Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Converting .mgz (or .nii) file to .hdr file (.hdr and .img)
by Kim, Gwang-Won 04 Apr '20

04 Apr '20

Dear expert, I'd like to convert .mgz (or .nii) file to .hdr file (.hdr and .img) to use .hdr in SPM software. I tried to convert the file using "mri_convert". But, there were the error messages below. Please, let me know how to onvert .mgz (or .nii) file to .hdr file (.hdr and .img). 1) convert .nii file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it nii -ot spm BB.nii RE mri_convert.bin -it nii -ot spm BB.nii RE $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from BB.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 2) convert .mgh file to .hdr file (.hdr and .img) [latifah:kim] (nmr-stable6-env) mri_convert -it mgh -ot spm AA.mgh RE.hdr mri_convert.bin -it mgh -ot spm AA.mgh RE.hdr $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from AA.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to RE.hdr... ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768

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Re: [Freesurfer] Freesurfer with Catalina
by fsbuild 03 Apr '20

03 Apr '20

External Email - Use Caution Hello Stephan, I’m assuming you’re running the freesurfer 6.0.0 release and used the Mac pkg file to install it on your Mac from,freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg You would need admin/root privileges to use the “Security and Privacy” tab from the System preferences window on the Mac to give the pkg file permission to install freesurfer as /Applications/freesurfer I have just done this install on a machine running Catalina (Mac OS 10.15.2).  Then I ran the commands below.  Please try them and see if you get the same results.  The first command I typed is “bash” to start a bash shell. % bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. Mac:~>  Mac:~> export FREESURFER_HOME=/Applications/freesurfer Mac:~> source /Applications/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer FSFAST_HOME       /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/subjects MNI_DIR           /Applications/freesurfer/mni Mac:~> which mri_convert /Applications/freesurfer/bin/mri_convert Mac:~> file `which mri_convert` /Applications/freesurfer/bin/mri_convert: Bourne-Again shell script text executable, ASCII text Mac:~> which mri_convert.bin /Applications/freesurfer/bin/mri_convert.bin Mac:~> file `which mri_convert.bin` /Applications/freesurfer/bin/mri_convert.bin: Mach-O 64-bit executable x86_64 Mac:~> bash -x /Applications/freesurfer/bin/mri_convert --help + source /Applications/freesurfer/sources.sh +++ uname -s ++ '[' Darwin == Darwin ']' ++ source /Applications/freesurfer/SetUpFreeSurfer.sh +++ '[' -z /Applications/freesurfer ']' +++ '[' -z /Applications/freesurfer/subjects ']' +++ '[' -z /Applications/freesurfer/sessions ']' +++ source /Applications/freesurfer/FreeSurferEnv..sh ++++ VERSION='$Id: FreeSurferEnv.sh,v 1.61 2016/06/09 14:54:31 zkaufman Exp $' ++++ '[' 1 -gt 1 ']' +++++ uname -s ++++ os=Darwin ++++ export OS=Darwin ++++ OS=Darwin ++++ '[' -n '' ']' ++++ output=1 ++++ [[ -z synpro ]] ++++ [[ -z '' ]] ++++ output=0 ++++ '[' -z /Applications/freesurfer ']' ++++ '[' '!' -d /Applications/freesurfer ']' ++++ [[ 0 == 1 ]] ++++ '[' -z /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ']' ++++ '[' -z 0 ']' ++++ [[ -z /Applications/freesurfer/fsfast ]] ++++ [[ 0 != 0 ]] ++++ [[ -z /Applications/freesurfer/subjects ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/bin ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/lib ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/data ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ '[' -n '' ']' ++++ '[' -e /Applications/freesurfer/fsl ']' ++++ '[' -e /usr/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/fsl ']' ++++ export FREESURFER_HOME=/Applications/freesurfer ++++ FREESURFER_HOME=/Applications/freesurfer ++++ export LOCAL_DIR=/Applications/freesurfer/local ++++ LOCAL_DIR=/Applications/freesurfer/local ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/fsfast ']' ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/subjects ']' ++++ [[ -z nii.gz ]] ++++ [[ 0 != 0 ]] ++++ [[ 0 == 1 ]] ++++ [[ 0 == 1 ]] ++++ [[ -z '' ]] ++++ export FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ SUF=/Users/synpro/matlab/startup.m ++++ '[' '!' -e /Users/synpro/matlab/startup.m ']' +++++ grep FSFAST_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp1='       1' +++++ grep FMRI_ANALYSIS_DIR /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp2='       0' +++++ grep FREESURFER_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp3='       1' ++++ [[        1 == 0 ]] ++++ [[ 0 == 1 ]] ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ '[' '!' -d /Applications/freesurfer/mni/bin ']' ++++ '[' -n /Applications/freesurfer/mni/lib ']' ++++ '[' '!' -d /Applications/freesurfer/mni/lib ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 '!=' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ PATH=/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ '[' -d /Applications/freesurfer/lib/misc/bin ']' ++++ '[' -d /Applications/freesurfer/lib/misc/lib ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/bin/freeview.app ']' ++++ '[' -d /Applications/freesurfer/lib/gcc/lib ']' ++++ '[' -z '' ']' ++++ export DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/tktools ']' ++++ PATH=/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export FIX_VERTEX_AREA= ++++ FIX_VERTEX_AREA= ++++ return 0 + mri_convert.bin --help mri_convert.bin --help  Help NAME mri_convert SYNOPSIS mri_convert [options] <in volume> <out volume> … rest of output deleted … On Apr 3, 2020, at 11:28, Stephan <stephan.wunderlich22(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurer team,I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina.Running mri_convert always leads to the following error://Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary fileAll security changes haven't helped yet.Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_robust_template: Internal Error: Rotation should not scale.
by Sebille, Sophie 03 Apr '20

