Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

recon-all: 'segmentation fault'
by Mark Plantz 28 Aug '13

28 Aug '13

Hello all, I recently created a .gca atlas for a set of special subjects. After running recon-all for one of these subjects, I was left with the following error during the 'Subcortical Segmentation' section: *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* * * I also attached a copy of the .gca atlas, the labels.mgz file, and the LUT I am using. Right now I have two probable causes of the problem: 1.) Since I did not include all of the regions as the normal .gca atlas, recon-all may be exiting with error. [I only included the following regions for labels: caudate, white matter, gray matter, cortex, thalamus, hippocampus, parahippocampus, putamen, pallidum, and amygdala]. 2.) I used a different look-up table [LUT] with different segmentation values for the previously listed regions. Do you think that either of these could be the reason for the segmentation fault? Any ideas on how to get around it? Thanks in advance. Best, MP atlas.gca<https://docs.google.com/a/u.northwestern.edu/file/d/0BzKLhN7P9kNQR0JYZTV6dG…>

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recon-all issue (CSF seg as gray matter)
by Alexandre Gramfort 28 Aug '13

28 Aug '13

Hi, after running recon-all on many datasets without any manual intervention, it looks like I finally have to. As you can see in : https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at… the CSF is segmented as gray matter while white+gray matters are merged. what's my best option to fix this? thanks Alex

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apply a label to an overlay in tksurfer
by Sarah Madsen 27 Aug '13

27 Aug '13

Hello, Is there a way to apply a label to a mgh file? I would like to show a gray brain with values from an mgh shown only in the significant areas (ie only within my label). Is there a way to do this? I have a set of mgh files with beta values from a regression. I also have a set of labels for the significant areas. Both sets of files were created in matlab and are in fsaverage space. I can open the two files together in tksurfer and see the entire beta map, along with the label for the significant regions. Is there a way to zero-out all of values in the mgh overlay which fall outside of my label? A command line option would be preferable, since I have several maps. Thank you very much!

2 1

Freesurfer dependencies
by ye tian 27 Aug '13

27 Aug '13

Dear Freesurfers, Where may I find a list of freesurfer dependent libraries? Thank you very much! Sincerely, Ye

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Otto: update freesurfer to latest version?
by Otto Muzik 27 Aug '13

27 Aug '13

Dear All, I would like to upgrade my freesurfer distribution to the latest version - Is there an automated procedure to do this? My current version is linux-gnu-stable5-20110522 Many thanks! Otto

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tutorial subject not found
by leila nasehy 27 Aug '13

27 Aug '13

Dear Supporter I am new to freesurfer and have started to download tutorial data for tracula.There is an error saying: "hostname: Host name lookup failure" what shall I do? Regards Leyla

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pb reading .annot in matlab/python
by Alexandre Gramfort 27 Aug '13

27 Aug '13

hi, when trying to read the following .annot file: https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig… using the following matlab code: -- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) -- there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)" the script outputs: -- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 -- in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out? thanks Alex

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Recon-all error
by pfotiad＠nmr.mgh.harvard.edu 27 Aug '13

27 Aug '13

Hi FS Commuity, I am using the stable version 5.3 of FS to recon-all a subject of mine, but the job is aborted and gives the following message: The command that I ran is: recon-all -all -subjid /cluster/ichresearch/Petechial/MEG/CAA_022_struc Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 Found 2 runs /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Exit 1 Also, I tried doing the same recon-all with the stable 5.0 version and it runs fine. Therefore, I was wondering whether you could tell me why is this happening. By the way I have also attached the recon-all.log. Thank you for your time. Best, Panos

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Clarification regarding bvec processing in TRACULA
by Salil Soman 27 Aug '13

27 Aug '13

Hi, After much searching, it appears to be pretty uniform that the product DTI sequence performed on GE requires the y gradient to be flipped. For the datasets with which I am working diffusion toolkit, vistalab and exploredti all require the y gradient to be flipped. However, Tracula makes appropriate outputs when I give it the default gradient table without flipping Y. When I flip Y and run it through Tracula, the forceps major is inverted (noted by checking the overlay of dtifit_fa and dtifit_V1 using fslview and by using TVglyphView using DTI-TK. I suspect that somehow Tracula is flipping the Y sign for the gradient (while the other programs I mentioned do not) - can anyone confirm this? Thanks! -Sal

2 1

bug reading BRIK
by Yuval Harpaz 27 Aug '13

27 Aug '13

Dear Team I tried to convert AFNI BRIK file to mgz using mri_convert. the MRI was shifted strangely. I overcame it by converting the MRI to nii using afni command (3dcopy) and from there to mgz with MRI convert. If you wish to fix the BRIK reader please see the info below. --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-51-generic x86_64 --------------------------------------------------------------------- shifted transformation matrix 0 0 -1 128.5 1 0 0 -127.5 0 -1 0 75.5 correct transformation matrix 0 0 -1 127 1 0 0 -127 0 -1 0 180 The MRI is aligned to a master supplied by brainhull<http://kurage.nimh.nih.gov/meglab/Meg/Brainhull>for MEG position using the procedure described in the link. I can attach a BRIK file if anyone wants to dig into it. thanks Yuval Dr .Harpaz BIU MEG lab <http://faculty.biu.ac.il/~goldsa/index.html>

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Freesurfer August 2013