Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

brainmask error
by Mads Jensen 25 Aug '14

25 Aug '14

Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log

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Crash
by D'anna, Lucio 25 Aug '14

25 Aug '14

Hi all, hope this email finds you well. I am a new user of this program. I tried to open lh.thickness opening a load surface but the program continues to crash. Please can you help me? Lucio Lucio D'Anna PhD Research Student Forensic & Neurodevelopmental Science Department Institute of Psychiatry King's College London Email: lucio.d'anna(a)kcl.ac.uk

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anatorig vs anat in dlabel
by Kirstie Whitaker 25 Aug '14

25 Aug '14

Hi I have a very minor question about the naming scheme for tracula output. I have the folders anat and anatorig in the dlabel folder. Am I right that: anatorig is the T1 image in "freesurfer space" (256 x 256 x 256; LIA) anat is a rotated version of the T1 image in freesurfer space that lines up with the standard orientation used by FSL (256 x 256 x 256; LAS) So neither is actually in the same space as the *original* file that was passed to recon-all (176 x 240 x 256; LAS)? I ran mri_label2vol with dlabel/anat/anat_brain_mask.nii.gz as the --temp argument and the labels didn't line up nicely. They did line up with anatorig though. Is this what you'd expect? 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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tracula: bvec-error
by Robby De Pauw 25 Aug '14

25 Aug '14

Dear FreeSurfer, When I try to use TRACULA I keep getting the following error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory after entering the following command: $ trac-all -prep -c dmrirc.preproc I tried to specify my bval and bvec in the config file, but that doesn’t seem to help. My data was assessed using a Siemens-scanner. Attached you can find the config-file. Thank you in advance, Best regards, Robby ————————————— the complete output can be found here: ~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc Badly placed ()'s. INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 trac-preproc -c /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 21 15:59:52 CEST 2014 mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 71 files in /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 4 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime 171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime 10800 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 60 IsMosaic 1 ImgPos 961.3685 959.9193 107.7635 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 60 Vc -1.0000 -0.0011 0.0062 Vr 0.0000 -0.9841 -0.1774 Vs 0.0063 -0.1774 0.9841 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: ( 96 96 60), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 10800, TR = 10800 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime 171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime 10800 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 60 IsMosaic 1 ImgPos 121.3850 132.3092 -36.0742 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 60 Vc -1.0000 -0.0011 0.0062 Vr 0.0000 -0.9841 -0.1774 Vs 0.0063 -0.1774 0.9841 VolCenter 1.8567 0.7748 17.1866 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = 0.0062587 -0.177391 0.98412 INFO: no Siemens slice order reversal detected (good!). TR=10800.00, TE=83.00, TI=-1.00, flip angle=90.00 i_ras = (-0.99998, -0.00111026, 0.00615943) j_ras = (3.52518e-09, -0.98414, -0.177395) k_ras = (0.0062587, -0.177391, 0.98412) writing to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz... flip4fsl /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 15.625 fslswapdim /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz x -y z /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Aug 21 16:00:45 CEST 2014 Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Some notes on getting Tracula to work for newbies
by Kirstie Whitaker 25 Aug '14

25 Aug '14

Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between < > then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in <NAME OF YOUR DTI NIFTI FILE> Try running the command: fslmaths <NAME OF YOUR DTI NIFTI FILE> <NAME OF YOUR DTI NIFTI FILE> eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open <SUBJECTS_DIR>/<SUBID>/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget <TRACULA_UPDATE_LINK>) and the untar it (tar -zxvf <TRACULA_UPDATE_TAR.GZ_FILE>). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 <SUBJECTS_DIR>/<SUBID>/dmri/dwi.nii.gz <SUBJECTS_DIR>/<SUBID>/dmri/lowb.nii.gz mri_convert: extra arguments ("41" and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2). Some fun facts from my experience: You can have decimal points (not commas though) in your bvals files. You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for) Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong! 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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Extracting Group Means for Cortical Thickness
by Bronwyn Overs 24 Aug '14

24 Aug '14

Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Transforming functional image while retaining voxel size
by Jackie Lam 22 Aug '14

22 Aug '14

Hello all, I’m trying to register and transform a functional image to my high resolution anatomical image. As I understand, it can be done with mri_vol2vol, but the resulting functional image is resampled into 1x1x1 voxels (the resolution of my high res anatomical). Is there a way to transform the functional image so that it is in the same space as the anatomical image while retaining its original voxel size? Many thanks, Jack

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installing mris_decimate
by Nicholas Heugel 22 Aug '14

22 Aug '14

So I just redownloaded the recent version of Freesurfer for Mac, Lion operating system, making sure to grab the most recent version. I need to use the tool mris_decimate but it is not in any of the files I downloaded, nor was it in any of the files I had previously. Where can I get mris_decimate, and what are the steps for installing it? Nicholas

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problem with format of CT dicoms
by Borzello, Mia 22 Aug '14

22 Aug '14

Hi Freesurfers, I'm in the process of creating the ct.mgz file, but it is erroring and saying there is a "segmentation fault (core dumped)." What can I do to remedy this? Thanks, m

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head surface
by Meryem Ayse Yucel 22 Aug '14

22 Aug '14

Hi Doug, I used mkheadsurf function. Meryem

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