03 Apr '20

Hi , I'm running Freesurfer's longitudinal pipeline and several of the participants generate the same error for the mri_robust_template step: cmd: mri_robust_template --mov sub-ECTRO103-V1/mri/norm.mgz sub-ECTRO103-V2/mri/norm.mgz /sub-ECTRO103-V3/mri/norm.mgz sub-ECTRO103-V4/mri/norm.mgz --lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V1_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V2_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V3_to_sub-ECTRO103.lta sub-ECTRO103/mri/transforms/sub-ECTRO103-V4_to_sub-ECTRO103.lta --template sub-ECTRO103/mri/norm_template.mgz --average 1 --sat 4.685 error: Internal Error for tp 2 -> template Rotation should not scale ( 1.44353e-05 ) Debug Info: A = [ ... 0.9994648269692 0.0051381533060 -0.0325665649690 -0.0062826679505 0.9993709272221 -0.0351399801222 0.0323652536320 0.0353254803840 0.9988599205733 ] R = [ ... 0.9994563704934 0.0051381078439 -0.0325662912834 -0.0062826179162 0.9993626623658 -0.0351396895455 0.0323649840458 0.0353251881385 0.9988516601031 ] S = [ ... 1.0000084609181 0.0000000029711 -0.0000000043613 0.0000000029711 1.0000082701461 0.0000000000049 -0.0000000043613 0.0000000000049 1.0000082701081 ] Internal Error: Rotation should not scale. Looking at the data, I don't see what could be the issue. Does anyone have any thoughts on this? I have attached the recon-all.log of one participant. I can also share the data if you'd like. FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20200403-65d465d Linux tonetti.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thanks, Sophie

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White matter hypointensities
by Rockers, Elijah D. 03 Apr '20

03 Apr '20

External Email - Use Caution Hello, When was the wm-hypointeisities label added to the Freesurfer segmentation? Is there any paper that explicitly mentions this, or should I just cite the 2002 paper? Thanks, -Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

1 0

Freesurfer with Catalina
by Stephan 03 Apr '20

03 Apr '20

External Email - Use Caution Hi Freesurer team, I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina. Running mri_convert always leads to the following error: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary file All security changes haven't helped yet. Best, Stephan

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Petsurfer: Gtmstats < 1, voxel wise mean is fine
by Eckbo, Ryan 03 Apr '20

03 Apr '20

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | --------------------- | --- | -------------------- | --------------- | ----------- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan

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HP and thalamic subfield quality with a bad aparc segmentation
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Apr '20

03 Apr '20

Hi all, >From my understanding from the log files, the subfield segmentations (and in general the aparc.mgz) relies on the norm.mgz (which is based off the brainmask.mgz). What if hypothetically, you have a not so good segmentation of the cerebral cortex, but willing to individually qc the subfields for the hippo, amyg and thal to see whether they are worth including in an analysis? I don't know if you would inherently discard a subject in a subfield analysis if it has a bad cerebral cortex segmentation (e.g ring artifacts) since the subfield segmentation retrieves some sort of cerebral cortex measurement in its calculations Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ 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.

