Freesurfer

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30132 discussions

Follow-Up: Longitudinal Processing - Retaining Manual Edits
by KALEY E ELLIS 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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error with mri_ca_register in long
by miracle ozzoude 27 Aug '18

27 Aug '18

External Email - Use Caution Hello All, When running the longitudinal pipeline for version 6, i encountered this error " TransformSample: gcam has not been inverted!; Numerical result out of range". I found a thread with similar error but the problem wasn't solved. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html . Just like the previous thread, it happens whenever I include the "-bigventricle" flag. Below is a sample of my recon-all scripts from cross-sectional to longitudinal. The error.log and recon.log files are too large to send. Thank you. Best, Paul Cross-sectional recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time Longitudinal recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles -3T -time

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Resample data for longitudinal comparisons
by James Gullickson 27 Aug '18

27 Aug '18

External Email - Use Caution All, I would like to compare cortical thickness between two timepoints. Timepoint 1 has 1mm^3 data. Timepoint 2 has 0.8mm^3 data. I realize that there are limitations with this change in resolution between timepoints and that no analysis is going to be perfect, but I am trying to come up with the best possible solution. Would it work to resample both timepoints' raw data into 0.9mm^3 ( mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data through Freesurfer 6.0 submilimeter recon? If so, are there any special considerations I need to take into account after the initial recon, or would longitudinal processing after this point be per normal? Thanks, James

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Longitudinal Processing question
by Nillo, Ryan Michael R 27 Aug '18

27 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas between a few months to < 2 years. I want to know what are appropriate/acceptable age deltas used for longitudinal processing. I looked through the archives and one researcher asked about age deltas. One of the answers was that “if the time delta is relatively small, this has good chances to work”. What does “relatively small” mean? If the time points exit the longitudinal pipeline without errors and the surfaces look correct, does this mean the data is relevant?? When I correct for head size, should I use the eTIV values from the cross-sectional directories or the longitudinal directories? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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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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