Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

flipping TRACULA tracts
by Barbara Kreilkamp 27 Jul '16

27 Jul '16

Dear Freesurfers, I've got data pertaining to patients with left and right-sided temporal lobe epilepsy (TLE). My aim is to group those tracts according to side of epilepsy for waypoint comparisons. Basically for patients with right TLE I'd like to look at right tracts and at the same time for patients with left TLE I'd like to look at left tracts (ipsilateral tracts), I need to do the same for the contralateral tracts. Is there a straightforward way of doing this? I've already copied the tracts to respective ipsi and contralateral byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_contraRTLE.}; done Now I have to flip the x-coordinates in the patients with right TLE (to make them more comparable to the tracts of the patients with left TLE). That will not be a problem, but I wonder if I am missing something? Can I then just go ahead and run trac-all -stats -c dmrircfile to generate the mean waypoint tracts etc.? Thank you very much, Best wishes, Barbara

2 2

TRACULA group stats visualization
by Derek Pisner 27 Jul '16

27 Jul '16

Dear Anastasia, I am running into an issue with the trac-all -stat option on our longitudinal TRACULA data. Everything runs smoothly through all earlier stages, and I checked individual subjects' merged outputs in freeview with -tv mode. Everything looks fine. Also, then when I run trac-all -c dmric_config -stat, everything finishes without error. But then when I open the results with the command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt I get the image seen in the attached .png file. Any idea what might be causing this? Many thanks in advance for you help. Best, Derek

2 8

When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
by Knut J Bjuland 27 Jul '16

27 Jul '16

flirt.fsl -ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 -verbose 0 -omat/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat-init/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.schterminate called after throwing an instance of'NEWMAT::SingularException'Abort (core dumped) ERROR: flirtFedora 24glibc-2.23.1-8.fc24.x86_64gcc-6.1.1-3.fc24.x86_64libstdc++-6.1.1-3.fc24.x86_64ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x00007ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x00007feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6(0x00007feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x00007feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x00007feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x0000557ba6f46000)Knut Jørgen Bjuland

2 3

New hippocampal subfields
by Jin Kyu Gahm 26 Jul '16

26 Jul '16

Hello, I was trying the new segmentation module of hippocampal subfields, but I also encountered the same errors as Pierre reported a week ago: ------------------------------------------------------------------------------------------------------------------ Invalid MEX-file '/tmp/MCR_1031368111/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared object file: No such file or directory Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 133) ------------------------------------------------------------------------------------------------------------------ Eugenio - I wonder if you already solved the problem. Thanks for your help! Best, Jin

2 1

fMRI Postdoctoral Fellow
by Thomas Yeo 26 Jul '16

26 Jul '16

Dear All, I am looking to hire a postdoc with either strong machine learning background OR system neuroscience background. Prior experience with fMRI is a plus. Topics are flexible. Example topics include individual-subject brain parcellations, relationships between behavior and brain networks, dynamic functional connectivity, meta-analysis, neural mass modeling, graph theoretic modeling of brain networks, etc. Other details below. Regards, Thomas Requirements: Ph.D. in neuroscience, computer science, electrical engineering, statistics or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (ythomas(a)csail.mit.edu) with your CV. Deadline: Whenever the position is filled.

1 0

question about reslicing
by Dorsa Haji Ghaffari 26 Jul '16

26 Jul '16

Hi, I re-sliced my left thalamus so that the size and number of slices correspond with the original MRI, but when I open it in freeview, it shows an extra part( like a cube) on the bottom of the image ( I have attached the mask). do you have any idea how to solve that? Also how can I make sure that the position and size of the thalamus makes sense since the thalamus mask has a different slice size and number than the original mri? Thank you Dorsa

