Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

CORRECTING DEFECT
by maryam koochaki 06 Jun '16

06 Jun '16

Dear freesurfer experts,I have a subject ending up with this error after recon-all.I tried to edit the aseg and run it, but it stuck at topological step. CORRECTING DEFECT 79 (vertices=54196, convex hull=8490) error in the retessellation normal vector of length zero at vertex 97187 with 0 faces vertex 97187 has 0 face No such file or directory Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test_emc_039 exited with ERRORS ..... Could you guide me how I can correct it.Thank you,Maryam Regards,Maryam Kouchakidivkolaei

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volumetric difference between 1.5 T and 3.0 T...
by Gonzalo Rojas Costa 06 Jun '16

06 Jun '16

Hi: There exist any difference between the volumetric values obtained using 1.5T and 3.0T images ? Any paper about it ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Build fsaverage
by shi yao wang 06 Jun '16

06 Jun '16

Hello, Thank you very much for the reply! 1. I copied calculated data into a new computer and I cannot find "fsaverage". 2. Bruce, thank you! I used make_average_subject command. However, it shows that error message: "lack of memory". I am wondering how can I do that. Thank you for helps again! Lawrence

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SOLVED: Re: convert FSL atlas label to individual freesurfer T1 space
by Jacobs H (NP) 05 Jun '16

05 Jun '16

I figured it out :) From: H Jacobs <h.jacobs(a)maastrichtuniversity.nl<mailto:h.jacobs@maastrichtuniversity.nl>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Saturday, June 4, 2016 at 7:48 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] convert FSL atlas label to individual freesurfer T1 space Hello! I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following: Flirt -in MNI15_T1_1mm.nii.gz -ref brainmask.nii -out converted.nii -omat convertedmatrix.mat -bins 256 -cost corratio -searchx -90 90 -searchy -90 90 -searchz -90 90 -dof 12 -interp trillinear Flirt -in JHUlabel.niig.gz -ref brainmask.nii -applyxfm -init convertedmatrix.mat -out newlabel.nii.gz (brainmask.nii is the brainmask.mgz converted to nii using mri_convert) Unfortunately this did not work, the label is still in the wrong position. Any idea what I am doing wrong or how I can solve this? Thanks! Heidi

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selxavg3-sess error with phase-encoded data
by Francesca Strappini 05 Jun '16

05 Jun '16

Hi Freesurfer experts, I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); I attached the Xtmp.mat file from the output folder in case is needed. Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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error at acfrun 762
by S.V.Shepherd [work] 04 Jun '16

04 Jun '16

Hi, I decided I should standardize my fMRI data across sessions by rescaling each voxel to have a run-mean of 100. Normalized data looked okay under manual inspection in FreeView. When I tried to analyze this data, however, I consistently get an error partway through: """ Index exceeds matrix dimensions. Error in fast_selxavg3 (line 762) acfrun = nrho1segmn(nthseg).^([0:flac.ntp-1]'); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n a_100_Av_s_task_fmov_bgrnd failed """ Any guess what might be causing this, or how to troubleshoot? Multiple analyses that worked on non-normalized data are mostly (but somehow not universally) failing in this same way. Thanks much. stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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convert FSL atlas label to individual freesurfer T1 space
by Jacobs H (NP) 04 Jun '16

04 Jun '16

Hello! I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following: Flirt -in MNI15_T1_1mm.nii.gz -ref brainmask.nii -out converted.nii -omat convertedmatrix.mat -bins 256 -cost corratio -searchx -90 90 -searchy -90 90 -searchz -90 90 -dof 12 -interp trillinear Flirt -in JHUlabel.niig.gz -ref brainmask.nii -applyxfm -init convertedmatrix.mat -out newlabel.nii.gz (brainmask.nii is the brainmask.mgz converted to nii using mri_convert) Unfortunately this did not work, the label is still in the wrong position. Any idea what I am doing wrong or how I can solve this? Thanks! Heidi

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Input for mris_fwhm to generate fwhm.dat file
by Chung, Yoonho 03 Jun '16

03 Jun '16

Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47480.html I have created a sig.mgh from my own stats code and need to also generate fwhm.dat file to run the monte carlo sim, which is estimated from the residuals. What are the specifics and dimension of this residual file I need to generate for mris_fwhm? Is this a residual of model fit at each vertex across all subjects (so [number of subjects x number of verticies] matrix in .mgh file)? or variance or standard deviation of the residuals? Perhaps pointing to an example file in the glmdir directory (created when running glmfit) will help me understand the process (for example is rstd.mgh or rvar.mgh is being used for mris_fwhm --i or something else?). Thank you for your help!

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Re: [Freesurfer] recon-all segmentation error
by Jaiashre Sridhar 03 Jun '16

03 Jun '16

Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre.

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Re: [Freesurfer] recon-all segmentation error
by Jaiashre Sridhar 03 Jun '16

03 Jun '16

Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could you please tell me how to fix this manually? Thanks, Jaiashre.

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Freesurfer June 2016