Freesurfer

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19 participants
30088 discussions

pvc error
by Donatienne Van Weehaeghe 26 Apr '19

26 Apr '19

External Email - Use Caution Dear freesurfer experts, I am running the rbv pvc correction on a mac system and encountered the following error. mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): could not open file The subjects directory is Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair, the orig files are located in Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname Thank you! Kind regards Donatienne

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How to get Euler number from amygdala or hippocampus segmentation?
by Reetta-Liina Armio 26 Apr '19

26 Apr '19

External Email - Use Caution Dear Freesurfer experts! I have run the hippocampus segmentation with FS 6 (stable version) and the amygdala segmentation with FS development version. I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper. Is it possible to get the Euler number from these specific segmentations or is the Euler number available only from subcortical segmentation? Thank you for the answer! Best, Reetta-Liina Armio

2 1

Questions about multiple test correction and quality assurance
by Zhi Li 26 Apr '19

26 Apr '19

External Email - Use Caution Dear FreeSurfer experts, I am reading your work 'False positive rates in surface-based anatomical analysis' and having several questions about multiple test correction in mri_glmfit-sim: 1. The permutation is permuting the design matrix, but how to permute it in a one-sample t-test? According to my understanding, all the subjects are listed as one group in the design matrix. 2. What's the difference between clustering-forming thresholds (CFT) and cluster-wise p value (CWP)? Whether the clustering-forming thresholds is set to the p map from the permutation test? Then how the CWP is calculated? 3. In the paper ''False positive rates in surface-based anatomical analysis, you suggested ''For surface area, one would need CFT 0.001 and FWHM>10 mm". Whether I could understand this as "the bigger smooth kernel the better"? The default smooth kernel in FSFAST is 5mm, which one should I use? 4. For the quality assurance in 'tkregister-sess', if I can use the QA value as a exclude criteria during analysis? If so is there any reference I can cite? Looking forward to your kind suggestions. Best regards, Lizhi

2 2

mri_convert : Error while loading library libGLdispatch.so.0
by Dev vasu 25 Apr '19

25 Apr '19

External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file: No such file or directory " Thanks Vasudev

2 1

fsaverage error with recon-all
by chen 25 Apr '19

25 Apr '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage/surf/lh.sphere.reg. According to the fsaverage-recon-all.log, it completed without error. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. I have attached an attachment about the recon-all.log.Secondly, i have studied the multi-site reliability of young traveling subjects which scanned in multi-site with the same scanner and protocol across 12 month. I ran these data with cross-pipeline. But, our results showed that the amygdala volumes have significantly lower reproducibility in inter-site than hippocampus and entorhinal cortex (ICC scores less than 0.5) with FreeSurfer rather than manual tracing. So, i want to assure that recon-all -all is the optimal process pipeline. If not, can you give me some advice? Should i use the longitudinal pipeline in multi-site study with traveling subjects? Thanks. ------------------ Capital Medical University

2 1

CORRECTING DEFECT 1 problem
by Abby tang 25 Apr '19

25 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error. CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : difference with theory (-32) = -52 CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) Segmentation fault (core dumped) Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I check files in blow command and attached picture. freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix 2851A_T1_w4/surf/lh.inflated.nofix almost all of subjects go wrong. I need your help. please give some advises with program statements in detail. I really appreciate your help 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz 2) Platform: ubuntu 18 3) recon-all.log:see attached

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recon-all stops in CORRECTING DEFECT
by Marina Fernández 25 Apr '19

25 Apr '19

External Email - Use Caution Dear freesurfer experts, We run recon-all in a specific subject and we can see in the terminal every commands until the following line: *CORRECTING DEFECT 21 (vertices=36576, convex hull=4845, v0=64547)* When the procedure is in this line it takes a lot of time (days) and it doesn't advance. When we open the lh.inflated and [l/r]h.orig.nofix files we can see that this subject has several errors *(see attached images)* but we don't know how we can repair it to finish the initial recon-all. Does anyone know how to solve this situation? What can we do? We will appreciate any help. Thank you very much in advance. Best regards, Marina Fernández Álvarez, PhD-student. Laboratory of Functional Neuroscience Pablo de Olavide University

2 1

calculation of the volume in mm3
by Schranzer René 25 Apr '19

25 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I was wondering about the volume calculation of the structures in the aseg.stats file. VoxelVolume_mm3 0.512 NVoxels 8616 Volume_mm3 4312.4 StructName Right-Hippocampus After my calculation of NVoxels * VoxelVolume I get a slightly different value. 0.512*8616 = 4411.4 Where does the difference come from? Thanks, René

2 1

recon-all error
by Ebru Ayyürek 25 Apr '19

25 Apr '19

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a full recon-all on the dicom/nifti file for test my freesurfer installation as described on the website https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall but I have an error like this; recon-all -s file1 -i /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/file1 mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm... Starting DICOMRead2() dcmfile = /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm dcmdir = /home/ebru/Desktop/den01_org/T1_1 Ref Series No = 201 Found 182 files, checking for dicoms Found 180 dicom files in series. First Sorting Computing Slice Direction Vs: -0.0462818 0.24329 0.968857 Vs: -0.0462815 0.243288 0.968849 Second Sorting Counting frames nframes = 1 nslices = 180 ndcmfiles = 180 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) writing to /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Çrş Nis 24 11:45:57 +03 2019 Found 1 runs /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1 mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz... TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/file1/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/file1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/file1/mri/orig.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Çrş Nis 24 11:46:09 +03 2019 /usr/local/freesurfer/subjects/file1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s file1 exited with ERRORS at Çrş Nis 24 11:46:11 +03 2019 For more details, see the log file /usr/local/freesurfer/subjects/file1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Ubuntu version:18.10 3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached DownloadAndInstall - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall> Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. surfer.nmr.mgh.harvard.edu

2 2

fsaverage error with recon-all
by chen 25 Apr '19

25 Apr '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage/surf/lh.sphere.reg. According to the fsaverage-recon-all.log, it completed without error. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. Secondly, i have studied the multi-site reliability of young traveling subjects which scanned in multi-site with the same scanner and protocol across 12 month. I ran these data with cross-pipeline. But, our results showed that the amygdala volumes have significantly lower reproducibility in inter-site than hippocampus and entorhinal cortex (ICC scores less than 0.5) with FreeSurfer rather than manual tracing. So, i want to assure that recon-all -all is the optimal process pipeline. If not, can you give me some advice? Should i use the longitudinal pipeline in multi-site study with traveling subjects? Thanks. ------------------ 首都医科大学宣武医院杜佳晨

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