Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

How to overlay Freesurfer and FSL outputs
by Mahmoud 24 Oct '14

24 Oct '14

Dear all, I have a set of T1-MPRAGE images and and conducted the following steps: 1- Converted the DICOM images to SPM8 (3D nifti nii) by dcm2niigui.exe 2- Used the following line to segment images by FreeSurfer: recon-all -i /xxx/IM-0009-0001.dcm -subject TEST -all recon-all -base TESTBASE -tp TEST -all recon-all -long TEST TESTBASE -all 3- Used FSL BET to skull strip the nii file from step 1 and then fed the output into FSL FAST segmentation to segment it to 3 classes. 4- Used the following line to convert the mgz file to nii mri_convert --in_type mgz --out_type nii --out_orientation RAS /xxx/mri/brainmask.mgz /xxx/test_brainmask.nii 5- Using the fslinfo it gives me the following info for test_brain.nii.gz data_type FLOAT32 dim1 192 dim2 240 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ while for the nii file from step 4 the fslinfo gives me: data_type UINT8 dim1 256 dim2 256 dim3 256 dim4 1 datatype 2 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 2.300000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ As you may see these two files are completly different so I am not able to overlay them using FSLVIEW. Any idea about how to overlay them ? Thank you, Mahmoud

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Trouble specifying contrast vectors
by Bronwyn Overs 24 Oct '14

24 Oct '14

Dear Freesurfer Mailing List, I wish to run a GLM in freesurfer with 3 categorical variables (haplotype-2levels, gender-2levels, group-2levels), and 1 continuous variables (age). Unfortunately, the MRI images I am using come from five different testing sites, so I also need to account for the potentially confounding effects of using different scanners. So my fsgd file like this: GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-numRiskNoRisk-genderMale-groupCase Class siteBrisbane-numRiskNoRisk-genderFemale-groupCase Class siteBrisbane-numRiskNoRisk-genderMale-groupControl Class siteBrisbane-numRiskNoRisk-genderFemale-groupControl Class siteBrisbane-numRiskanyRisk-genderMale-groupCase Class siteBrisbane-numRiskanyRisk-genderFemale-groupCase Class siteBrisbane-numRiskanyRisk-genderMale-groupControl Class siteBrisbane-numRiskanyRisk-genderFemale-groupControl Class siteMelbourne-numRiskNoRisk-genderMale-groupCase Class siteMelbourne-numRiskNoRisk-genderFemale-groupCase Class siteMelbourne-numRiskNoRisk-genderMale-groupControl Class siteMelbourne-numRiskNoRisk-genderFemale-groupControl Class siteMelbourne-numRiskanyRisk-genderMale-groupCase Class siteMelbourne-numRiskanyRisk-genderFemale-groupCase Class siteMelbourne-numRiskanyRisk-genderMale-groupControl Class siteMelbourne-numRiskanyRisk-genderFemale-groupControl Class siteNewcastle-numRiskNoRisk-genderMale-groupCase Class siteNewcastle-numRiskNoRisk-genderFemale-groupCase Class siteNewcastle-numRiskNoRisk-genderMale-groupControl Class siteNewcastle-numRiskNoRisk-genderFemale-groupControl Class siteNewcastle-numRiskanyRisk-genderMale-groupCase Class siteNewcastle-numRiskanyRisk-genderFemale-groupCase Class siteNewcastle-numRiskanyRisk-genderMale-groupControl Class siteNewcastle-numRiskanyRisk-genderFemale-groupControl Class sitePerth-numRiskNoRisk-genderMale-groupCase Class sitePerth-numRiskNoRisk-genderFemale-groupCase Class sitePerth-numRiskNoRisk-genderMale-groupControl Class sitePerth-numRiskNoRisk-genderFemale-groupControl Class sitePerth-numRiskanyRisk-genderMale-groupCase Class sitePerth-numRiskanyRisk-genderFemale-groupCase Class sitePerth-numRiskanyRisk-genderMale-groupControl Class sitePerth-numRiskanyRisk-genderFemale-groupControl Class siteSydney-numRiskNoRisk-genderMale-groupCase Class siteSydney-numRiskNoRisk-genderFemale-groupCase Class siteSydney-numRiskNoRisk-genderMale-groupControl Class siteSydney-numRiskNoRisk-genderFemale-groupControl Class siteSydney-numRiskanyRisk-genderMale-groupCase Class siteSydney-numRiskanyRisk-genderFemale-groupCase Class siteSydney-numRiskanyRisk-genderMale-groupControl Class siteSydney-numRiskanyRisk-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyRiskAnyRisk-genderMale-groupCase 23 ... As the number of categorical variables really complicates the specification of contrast vectors, I was wondering if you could confirm whether these vectors are correct: Main effect for haplotype (Risk vs No Risk): 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Main effect for gender (Male vs Female): 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Main effect for group (Case vs Control): 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Interaction between gender & group: 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Interaction between gender & haplotype: 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Interaction between group & haplotype: 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Interaction between gender, group, & haplotype: 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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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LME tools with FS ver. 5.1?
by Manabu Kubota 24 Oct '14

24 Oct '14

Hi experts, I'm planning to apply linear mixed effects models to my longitudinal MRI dataset. I found the LME Matlab tools are not included in FreeSurfer ver. 5.1. Is it possible to use the standalone copy of the tools linked in the website with FS ver. 5.1? Do I need to run an extra command to my data before using them? I have done all the data preprocessing with FS ver. 5.1, and I hope I don't have to do it again from the beginning with a newer FS version… Thanks! Best, Manabu

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Research Assistant I position in Neuroimaging
by Dana DeMaster 23 Oct '14

