Freesurfer

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30132 discussions

Fw: Parcellation label error
by Ali,Mohamed Tarek Mohamed 20 Aug '18

20 Aug '18

External Email - Use Caution ________________________________ From: Ali,Mohamed Tarek Mohamed Sent: Saturday, August 18, 2018 10:59 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Parcellation label error Hello FreeSurfer Developers, While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am getting values in labels which are not found in cnames.table(:,5). These values are 0. I assigned the values to the unknown area. However, when I looked at the number of vertices per brain regions I found that corpuscallosum has no vertices in the DK atlas. This is my first week using a neuroimaging software and Freesurfer is my first software to work on, so I just don't know if that's ok or if there is something wrong. I am attaching the output of a python code I wrote to count the number of vertices per brain region in the left hemisphere of a structural MRI image from our dataset. Thanks in advance, Mohamed T. Ali Ph.D. student, Bioengineering, University of Louisville.

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segmentHA_T1.sh exits with error
by Antonin Skoch 20 Aug '18

20 Aug '18

External Email - Use Caution Dear experts, I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits with following error: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch Command exited with non-zero status 255 Full log file is attached. I have also uploaded whole subject (named segmentHA_T1_error.tar.gz ), including content of temporary directory hippoSF_T1_v21_right, to your server. I am using dev version, build 2018-07-28. I am using customized recon-all, but it should not relate to this error. Could you please look at this issue? Regards, Antonin Skoch

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How to register fMRI data without upsampling voxel size?
by Maria Hakonen 20 Aug '18

20 Aug '18

External Email - Use Caution Dear Freesurfer experts, Could you please let me know how to normalize fMRI data without upsampling the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried this as follows: 1. Register functional (data.nii) to anatomical matrix bbregister --s $subject --bold --init-fsl --mov data.nii --reg register.dof6.dat 2. Register anatomical to mni152: mni152reg --s $subject 3. Create registration between functional and mni152 mri_matrix_multiply -im register.dof6.dat -iim reg.mni152.2mm.dat -om reg.mni152.dat 4. Resample func to mni152 space mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov data.nii --reg reg.mni152.dat --o data.mni152.nii --no-resample I checked the registrations after each step. After step 4, the functional data and the template are not fully aligned if I use “no-resample”. Without no-resample, the registration seems successful, but the fMRI data has a voxel size of 2mm. Best, Maria

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How to install Biomedical Toolkit examples in Labview 2015?
by Bellamy Baron 20 Aug '18

20 Aug '18

External Email - Use Caution Hi freesurfers, Does anyone know how to install Biomedical Toolkit examples in Labview 2015? I installed an evaluation version of Labview 2015, 2015DFDT, and 2015ASPT under Windows 7. Then, I installed the 2014BMTK but only one, I get the Biomedical Workbench, but examples (source codes) are not installed. In a second time, I marked the option of 2014_Support in the installation of 2014BMTK, then examples are installed but in another file (Labview 2014) and there are missing modules when I try to test these examples. Thanks, -------------------------------------------------------------------------------------------------------- Bellamy Specialist - iWYZE https://www.iwyze.co.za <https://www.iwyze.co.za/products/car-insurance>

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3 positions to post
by Florence M 20 Aug '18

20 Aug '18

External Email - Use Caution Hi, I want to post a positions bellow, thanks to reply where I should go to post it on free surfer please. Best, Florence

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Freesurfer v6.0: Using FLAIR for hippocampal subfields
by Ole Johan Evjenth Sørhaug 20 Aug '18

20 Aug '18

External Email - Use Caution Dear freesurfer experts, I'm interested in doing subfield segmentations of the hippocampus in version 6.0. What I am specifically interested in, is that if I can expect better segmentations if I use a 1mm isotropic FLAIR series in addition to the 1mm isotropic T1 series, rather than using the T1 series alone. Regards Ole Johan Sørhaug

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mri_cvs_register using fsaverage
by Peled, Noam 19 Aug '18

19 Aug '18

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command: mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K) Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas? Thanks, Noam

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Re: [Freesurfer] segmentHA_T1.sh exits with error
by Antonin Skoch 17 Aug '18

17 Aug '18

External Email - Use Caution Dear Eugenio, here it is: asegModBinDilated.mgz asegModBinDilatedResampled.mgz asegModCHA.mgz asegMod.mgz asmr1.mgz asmr2.mgz asmr3.mgz compressionLookupTable.txt discreteLabels_all.mgz discreteLabelsMergedBodyHead.mgz discreteLabels.mgz discreteLabelsWholeBodyHead.mgz error.log hippoAmygBinaryMask_autoCropped.mgz hippoAmygBinaryMask.mgz hippoMaskDilated5mm.mgz hippoMask.mgz hippoMaskResampledDilated.mgz hippoMaskResampled.mgz imageDump.mgz image.mgz T1resampled.mgz trash.lta volumesAmygdala.txt volumesHippo.txt warpedMeshNoAffine.txt.gz warpedMesh.txt.gz warpedOriginalMesh.txt.gz Antonin Dear Antonin, Can you please send me a listing of the files in: /hydra-db/hydra_io/vypocty/freeSurfer/A_analysis_HPC_PFC/A_links_all/ESO_C00577_20160303_1246_1/tmp/hippoSF_T1_v21_right/ Kind regards, /Eugenio-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Antonin Skoch <a...(a)ikem.cz> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 17 August 2018 at 18:16 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T1.sh exits with error External Email - Use Caution Dear experts, I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits with following error: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch Command exited with non-zero status 255 Full log file is attached. I have also uploaded whole subject (named segmentHA_T1_error.tar.gz ), including content of temporary directory hippoSF_T1_v21_right, to your server. I am using dev version, build 2018-07-28. I am using customized recon-all, but it should not relate to this error. Could you please look at this issue? Regards, Antonin Skoch

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Freeview heat map
by James Brown 16 Aug '18

16 Aug '18

External Email - Use Caution Dear Freesurfer developers, I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to measure a parameter of interest for every ROI in DKT atlas. I would like to load the mean values of this parameter to Freeview (every ROI in DKT has one value of the parameter represent the mean signal in the ROI). The objective is to give color code for every ROI in DKT that fit the values of the computed parameter. Is there any way of doing this in Freeview? Thanks john

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DOWNLOAD LINK
by FabLab HGUGM 16 Aug '18

16 Aug '18

External Email - Use Caution Hello, At the FabLab in Hospital Gregorio Marañon in Madrid we have tried to download Free Surfer several times but the download link for mac seems to no longer be working. Is there any other link available? Thanks!

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