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recon-all tries to call mri_relabel_hypointensities -all-info
by Drucker, Daniel 19 Feb '19

19 Feb '19

freesurfer-6.0.1/bin/recon-all line 630 calls: mri_relabel_hypointensities -all-info However, -all-info is not a valid option: $ mri_relabel_hypointensities usage: mri_relabel_hypointensities [options] <input aseg> <surface directory> <output aseg> This program measures a variety of anatomical properties valid options are: -l <label file> - limit calculations to specified label -a <annotation file> - compute properties for each label in the annotation file separately $ mri_relabel_hypointensities -all-info unknown option -all-info -- Daniel M. Drucker, Ph.D. Director of IT, McLean Imaging Center

2 1

Information about argument -erode in command mri_extract_label
by Viktor Domazetoski 19 Feb '19

19 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I would like to enquire about the command mri_extract_label. More specifically I am looking for information about the -erode argument. Therefore I have a few questions: 1. Is a 3D erosion of the entire brain or a 2D slice by slice erosion used? 2. What structuring element (regarding the shape and size of the kernel) is used for the erosion for a given argument value (e.g. for the command mri_extract_label -erode 1)? Thank you in advance! Kind regards, Viktor

2 1

Average subject
by Laboratorio de Neurociencia Funcional 19 Feb '19

19 Feb '19

External Email - Use Caution Dear all, I am planning to run separate regression analysis with cortical thickness in two very different populations (young and elderly subjects). Depending on results, it may happen that I am interested in comparing regression slopes between the two groups. My question is: should I build one average subject for each within-group regression analysis (one for young and another for elderly), and another different average subject merging all subjects of the two samples to compare regression slopes? Or I should preferably use only one average subjects with all subjects in all within and between regression analysis? Many thanks in in advance. Best regards, Jose

2 3

dt_recon error
by Daniel Davidson Callow 18 Feb '19

18 Feb '19

External Email - Use Caution Hello, I am still trying to run dt_recon and am having issues. The code I am running is attached...and an abbreviated version is below. foreach subj (`ls -d /Volumes/DANIEL/AES101 | sed 's/\// /g' | awk '{print $3}'`) foreach cond (Ex Rest) echo "subj = " ${subj} ", cond = " ${cond} cd /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/ mri_convert image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/dwi.nii.gz dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}. and the following is the output and errors I am getting from running the above code. I have also attached a screenshot of the path and folder with the various file inputs and outputs. subj = AES101 , cond = Ex mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from image000001.dcm... Getting Series No Scanning Directory INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz... Saving bvals and bvecs -rwxrwxrwx 1 administrator staff 1276058 Feb 18 10:18 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/ dt_recon logfile Mon Feb 18 10:19:18 EST 2019 VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/ cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex /Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. hlhp-105.umd.edu administrator /usr/local/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Mon Feb 18 10:19:18 EST 2019 cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm... Getting Series No INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii... Saving bvals and bvecs #@#------------------------------- Eddy/Motion Correct Mon Feb 18 10:19:30 EST 2019 cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi /usr/local/fsl/bin/eddy_correct: line 94: 64175 Abort trap: 6 fslsplit $input ${output}_tmp Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp????.*: No such file or directory rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_ref*: No such file or directory Any help you could provide for trouble shooting the issue would be greatly appreciated! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

1 1

midbrain mask for LGI
by Sanfelici, Rachele 18 Feb '19

18 Feb '19

1 0

Excluding Specific Regions from a Volumetric File
by Maedeh Khalilian 18 Feb '19

18 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder how to do that. I would be grateful if u could help me with that. Best regards, Maedeh

2 1

Excluding Specific Regions from a Volumetric File
by Maedeh Khalilian 17 Feb '19

17 Feb '19

2 1

Fix topology correcting defect
by "Milene Bürger" 17 Feb '19

17 Feb '19

4 7

automatically save the selected plane
by Sadia Sheikh 17 Feb '19

17 Feb '19

External Email - Use Caution Dear FreeSurfer experts It is possible to automatically save the selected planes or set of planes from the specific region? Since I have a large number of data and I want to save all the planes that lie in the midbrain region. Regards Sadia Research Student

2 3

Re: [Freesurfer] problem using recon-all
by Shachar Gal 17 Feb '19

17 Feb '19

External Email - Use Caution Actually Im not really sure why Matlab pops up here.. this is ran there is nothing that is Matlab dependent in the PreFreesurfer Pipeline...

2 1

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