Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

head surface
by Meryem Ayse Yucel 25 Aug '14

25 Aug '14

Sorry about that, here is the whole correspondance: Hi Doug, I used mkheadsurf function. Meryem Hi freesurfer community, I am trying to get faces and vertices of the head surface mesh in Matlab. freesurfer_read_surf works perfectly when I extract faces and vertices for the pial surface (from lh.pial), but I get an "unknown magic number in surface file" error when I use the same function for lh.seghead (which I assume is the head surface?). Any help on what I am doing wrong? Thanks! Meryem

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Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 25 Aug '14

25 Aug '14

Hi Anastasia Thanks for your quick reply. I’ve changed the command and I got one step further. Now I get another 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 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 Mon Aug 25 14:23:03 CEST 2014 Somehow the folder bvecs was not created? Regards, Robby Hi Robby - It looks like in your config file "setbveclist" is one word, instead of "set bveclist". This may be why you're getting the "Badly placed ()'s." error at the very beginning of your trac-all output. And it would explain why it can't find the files. Hope this helps, a.y On Thu, 21 Aug 2014, Robby De Pauw wrote: 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.dep...(a)ugent.be ____________________________________ 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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Correlation of symptom severity and significant clusters
by Katharina Zech 25 Aug '14

25 Aug '14

Dear all, I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD. As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps? Thanks a lot! Katharina

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Re: [Freesurfer] GLM: Error Matric-Scale
by Robby De Pauw 25 Aug '14

25 Aug '14

Dear Douglas, The file is created on a mac using the open -e command. I’ve tried running your command: cat whiplash.fsgd | sed 's/\r/\n/g' > new.whiplash.fsgd However, this makes the file unreadable for FreeSurfer. Any ideas? Thank you in advance, Robby Date: Thu, 21 Aug 2014 13:30:19 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] GLM: Error Matric-Scale To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53F62CAB.1060307(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It looks like your fsgd file may have been created on a windows computer. Is that possible? Try reformatting it in linux or mac. doug On 08/20/2014 12:58 PM, Robby De Pauw wrote: > > > > > > > > Hi there FreeSurfer > > When trying the GLM-analysis I keep getting the following error. Could > you help me with fixing it? > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > -------------------------------- > 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.whiplash.thickness.10B.mgh --fsgd whiplash.fsgd dods > --C group_diff.mtx --surf fsaverage lh --cortex --glmdir > lh.whiplash.glmdir > 2. The FSGD file (if using one) > 3. And the design matrix above > > Thank you in advance, > > > Robby > > > Robby De Pauw, dra. > *Ghent University* > Department of Physiotherapy and Rehabilitation Sciences > 3B3 > De Pintelaan 185 > B-9000 Ghent > > Robby.DePauw(a)Ugent.be <mailto:Robby.DePauw@Ugent.be> > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be On 22 Aug 2014, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Re: [Freesurfer] GLM: Error Matric-Scale

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BBRegister Patch
by Zamroziewicz, Marta Karolina 25 Aug '14

25 Aug '14

Good morning! Is the bbregister patch available yet (original email below)? Thank you for your time and assistance! Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2(a)illinois.edu<mailto:mzamro2@illinois.edu> 815-980-3882 This email is related to the archived “bbregister and FLAIR” email chain posted by Kayle Sawyer on 5/23/2014 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html) We have also been registering with FLAIR scans, and have run into a problem with approximately half of our subjects. Recon-all completes successfully but a bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve attached two screenshots, the first of which shows a bad registration and the second of which shows a good registration. Per your previous suggestion, we ran bbregister using the following flag: bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat --t2 --lta reg.test.lta This did result in a good registration, and we are hoping to incorporate this into our processing pipeline to ensure that we can use the FLAIR for refining the pill surface. The problem that we’ve run into is that we aren’t sure at which point this bbregister step occurs within the recon-all process flow. We were thinking there are a couple of possibilities: 1. manually create the transformation matrix for the FLAIR using the command mentioned above, and then re-run whichever steps necessary in recon-all to include this manually created xform; 2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with whatever steps/flags we need to include this FLAIR image to refine the pial surface. Unfortunately we're not exactly sure which flags to include in recon-all in order to most efficiently re-process our data with the manually created FLAIR transformation, and we were hoping you might offer some advice on this point. Please let me know if I can provide any additional information. [cid:32781EBE-87CB-4FF9-815F-4D732E675168@beckman.uiuc.edu][cid:45A8FE84-7BD3-4C2E-8618-AE9786828CF2@beckman.uiuc.edu]

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International PhD Course in Molecular Medicine, Experimental Neurology Section, San Raffaele Hospital, Milan, Italy.
by Zonca Lucia 25 Aug '14

25 Aug '14

The Neuroimaging Research Unit, Vita-Salute San Raffaele University, Milan, Italy, headed by Prof. Massimo Filippi, is looking for graduate students interested in a three-year PhD program in the frame of the International PhD Course in Molecular Medicine, Experimental Neurology Section. Titles and Directors of Study of the programs are the following: 1. Network degeneration in motor neuron diseases (MND): a study of the structural and functional connectomes in amyotrophic lateral sclerosis and other MND. Prof. Massimo Filippi 2. Brain plasticity in multiple sclerosis. Prof. Massimo Filippi 3. Investigation of the functional and structural correlates of cognitive network function in pediatric MS patients. Dr Maria A. Rocca 4. Cervical cord atrophy as a tool for monitoring disease evolution and for predicting long-term disability in patients with multiple sclerosis. Dr Maria A. Rocca 5. The morphological, microstructural and functional MRI correlates of motor, cognitive and neurobehavioral impairment in patients with movement disorders. Dr. Federica Agosta 6. Multimodal magnetic resonance imaging diagnosis of frontotemporal lobar degeneration (ftld): using supervised machine learning techniques to classify individual FTLD and Alzheimer's disease patients. Dr. Federica Agosta The lab has a strong background in multiple aspects of neuroimaging from sequence programming and software design to the analysis of structural and functional images from patients with different disorders of the central nervous system. The candidate will join a group with multiple interests in the field in a positive and productive environment. The ideal candidate should have expertise in the acquisition and analysis of advanced MRI techniques (volumetric, diffusion tensor MRI and functional MRI). Expertise in voxel-based morphometry, tract-based spatial statistics, resting state and active fMRI analyses would be an advantage. She/he will have a good team-working attitude, be self-motivated and have a strong interest in pursuing research in a stimulating and competitive field of science. Admission requirements and procedures are described at http://www.unisr.it/view.asp?id=8802 Deadline for application submission is 11 September 2014. [cid:5x100osr2014ecc.jpg] <http://www.5xmille.org/> Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.com<http://www.codetwo.com>

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The influence of cortical talairach on final surfaces
by will brown 25 Aug '14

25 Aug '14

Hi all, In the freesurfer pipeline, is cortical segmentation (and the subsequent surface construction) based on the actual scans or on the scan in talairach space? Thanks, Will Brown

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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

2 3

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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