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30099 discussions

Creat ROI from annotation file
by wangzhiwei3233 01 Dec '14

01 Dec '14

Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture). Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter. Could anyone help me creat good masks? Thanks a lot! Zhiwei

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mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
by lindsay hanford 01 Dec '14

01 Dec '14

Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanford(a)gmail.com

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Number of slices generated in the brainmask.mgz
by Gunjan Gautam 01 Dec '14

01 Dec '14

Hi FreeSurfers, brainmask.mgz is generating 256 slides per volume. How can I have control over it, in terms of generating less number of slides (say 181) per volume? Gunjan

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ALLvsFIX contrast
by Reza Rajimehr 01 Dec '14

01 Dec '14

Hi, In an fMRI experiment, I have 60 conditions. I want to make ALLvsFIX contrast to select vertices that are visually responsive, by finding vertices that have ces values greater than zero in this contrast. For this, I can run: mkcontrast-sess -analysis analysisname -contrast allvsfix -a 1 -a 2 -a 3 ... -c 0 Since this is a very long command, is there a smarter way to make such contrast? Thanks, Reza

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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/

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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

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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'

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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

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