_data()==label).astype(float) Y = (imageY.get_data()==label).astype(float) VolX = X.sum() VolY = Y.sum() XY = (X*Y).sum() # X*Y prod element by elements. XY=volume of intersection diceXY = 2.0 * XY / (VolX + VolY) return diceXY Best regards, Luigi Antelmi

1 0

recon-all error in freesurfer 4.5
by elahe' yargholi 28 Nov '14

28 Nov '14

Dear Freesurfer experts, I used 'recon-all' command ('recon-all -i path/EYT1.mgz -s EYrecon -all) in freesurfer 4.5 and after 8 hours of process, I received the an error and it stopped. The error says it can not find files in surf folder... recon-all.log is attached. I use virtual machine 10- Ubuntu 12.04 - freesurfer 4.5. I do appreciate your attention. BR, Elahe'

1 0

mri_vol2surf --prodist measuring from pial surface
by Kirstie Whitaker 27 Nov '14

27 Nov '14

Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

1 0

Freeview - Vector and Spline information for Sufaces
by Güllmar, Daniel 27 Nov '14

27 Nov '14

Dear all, I'm currently trying to view face and/or vertex normals in freeview (of an existing surface). I've seen the option to load "vector display" data, but I do not know the format of such a file. Can someone help me with that issue? Regards, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.html

1 0

TRACULA mask error
by Worker, Amanda 27 Nov '14

27 Nov '14

Dear All, I have run all of the pre-processing steps on my DTI data and as I am checking my nodif_brain_mask I have realised that some of the masks have become distorted and twisted in some way. I have attached screenshots of both the raw data (which looks fine) and the white mask (which is distorted). In addition, as I have read that it is important to check the dtifit_V1 and dtifit_FA I have also included these in the word document, incase this helps. This distortion has occured for approximately a quarter of the subjects that I have processed and the rest look good. Please can you let me know if you have any ideas about what has gone wrong and how to fix this? Thanks in advance for your help, Amanda

1 0

Eccentric lesions
by Octavian Lie 27 Nov '14

27 Nov '14

Dear All, I am interested at getting as good pial/cortical reconstructions as possible on a series of epilepsy pt scans, some showing eccentric (cortical) lesions (focal encephalomalacias, infarcts, or after focal resections). One particularly difficult lesion type to get an accurate cortical surface is where there are prongs of grey matter bulging out (like a bag of worms), (mostly) without visible wm, see attached picture. These prongs are maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not included in the pia with the default recon. Lesion voxel intensities vary from 30-90. I tried cp, wm edits (using brainmask or T1 as referece), both, did not matter, it did not work. Since I am not intested in wm/subcortical segmentation but just in a good pia, I was wondering if I 'create' thin wm tracts through the center of these gm prongs to help pial segmentation. If this is a valid option, should I create those in brainmask, brain.finalsurfs or wm.mgz, and should I use 110 or 255 for the brush? Any other suggestions are appreciated. Nevertheless, I know there is a lot of tweaking of each lesion, and I try for more of a global approach to these kinds of lesions. Thank you, Octavian.

3 9

Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
by Jens Offenbach 27 Nov '14

27 Nov '14

We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens

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