Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

saving in GIFTI .func.gii format
by SHAHIN NASR 08 Nov '13

08 Nov '13

Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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algorithm developer position open
by Gennan Chen 07 Nov '13

07 Nov '13

Hi! All, We have an algorithm developer position open at Synarc. If you are interested, please send me your resume. Position Description: The algorithm developer engineer works with our scientific groups to come up innovative image processing and data mining/pattern recognition algorithms to maintain scientific lead in all TA areas Responsibilities: Work with Scientists and TA lead on surveying literature /algorithms and existing commercial implementation for specific tasks. Prototype and validating algorithms on large dataset by using in house cluster or Amazon EC2. Prototype related UI elements and addressing integration on Synarc internal proprietary platform. Work with Scientists and TA lead on journal/conference publications and intellectual properties related document. Qualifications: Education: PhD in biomedical engineering, physics, applied math or computer science Experience: Must be expert in ITK and Matlab Familiar with HPC like condor or SGE is a must have Experience with EC2 will be a plus Experience with VTK or QT will be a plus. Experience with Python/Java/SQL will be a plus Skills: Good written and verbal communication skills. Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Gennan Chen Engineering Manager, Synarc ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?
by Emad Ahmadi 07 Nov '13

07 Nov '13

Hello, I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle. I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD ------------------------------------------------ Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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Segmentation question
by Rashmi Singh 07 Nov '13

07 Nov '13

FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi

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Re: [Freesurfer] Segmentation question
by Louis Nicholas Vinke 07 Nov '13

07 Nov '13

Hi Rashmi, Several of the morphometry stats were changed between 5.1 and 5.3. I don't remember the specifics, but Doug or someone else on the list may know. Alternatively, you could use the mri_segstats from 5.3 to calculate the morphometry stats for your 5.1 data. -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: > I am using version V5.1.0 is it different for that or the information is > the same irrespective of the version I use. > Rashmi > > On 11/7/13 1:57 PM, "Louis Nicholas Vinke" <vinke(a)nmr.mgh.harvard.edu> > wrote: > >> Hi Rashmi, >> This page has the definition you are looking for (FS v5.3). >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >> >> -Louis >> >> On Thu, 7 Nov 2013, Rashmi Singh wrote: >> >>> FreeSurfer experts, >>> May you please educate me how the supra tentorial volume (STV) >>> measured by >>> FreeSurfer and which date does it take as input file to calculate this >>> variable. >>> Thanks, >>> Rashmi >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > >

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fMRI-data mri_convert, missing header
by Philipp Heimbeck 07 Nov '13

07 Nov '13

Hello! I'm encountering a problem with converting fMRI-Data from dicom- to NIfTI-files (single file). The problem only occurs with data aquired on Siemens Vision, data from Siemens Trio work just fine. The "Siemens ASCII header" is missing (files have not been anonymized) and every dicom-file has its own series number. This is true for all functional data (10 subjects, one run each). Other programs can't convert these dicom-files either (dcm2nii, NIfTI-1 converter for BVQX). Do you know if there is a possible solution for this problem? In more detail, when running mri_convert, the following happens: ... Getting Series No Scanning Directory INFO: Found 218 files in ../run INFO: Scanning for Series Number 67 INFO: found 1 files in series INFO: loading series header info. INFO: sorting. RunNo = 66 WARNING: file ../MR.9500.260 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (512 512 1), nframes = 1, ismosaic=0 PE Dir COL COL FileName ../MR.9500.260 Identification NumarisVer VB33D ScannerModel MAGNETOM VISION PatientName deleted, shows correctly Date and time StudyDate deleted, shows correctly StudyTime 150948.046000 SeriesTime 153015.877000 AcqTime 153606.293000 Acquisition parameters PulseSeq ep_fid Protocol unknown PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 60 InversionTime -1 RepetitionTime 60 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 66 SeriesNo 67 ImageNo 260 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 96.0000 80.1658 98.1990 VolRes 0.3750 0.3750 3.0000 VolDim 512 512 1 Vc -1.0000 0.0000 -0.0000 Vr -0.0000 -0.9848 -0.1736 Vs -nan -nan -nan VolCenter -nan -nan -nan TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=60.00, TE=60.00, TI=-1.00, flip angle=90.00 i_ras = (-1, 0, -0) j_ras = (-0, -0.984808, -0.173648) k_ras = (-nan, -nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -0.375 -0.000 -nan -nan; 0.000 -0.369 -nan -nan; -0.000 -0.065 -nan -nan; 0.000 0.000 0.000 1.000; If there's any help, I'm glad to hear it. And if the answer is "no, the data is gone forever", this would be a helpful response, too. Philipp

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Re: [Freesurfer] Freesurfer Digest, Vol 117, Issue 9
by Jonathan DuBois 07 Nov '13