3 7

mri_glmfit problem/2 group 6 covariates
by miracle ozzoude 26 Jul '16

26 Jul '16

Hello doug, while running the mir_glmfit problem, i encountered this problem “ INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 1 Education 15.5625 1.99902 2 Firstscore 1.03375 0.341785 3 Secondscore 1.03906 0.370678 4 Thirdscore 1.13844 0.4768 5 Averagescore 1.07375 0.364046 Class Means of each Continuous Variable 1 Group1 35.6316 15.0526 1.0342 1.2111 1.4289 1.2305 2 Group2 46.2308 16.3077 1.0331 0.7877 0.7138 0.8446 INFO: gd2mtx_method is dods Reading source surface /Users/paul/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/paul/Desktop/improvervsdeclinermri cmdline mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd new.MOT.fsgd dods --C new.firstmatrix.mtx --C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir sysname Darwin hostname TC-CT-LAB4-iMAC.local machine x86_64 user paul FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh logyflag 0 usedti 0 FSGD new.MOT.fsgd labelmask /Users/paul/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.new.MOT.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.new.MOT.glmdir Loading y from /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.new.MOT.glmdir/Xg.dat Normalized matrix condition is 1.27568e+06 Design matrix ------------------ 1.000 0.000 23.000 0.000 15.000 0.000 1.680 0.000 1.780 0.000 2.110 0.000 1.860 0.000; 1.000 0.000 43.000 0.000 16.000 0.000 0.840 0.000 0.890 0.000 1.190 0.000 0.970 0.000; 1.000 0.000 39.000 0.000 17.000 0.000 0.790 0.000 0.840 0.000 1.220 0.000 0.950 0.000; 1.000 0.000 19.000 0.000 13.000 0.000 0.840 0.000 1.060 0.000 1.260 0.000 1.050 0.000; 1.000 0.000 28.000 0.000 13.000 0.000 1.060 0.000 1.120 0.000 1.370 0.000 1.180 0.000 …………………………………………………………………………………………………………………... ERROR: matrix is ill-conditioned or badly scaled, condno = 1.27568e+06 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd new.MOT.fsgd dods --C new.firstmatrix.mtx —C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir 2. The FSGD file (if using one) 3. And the design matrix above” Below are my fsgd file and contrast matrix. I can’t add DeMeanFlag 1 because I am using dods and interested in group difference. Also, none of the responses from people with similar error helped me. I am using version 5.1 Thank you very much. Paul GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Education Firstscore Secondscore Thirdscore Averagescore Input 01053p/fsdir Group1 23 15 1.68 1.78 2.11 1.86 Input 01054p/fsdir Group1 43 16 0.84 0.89 1.19 0.97 Input 01061p/fsdir Group1 39 17 0.79 0.84 1.22 0.95 Input 01062p/fsdir Group1 19 13 0.84 1.06 1.26 1.05 Input 01074p/fsdir Group1 28 13 1.06 1.12 1.37 1.18 Input 01080p/fsdir Group1 28 18 0.97 1.26 1.33 1.19 Input 01099p/fsdir Group1 37 16 0.87 1.15 1.37 1.13 Input 01101p/fsdir Group1 20 14 1.00 1.37 1.45 1.27 Input 01102p/fsdir Group1 58 16 0.97 1.12 1.41 1.27 Input 01121p/fsdir Group1 28 18 0.87 1.00 1.00 0.96 Input 01127p/fsdir Group1 46 16 0.77 1.06 1.58 1.14 Input 01128p/fsdir Group1 21 16 1.58 1.78 1.78 1.71 Input 01130p/fsdir Group1 22 16 1.50 1.22 1.63 1.45 Input 01131p/fsdir Group1 19 13 1.54 1.68 2.11 1.78 Input 01141p/fsdir Group1 17 12 1.00 1.09 1.30 1.13 Input 1044pp/fsdir Group1 51 16 0.94 1.54 1.68 1.39 Input 1053pp/fsdir Group1 44 16 1.22 1.30 1.50 1.34 Input 1058pp/fsdir Group1 78 12 0.61 1.12 1.15 0.96 Input 1060pp/fsdir Group1 56 13 0.60 0.63 0.71 0.65 Input 01047p/fsdir Group2 50 18 1.12 0.94 0.94 1.00 Input 01075p/fsdir Group2 20 15 1.12 0.84 0.60 0.85 Input 01077p/fsdir Group2 48 16 0.43 0.35 0.35 0.38 Input 01091p/fsdir Group2 23 16 1.58 1.22 1.22 1.34 Input 01096p/fsdir Group2 17 17 1.50 1.26 1.19 1.32 Input 01113p/fsdir Group2 51 18 0.75 0.69 0.60 0.68 Input 01124p/fsdir Group2 43 18 1.33 0.89 0.87 1.03 Input 01134p/fsdir Group2 59 16 0.82 0.60 0.60 0.67 Input 1004pp/fsdir Group2 46 19 0.82 0.79 0.71 0.77 Input 1040pp/fsdir Group2 64 13 0.92 0.55 0.46 0.64 Input 1043pp/fsdir Group2 49 16 1.58 1.03 0.89 1.17 Input 1064pp/fsdir Group2 78 12 0.40 0.11 0.10 0.20 Input 1067pp/fsdir Group2 53 18 1.06 0.97 0.75 0.93 first contrast matrix 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 group1 greater than group 2 regressing out age, education, first, second, third and average second constrast matrix -1 1 0 0 0 0 0 0 0 0 0 0 0 0 group 2 greater than group 1 regressing out age, education, first, second, third and average third contrast matrix 0 0 0 0 0 0 0.5 -0.5 0 0 0 0 0 0 group 1 showing increasing correlation with first score compared to group 2 fourth contrast matrix 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 0 0 group2 showing showing increasing correlation with first score compared to group 1 fifth contrast matrix 0 0 0 0 0 0 0 0 0.5 -0.5 0 0 0 0 group1 showing showing increasing correlation with second score compared to group 2 sixth contrast matrix 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 group2 showing showing increasing correlation with second score compared to group 1 seventh contrast matrix 0 0 0 0 0 0 0 0 0 0 0.5 -0.5 0 0 group1 showing showing increasing correlation with third score compared to group 2 eighth contrast matrix 0 0 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 group2 showing showing increasing correlation with third score compared to group 1 ninety contrast matrix 0 0 0 0 0 0 0 0 0 0 0 0 0.5 -0.5 group1 showing showing increasing correlation with average score compared to group 2 tenth contrast matrix 0 0 0 0 0 0 0 0 0 0 0 0 -0.5 0.5 group2 showing showing increasing correlation with average score compared to group 1