2 3

CORONA Research study in India - an online survey !
by Sahil Bajaj 02 Apr '20

02 Apr '20

External Email - Use Caution Dear all, Our research group is looking for participants (age 19 years or older) who are currently staying in India amid 21-days COVID-19 lock down, and can complete an online 15 min survey about human behavior related to COVID-19. If you meet these two eligibility conditions: (i) age 19 years or older, and (ii) you are/were staying in India during 21-days lock-down period due to CORONA virus, and are interested in participating in the study, please email me back at sahil.brain(a)gmail.com to get the survey link. Details about my research: https://www.boystownhospital.org/research/faculty/sahil-bajaj Given the seriousness of the disease, I would really appreciate if you can contribute to scientific research related to COVID-19. Thanks a lot ! Best, Sahil -- ------------------------------------- *Sahil** Bajaj, Ph.D.* Director, Multimodal Clinical Neuroimaging Laboratory (MCNL) Center for Neurobehavioral Research *E-mail:* sahil.bajaj(a)boystown.org | *p:* 531.355.1053 | *f:* 531.355.1213 Boys Town National *ResearchHospital* Boys Town, NE 68010 Twitter <https://twitter.com/BoysTown> | LinkedIn <https://www.linkedin.com/company/boys-town-national-research-hospital/>

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PhD position, University of Oldenburg, Germany
by Peter Soros 02 Apr '20

02 Apr '20

External Email - Use Caution Dear All, The University Clinic of Neurology, University of Oldenburg, Germany, seeks a highly motivated PhD student (m/f/d) for a TV-L 13 position (65 % of full time, 3 years): Neuroimaging, behavioral, and neurochemical markers of Parkinson's disease progression This position is embedded in a larger project on healthy aging and neurodegenerative disease at the University of Oldenburg and is funded by an intramural grant from the School of Medicine and Health Sciences. The successful PhD student will investigate large neuroimaging, behavioral, and clinical data sets available to us, using sophisticated statistical and neuroimaging software installed on the High-performance Computer Cluster in Oldenburg (uol.de/en/school5/sc/high-performance-computing/hpc-facilities). The overarching aim of the project is to determine biomarkers for disease progression and cognitive decline in Parkinson's disease. This project is a close collaboration between Neurology (Dr. Peter Sörös, Prof. Dr. Karsten Witt) and Anatomy (Prof. Dr. Anja Bräuer) in Oldenburg and Biostatistics at the Helmholtz Centre for Infection Research in Braunschweig (Prof. Dr. Frank Klawonn). The successful PhD student will also analyze biochemical markers of neurodegeneration in Prof. Bräuer's lab (uol.de/anatomie), participate in the development of novel software tools based on R Shiny together with Prof. Klawonn's group (www.helmholtz-hzi.de/en/research/research-topics/bacterial-and-viral-pathog…) and acquire own MRI data sets of patients and controls in the Neuroimaging Unit, School of Medicine and Health Sciences, University of Oldenburg (uol.de/en/medicine/biomedicum/neuroimaging-unit). The Neuroimaging Unit houses a research-only Siemens Prisma MRI at 3 Tesla with 64-channel head coil. Applicants are required to have an academic university degree, such as a master's degree in the field of psychology, neuroscience, physics or a related discipline, or a medical degree. A strong research background with experience in neuroimaging analysis (e.g. FreeSurfer, FSL, SPM), statistics (R), and programming (R Shiny, Python) is highly desirable. Excellent skills in written English are important. Oldenburg is an attractive city with a population of 170.000 in the northwest of Germany, close to Bremen, Hamburg, and Groningen. In order to increase the percentage of female employees in the field of science, female candidates with equal qualification will be given preference. Applicants with disabilities will be preferentially considered in case of equal qualification. Applications including a detailed letter of motivation, a complete CV, copies of university diplomas and transcripts, a copy of the B.Sc. or M.Sc. thesis (or other written work), and contact details of two academic referees should be sent to Dr. Peter Sörös: peter.soros(a)uni-oldenburg.de or to: Dr. Peter Sörös, Neurology, School of Medicine and Health Sciences, University of Oldenburg, Heiligengeisthöfe 4, 26121 Oldenburg, Germany. Application by email (one PDF document) is preferred. Deadline for application: April 30, 2020 https://uol.de/stellen/?stelle=67239 <https://uol.de/stellen/?stelle=67239>

1 0

Help Segmentation of Hippocampal subfields
by ioana cracana 02 Apr '20

02 Apr '20

External Email - Use Caution Hello, I'm doing a study about hippocampal atrophy and I'm using the Segmentation of Hippocampal subfields tool. There were some minor errors and I edited them using Freeview, voxel edit tool. I would like to generate a new [lr]h.hippoSfVolumes-T1.v10.txt file using the edited [lr]h.hippoSfLabels-T1.v10.mgz . What command do i have to use? I'm using Freesurfer v6.0.0. Thanks, Ioana

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Freesurfer April 2020