07 Nov '13

Hi Doug, Sorry, the ${s} was typo, and the ${h} was for hemisphere, but I modified the commands below to make them more straight forward. With the first command I am running mris_preproc with multiple controls and one patient together and then running mri_surf2surf to do smoothing, and mri_glmfit with the fsgd and mtx files displayed below. In the second command I am running mris_preproc and mri_surf2surf on the control group and patient separately. Then I use mri_concat to get the mean and sd from the control group, which I compare to the patient file using fscalc.fsl to generate the zmap. I attached a screen shot from one subject to show how different the results are (fscalc method is the one with the large negative cluster in the prefrontal). The results of the fscalc.fsl method seem to be correct, but I am not sure why they differ so much. So my question is, if I use the fscalc.fsl method, is there a way to do the monte carlo based cluster correction? Alternatively, is there something wrong with the way I am running mri_glmfit that it is not running a z-test? Thanks again, Jonathan [image: Inline image 2][image: Inline image 1] ------------------------------ > > Message: 21 > Date: Tue, 05 Nov 2013 18:26:14 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] z-test differences from fscalc and > mri_glmfit > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52797E96.704(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > When you say that you are getting very different results, what are you > comparing exactly? I can't tell what your mri_glmfit command is because > it is embedded in a script with lots of variables. Have mercy on me and > just give me a simple command line that I don't have to struggle with:) > doug > > > > > > On 11/05/2013 02:21 PM, Jonathan DuBois wrote: > > Hi All, > > > > In a previous post Doug suggested two methods for generating > > voxel-wise z-score maps, one using glmfit with one subject in one > > group and the second using fscalc.fsl. Link to post: > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html > > > > > > I have tried both methods using PET data registered to the surface, > > but get very different results from fscalc and mri_glmfit. The results > > I expect are given by fscalc, but I would also like to run the Monte > > Carlo-based MCC, which requires a glmdir. Is there another way to run > > MC MCC on the z-map generated by fscal or alternatively, is the code > > that I am using for glmfit wrong? A simplified version of the code for > > both analyses is below. I am using FS 5.3 with the fsl binaries from > > the release notes on mac OS 10.8. > > > > > > Thanks for your help > > Jon > > > > ----------------------------------mri_glmfit: > > mris_preproc --target fsaverage --hemi lh --iv > > nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv > > nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv > > nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --iv > > pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 > > --out lh.pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh > > > > mri_surf2surf --hemi lh --s fsaverage --fwhm 10 > > --cortex --sval > > lh.pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh --tval > > lh.pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh; done > > > > mri_glmfit --y > > lh.pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh --fsgd > > patient1_allcontrols_ztest.fsgd dods --C group2_cov0_diff.mtx --surf > > fsaverage lh --cortex --glmdir > > lh.pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.glmdir > > > > *patient1_allcontrols_ztest.fsgd*: > > GroupDescriptorFile 1 > > Title patient01_ztest > > Class Patient > > Class Control > > Input pat01 Patient > > Input nc01 Control > > Input nc02 Control > > Input nc03 Control > > > > *group2_cov0_diff.mtx*: > > -1 1 > > > > ----------------------------------fscalc.fsl: > > mris_preproc --target fsaverage --hemi lh --iv > > nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv > > nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv > > nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --pf 0.5 > > --out lh.allcontrols_pet_ztest_pf05_fsaverage.mgh > > > > mris_preproc --target fsaverage --hemi lh --iv > > pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 > > --out lh.patient01_pet_ztest_pf05_fsaverage.mgh > > > > for stat in mean std; do mri_concat > > lh.allcontrols_pet_ztest_pf05_fsaverage.mgh --o > > lh.allcontrols_pet_ztest_pf05_fsaverage_${stat}.mgh --${stat}; done; > > done > > > > fscalc.fsl --surf fsaverage lh > > lh.patient01_pet_ztest_pf05_fsaverage.mgh -sub > > lh.allcontrols_pet_ztest_pf05_fsaverage_mean.mgh -div > > lh.allcontrols_pet_ztest_pf05_fsaverage_std.mgh > > lh.patient01_vs_allcontrols_pet_ztest_pf05_fsaverage_zmap.mgh; done > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > >

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mris_fix_topology hangs (?)
by Martin Luessi 07 Nov '13

07 Nov '13

Hi, I'm running recon-all on a subject from the human connectome project, and for some reason "mris_fix_topology" seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem? Best, Martin PS: I'm using FS 5.3 ... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514 CORRECTING DEFECT 0 (vertices=65102, convex hull=346)

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MRISalloc: could not allocate vertices
by Ray, Siddharth 07 Nov '13

07 Nov '13

Hi Freesurfers, Got this error while running some of my subjects: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory Do anyone know how to fix this? Thanks, -Siddharth

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ltaReadFile error while running recon-all -long
by Jonathan Holt 07 Nov '13

07 Nov '13

FS experts, I’m having a bit of an issue with a single subject. Recon-all -long errors out after it tells me it cannot open the subjid_to_template.lta file. I’m very confused, because the file it’s looking for exists in the exact location it’s looking for but the recon-all.log suggests that there is no such file or directory. It proceeds to map control points and runs into a segmentation fault, after which it exits with errors. Any help would be appreciated.

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