23 Oct '14

Position: Research Assistant I (full-time research assistant position in Brain Research Analysis in Neurodevelopment (BRAIN) Laboratory) Location: University of Texas-Health Science Center at Houston Apply at: jobs.uth.tmc.edu/applicants/Central?quickFind=100904 A full-time research assistant position in Brain Research Analysis in Neurodevelopment (BRAIN) Laboratory, at the Children's Learning Institute. Our laboratory uses neuroimaging techniques to investigate the neural systems underlying a variety of developmental disorders. The BRAIN Lab is a lively, collaborative, supportive intellectual environment. Duties will include assisting with all aspects of neuroimaging data collection including, but not limited to, running the MRI scanner, organizing structural and functional data, basic processing of structural and functional data, and coordinating lab activities. Departmental Requirements/Preferences - BA/BS in Psychology, Cognitive Science, Neuroscience or other related scientific field - Fluent or nearly fluent Spanish speaker - Strong computer skills - An ability to solve technical problems independently - Strong organization skills - Detail oriented - Prior research experience - Experience working with elementary school aged children - Flexible schedule with willingness to work nights and weekends. This would be an excellent position for an individual desiring to hone their research skills before continuing on to postgraduate study. Applications must be submitted at jobs.uth.tmc.edu/applicants/Central?quickFind=100904 -- Dana DeMaster

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Re: [Freesurfer] using mri_convert with multiframe dicom
by Flavin, John 23 Oct '14

23 Oct '14

Hi Timothy you should be able to. You can use the -nth <frame #> switch to convert each frame individually cheers Bruce On Mon, 11 Jul 2011, Timothy Brown wrote: > Hi All, > > Can mri_convert be used with multiframe dicom? Is this advice still valid? I tried converting a multi frame DICOM (176 frames in one file) using the -nth flag in mri_convert in Freesurfer 5.3 and it did not work as I expected. $ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o PROCESSED/subj/mri/orig/001.mgz -nth 0 /path/to/bin/mri_convert -i RAW/301/foo.dcm -o PROCESSED/subj/mri/orig/001.mgz -nth 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from RAW/301/foo.dcm... Starting DICOMRead2() dcmfile = RAW/301/foo.dcm dcmdir = RAW/301 WARNING: tag image orientation not found in RAW/301/foo.dcm Ref Series No = 301 Found 3 files, checking for dicoms WARNING: tag image orientation not found in RAW/301/foo.dcm Found 1 dicom files in series. WARNING: tag image orientation not found in RAW/301/foo.dcm First Sorting Computing Slice Direction WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented. Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 MRIresample(): error inverting matrix; determinant is -nan, matrix is: -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; I get the exact same output running with -nth 0 as I do not using the -nth flag at all. If I try using -nth 1 (or -nth i for any integer i > 0) I get mri_read(): start frame (1) is out of range (1 frames in volume) mri_convert reports nframes = 1. I can look in the DICOM headers of the file and find (0028, 0008) Number of Frames IS: ‘176’ and (2001, 1018) [Number of Slices MR] SL: 176 Anything I can do to tell mri_convert the correct number of frames? Flavin ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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FS-FAST par file ?
by dgw 23 Oct '14

23 Oct '14

If I have events which precede the first MR volume, can I input negative values in my par file? I understand my power, and the advantage of doing this will be minimal, but I wanted to inquire if FS-FAST is capable of handling this case. Thanks, Dan

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strange artefact in T1 - stripe pattern
by Corinna Bauer 23 Oct '14

23 Oct '14

Hello, I am analysing some structural data for collaborators and one of the datasets has a strange artefact in it. Is there any way to adjust for the intensity bands or is this a lost cause? Thanks, Corinna

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Sulcal CSF Volume
by Mohammed Goryawala 23 Oct '14

23 Oct '14

Hello FreeSurfer Experts, Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate? Thank you Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami

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Re: [Freesurfer] longitudinal base template creation with one timepoint
by Martin Reuter 23 Oct '14

23 Oct '14

Hi Tracy, When you call recon-all -base simply pass only the single time point -tp. Best Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Tracy Melzer <tracy.melzer(a)otago.ac.nz> </div><div>Date:10/22/2014 10:59 PM (GMT-05:00) </div><div>To: freesurfer(a)nmr.mgh.harvard.edu </div><div>Subject: [Freesurfer] longitudinal base template creation with one timepoint </div><div> </div>Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer

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Research Assistant Job: Northwestern Univ. Alzheimer's Disease Center (Chicago, IL)
by Emily Rogalski 23 Oct '14

23 Oct '14

Research Study Assistant job available at Northwestern University’s Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathological aging. Duties include coordinating PET and MRI scans, and analyzing the resultant structural and functional imaging data. The RA will also have the opportunity to administer and score neuropsychological tests. Additional duties include working on graphics for manuscripts and grants or other general lab responsibilities. Candidates must have proficiency with computer programming, ideally with relevant technical languages such as MATLAB or Python. They must be willing to learn new MRI analysis software and troubleshoot problems independently. Prior experience with neuroimaging analysis suites such as Freesurfer, FSL, or SPM would be extremely useful. Relevant backgrounds would be in Neuroscience, Biology, Psychology, Computer Science, Mathematics, and Biomedical Engineering. *Minimum Qualifications: * - The candidate must hold a Bachelor degree. - Candidate must be fluent in at least one programming language. - A two-year commitment is requested. *Preferred Qualifications: * - Experience using Freesurfer or other neuroimaging platforms. Interested applicants can apply online here: http://www.northwestern.edu/hr/careers/ Job ID: 24257 If you have specific questions please email: e-rogalski(a)northwestern.edu To learn more about our center please go to: www.brain.northwestern.edu -- Emily J Rogalski, PhD Associate Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Freesurfer October 2014