Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

GNU R package to read and write FreeSurfer data
by Tim Schäfer 18 Sep '19

18 Sep '19

External Email - Use Caution Dear list, I needed some GNU R functions which read and write MGH/MGZ files including all the header information, so I wrote them and also put them into a package to share them. Support for binary 'curv' format morphometry files (like 'surf/lh.area') and annotations (like 'labels/lh.aparc.annot') in also included. The package is on CRAN: https://cran.r-project.org/package=freesurferformats Docs, examples and vignettes are included. Unit tests can be found (with the full source code) on GitHub: https://github.com/dfsp-spirit/freesurferformats Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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How to fasten recon-all execution time without using CUDA
by Dev vasu 18 Sep '19

18 Sep '19

External Email - Use Caution Dear all, I am using - openmp 30 to run recon-all, i see now change in the execution time period. Could you please highlight me a method to reduce the execution time for recon-all, if possible some parallel script to do that same. Thanks Vasudev

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Names of the segmentation volumes in lh.hippoSfLabels-T1.v10.mgz
by Kai Liu 18 Sep '19

18 Sep '19

External Email - Use Caution Hi FS experts, I am using the module of segmentation of hippocampal subfields. About the output of lh.hippoSfLabels-T1.v10.mgz, could you pls provide the correspondence between the values of segmentation volumes in the image file and the anatomical names in the file of lh.hippoSfVolumes-T1.v10.txt? I am pretty confused because there are totally 12 regions as described in the .txt file, and I was anticipating 12 values corresponding to 12 segmentation volumes in the .mgz file (like aseg). However, I found 14 discontinuous values in the .mgz ranging from 203 to 226. Looking forward to your kind reply. Kai

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mri_convert for Philips dicoms
by Mun, Anna 17 Sep '19

17 Sep '19

Dear FreeSurfer team, I am working with data sent to us from other research site. They use Philips scanner and I can not run mri_convert on the dicoms. Is there other way to mri_convert and reconstruct Philips dicoms. error log is: WARNING: tag SeriesNumber not found WARNING: tag image orientation not found ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 break DICOMRead.c:5228 Ref Series No = 0 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu Thank you in advance! Best, Anna

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Freeview error
by Miguel Ángel Rivas Fernández 17 Sep '19

17 Sep '19

External Email - Use Caution Dear Freesurfer devs, I tried to open the brainmask.mgz file in freeview but I obtained this error: mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly. Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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mris_sphere question
by Lauricella, Michael 17 Sep '19

17 Sep '19

External Email - Use Caution Dear Freesurfer Experts, I'm fairly new to freesurfer, but have a set-up in which I have been able to run many successful recon-all runs. One problem that I have sometimes, maybe about 20% of the time, is that the run will freeze and crash at this step: mris_sphere -rusage /mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere here's the end of the logfile: "== Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.287... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.21 pass 1: epoch 2 of 3 starting distance error %20.95 unfolding complete - removing small folds... starting distance error %20.57 removing remaining folds... final distance error %20.59 MRISunfold() return, current seed 1234" Does anyone have any ideas why this might be happening? Maybe this is a computationally intensive step? If I run a few recon-alls concurrently it almost always crashes at this step. The command I run is: recon-all -all -openmp 2 -qcache -nuintensitycor-3T -s SUBJECT_ID -sd /mnt/freesurfer_subjs/ Thank you so much for your help! Best, Michael

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PET input file for mri_gtmpvc
by Jane Tseng 17 Sep '19

17 Sep '19

External Email - Use Caution Dear Freesurfer experts, I was wondering if there is any recommendation on the PET input file for partial volume correction using mri_gtmpvc? Should I use a non-skullstripped SUV or a skullstripped SUV? If a skullstripped SUV can be used, would a tight (just aparc+aseg binarized) or a lenient (e.g. aparc+aseg binarized and dilated by 2mm) mask be better? I am interested in using the GTM regional values. Thank you for your help! Best wishes, Jane

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Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects
by vin rasa 16 Sep '19

16 Sep '19

External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4 structures only. I found aparcstats2table command, which seems to extract all the segmented regions. https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table Thanks in advance

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Questions about labels and tkmedit
by Zeng,Victor (BIDMC - Psychiatry) 16 Sep '19

16 Sep '19

Hi all, ? I know tkmedit has been deprecated, but we're thinking about using it just for quality check purposes since we found that it is less resource intensive. We're trying to load multiple labels, is there a way to do that so that each label is assigned a different color (we know that's possible for Freeview). best Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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001 vs brainmask views in freeview
by Alexopoulos, Dimitrios 16 Sep '19

16 Sep '19

External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. [cid:image001.jpg@01D56C83.BD016B00] [cid:image002.jpg@01D56C83.BD016B00] Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. [cid:image003.jpg@01D56C83.BD016B00] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer September 2019