Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

Missingness and recent developments in longitudinal pipeline for pediatric samples
by Mohn, Johannes 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FS Experts and Community, we are working on a longitudinal dataset of structural T1w images in a pediatric sample assessed at 2 waves, 2 years apart (aged 6/7 and 8/9). As far as we know, it is yet unresolved whether the Freesurfer longitudinal pipeline is robust in pediatric samples, where the head size is still changing or have there been any recent developments? Also, is there any documentation on how missingness affects this Pipeline? We look forward to your response Thank you, Laurel and Johannes Jacobs Entwicklungsstudie Max-Planck-Institut für Bildungsforschung Max Planck Institute for Human Development Lentzeallee 94 14195 Berlin Tel.: 030-824 06 371 E-Mail: jacobs-studie(a)mpib-berlin.mpg.de<mailto:jacobs-studie@mpib-berlin.mpg.de>

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Seeing the Parcels as Volumes
by Maedeh Khalilian 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_annnotation2label" and "mri_label2vol" to change the parcellation output of FreeSurfer e.g the lh.aparc.annot into an ".nii" so i can see the parcels in Mricro. Now I can see the parcels just on the cortex not on the whole graymatter. The first question I have is that, is the parcellation done on the whole graymatter? And if yes, is there a way that I can see the volumes on the whole graymatter, not just on the cortex? I would be grateful if you could help me. best regards, Maedeh,

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Available postdoc position linked to ENIGMA Brain Injury
by Alexander Olsen 27 Aug '18

27 Aug '18

External Email - Use Caution There is a temporary position available at the Department of Psychology as postdoctoral fellow in multimodal neuroimaging for a period of 2 years.The postdoctoral fellow will work at the Clinical Neuroscience Laboratory (CNL)<http://www.ntnu.no/web/psykologi/cnl>, headed by Associate professor Alexander Olsen. The successful candidate will develop work that contributes to, and complements, ongoing research studies. The postdoctoral fellow will have a key role in our research activities linked to the ENIGMA Brain Injury<http://enigma.ini.usc.edu/ongoing/enigma-tbi/> working group. ENIGMA is a framework with harmonized protocols for data processing and analysis across multiple sites and cohorts. The postdoctoral fellow will work in close collaboration with our world-wide partners to provide new knowledge on the consequences of traumatic brain injury by utilizing an unprecedented sample size compared to typical neuroimaging studies. Salary starting at 515 200 NOK ($ 62 000) per year. Read more about the position, and how to apply: https://www.jobbnorge.no/ledige-stillinger/stilling/149964/postdoctoral-pos… Feel free to contact me for any questions. Sincerely, Alexander Olsen Associate Professor Clinical Neuropsychologist Norwegian University of Science and Technology St. Olavs Hospital Trondheim, Norway Telephone: +47 917 22 824 http://www.ntnu.edu/employees/alexander.olsen

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3 positions to post on your platform
by Florence M 27 Aug '18

27 Aug '18

External Email - Use Caution Hi, Could you post this 3 positions on your forum please? Best regards, Florence Majri

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mris_smooth error: can't allocate region
by Paysing Wu 25 Aug '18

25 Aug '18

External Email - Use Caution Hi FreeSurfer Developers, I was running recon-all and it stoped at smooth1. The command is: recon-all -i T1image.nii.gz -s subject_name -all Below is error message on the screen: #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix \n setting seed for random number generator to 1234 mris_smooth(27701,0x7fffec01b3c0) malloc: *** mach_vm_map(size=13835344293369151488) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug TAGskip: tag=-8454144, failed to calloc 4286513152 bytes! Cannot allocate memory Darwin lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 Although the message looks like the shortage of memory, it could run a few weeks ago. So, I really doubt memory is the main reason (the physical memory is 40GB)...The only difference before and after I can run is I reinstall the same version of Matlab 2016b by accident. Do you think I have to change some setting to run it? Also, I've looked for solutions and couldn't find a one which really fits my problem. Would you please help me trouble-shoot this issue? Thank you so much. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: macOS Sierra version 10.12.6, with physical memory 40GB 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached Best, PH

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questions about hippocampus subfield error
by 姜时泽 25 Aug '18

25 Aug '18

External Email - Use Caution | | Dear freesurfer experts, I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm. below is the commands I used to run freesurfer and attached is the recon-all log file. recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all I am not sure if there are something wrong with my inputs. Thank you all all the best Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

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Recon-all crash at Talairach
by Meaghan Perdue 25 Aug '18

25 Aug '18

External Email - Use Caution Hello experts, I am processing a data set through Freesurfer v. 5.3 and many subjects are crashing at the following point: #@# Talairach Sat Aug 25 10:06:26 EDT 2018 /Volumes/freesurfer/PID/Time3/sn9885/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n The command I've used to initiate recon all is: recon-all -all -s sn9885 -i sn9885.nii.gz -cw256 -qcache Any advice for trouble-shooting this? Many thanks! Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Unable to copy the license.txt file into $FREESURFER_HOME
by Tsz Wai (Bentley) Lo 24 Aug '18

24 Aug '18

External Email - Use Caution Hi FreeSurfer Developers, I am attempting to copy my license.txt into $FREESURFER_HOME. I have already open a terminal window and define and environment variable called freesurfer_home but I am not sure where FreeSurfer home is. I am not sure how to source the set up script as well. I am on macOS high Sierra. Bentley This email is intended only for the named recipient(s) and may be confidential. Any unauthorized use, dissemination or copying of this email is strictly prohibited. If you have received this email in error, please notify the sender immediately and destroy all copies of this email.

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Error with mris_anatomical_stats
by Davide Momi 24 Aug '18

24 Aug '18

External Email - Use Caution Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? this is the command which I used: mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh computing statistics for each annotation in label/lh.aparc.annot. reading volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz... mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz Thanks in advance Davide

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bbregister error
by Nada Naguib 24 Aug '18

24 Aug '18

External Email - Use Caution Hello, I have been using bbregister in this format bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta NewT2out is the output of the free surfer processing on the T1 image and dkti4d.nii is the template file I want to use for the registration. it has worked before but now there is a new error ERROR: cannot find NewT2out in /project/iconic/apps/freesurfer/5.3.0/install/subjects even though I have already ran the command: setenv SUBJECTS_DIRECTORY /project/bil/Nada This path is where both NewT2out and dkti4d.nii are located. I don’t understand what is going wrong Best Nada

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Freesurfer August 2018