4 7

normalizing in fsgd
by miracle ozzoude 26 Jul '16

26 Jul '16

Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it? GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8 Thank you, Paul

3 5

Projecting AAL atlas to fsaverage
by Salim Arslan 26 Jul '16

26 Jul '16

Hi, We are trying to project the AAL labels from volume to surface in order to be able to include the AAL atlas to our surface-based experiments. What we have done so far is that we projected the volume labels to the fsaverage white surface using mri_vol2surf function in the following setting: mri_vol2surf --mov ROI_MNI_V5.nii --mni152reg --hemi lh --surf white --o $OUT_FOLDER/lh.fsaverage.white.ROI_MNI_V5.asc.w --out_type paint --trgsubject fsaverage where ROI_MNI_V5.nii corresponds to the ALL atlas in MNI space. After converting the output asc.w file first to a FreeSurfer-compatible format, and then to gifti, we realized that the result was garbage (Please see Fig. 1). Following a suggestion from a member of our research group, we applied dilation to the input atlas (ROI_MNI_V5.nii) and re-ran the function with the same setting as above. This way, the final cortical parcellation was not perfect but still seemed to be usable (Please see Fig. 2). The problem here is that, as you may have also noticed, some of the cortical parcellation boundaries do not follow the folding patterns across the surface. Besides, some parcels just do not seem to be right (see the arrows in the motor area). Having said that, I have the following questions:1- Why is not possible to properly project the labels onto the surface without first dilating the input atlas?2- If dilation is not a big issue, how would the experts in the mailing list interpret the distortions, especially in the motor area? Is it kind of a side effect we should expect after such process between volume and surface? >From the archive I can see that similar questions have been posted a few years back (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27586.html, https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23761.html) Although these messages are highly useful, apparently there is still not a standard solution to this problem. Please accept my sincere apologies if this is still considered as re-posting. Any feedback is greatly appreciated. Thanks for your attention. Kind regards,Salim

1 0

GLM significance table
by Caroline Beelen 26 Jul '16

26 Jul '16

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example): Mri_glmfit -- table aparc_rh_thickness_stats.txt -- fsgd gender_dys.fsgd (see attached; example of a fsgd-file) -- C Int.mtx -- C Dys.mtx -- C Gender.mtx -- glmdir roi.gender_dyslect.rh.thickness.glmdir The file was created and it contained a sig.table.dat folder. However, the values in this folder are all quite low. According to information found on your website they should correspond to (-)log10(p) values. I found mainly values between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 (non-existing). Could you please explain to me what I did wrong? Thank you very much! Kind regards, Caroline

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer