Freesurfer

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30132 discussions

Extracting both the GM and WM ROIs
by Song, Da-Yea 14 Dec '18

14 Dec '18

External Email - Use Caution Hello, I've been trying to extract ROIs directly from the Desikan atlas by using the mri_annotation2label and the aparc.annot files from the fsaverage folder. I noticed that this pulls out the grey matter portion for these regions but was wondering if there was a command or file that I could use to do the same for both the grey and white matter. For example, is it possible to extract the grey and white matter region of the posteriorcingulate (in one file)? Thank you so much in advance for your help! Best regards, Da-yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Inferior colliculus and Brainstem-cochlear-nucleus
by Chama Belkhiria 14 Dec '18

14 Dec '18

External Email - Use Caution Dear comittee, I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can freesurfer distinguish it from other brainstem structures in segmentation? I have found these references in the LUT "7100 Brainstem-inferior-colliculus and 7101 Brainstem-cochlear-nucleus", but idid not find them in the aseg or aparac files. How to measure the volume and thickness of these regions? Thank you in advance Chama ***** Post Doctoral Researcher Audition and Cognition Center Neurosciences Department Faculty of Medicine, University of Chile

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Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results
by Bruce Fischl 14 Dec '18

14 Dec '18

what is your input data format? On Fri, 14 Dec 2018, Geha, Paul wrote: > Dear Bruce, > > Thank you for your reply. > > However, we are obtaining an odd result with FreeSurfer when we examine the volume of the left and right accumbens. In the UK BioBank data >20K subjects freesurfer segmentations the left accumbens is clearly significantly larger than the right accumbens ( http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110 <http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110>). Also, the attached paper used freesurfer and found left accumbens > right. In our hands, and in 2 different data sets collected in two different sites, we obtain the opposite with FreeSurfer (right accumbens > left accumbens). > > Furthermore, when we segment these same data sets with FIRST from FSL we do obtain Left accumbens > right Accumbens in both data sets in agreement with the literature. > > Any help in solving this discrepancy is much appreciated. > > Regards, > Paul > —————————————————— > Paul Geha, MD > Assistant Professor of Psychiatry > Yale School of Medicine > Assistant Fellow, The John B. Pierce Laboratory > Email: paul.geha(a)yale.edu > Tel:(203)903-4334 > > > >> On Dec 13, 2018, at 3:49 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Meena >> >> it shouldn't. We reorient everything to radiological >> >> cheers >> Bruce >> On Thu, 13 Dec 2018, Meena M. Makary wrote: >> >>> External Email - Use Caution >>> Hi; >>> I am wondering if the orientation of the input data to recon-all (i.e. Neurological Vs. Radiological) >>> produces different results in terms of laterality (right vs. left)? >>> Thanks; >>> --Meena >>> — >>> Meena M. Makary, Ph.D. >>> Assistant Professor | Cairo University >>> Postdoctoral Fellow | Yale University School of Medicine >>> Postdoctoral Associate | The John B. Pierce Laboratory >>> Postdoc Committee Chair | The John B. Pierce Laboratory >>> Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG >>> 290 Congress Avenue, New Haven, CT 06519 >>> +1 (475) 731-5592 > >

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Segmentation Query
by Fariha Muazzam 14 Dec '18

14 Dec '18

External Email - Use Caution Hi I am working in Freesurfer for subcortical segmentation of brain, I did segmentation of a volume and I got around 45 regions. Is it possible that I could customize the regions I want or number of segments that I want? Thank You Regards *Fariha Muazzam* Research Officer -------------------------------------------------------------------------- Al-Khawarizmi Institute of Computer Science (KICS) University of Engineering and Technology (UET), Lahore *Email:* fariha.muazzam(a)kics.edu.pk * |* *Web:* www. <http://www.ictrdf.org.pk/>kics.edu.pk

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GPU/supercomputer adaptation of freesurfer?
by John Absher 14 Dec '18

14 Dec '18

External Email - Use Caution Hi, I'm planning a freesurfer analysis of a large MRI dataset, and want to use the "380 GPU nodes" (and other cores/nodes) on the Palmetto Cluster (https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) to speed up the process. Since I am not a programmer, I'm hoping someone can give me a quick tutorial: a) Is this going to speed up recon-all and the data analysis? b) How much programming/expertise is required to enable freesurfer to take advantage of a supercomputer's resources? c) Has anyone done this already? d) The Palmetto Cluster is more or less limited to command-line. As long as I visualize the data on another system, I assume this will not be a problem, right? Thanks, John R. Absher, MD jabsher(a)ghs.org<mailto:jabsher@ghs.org> GHS Neuroscience Associates University of South Carolina School of Medicine Greenville 864-350-6655 (mobile)

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Longitudinal stream : LME and limits of model
by Matthieu Vanhoutte 14 Dec '18

14 Dec '18

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would miss the first timepoint but got the others ? 3) Considering a group in longitudinal study, which is the number of subjects minimal of this group accepted for LME modeling ? 4) Finally, concerning quality control and among a big number of total time points, which essential controls are necessary ? (Control of norm.mgz of the base, alignment of longitudinal timepoints on base,… ?) Best regards, Matthieu

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Longitudinal processing - LAS and RAS orientation baseline vs follow-up
by Elena Pozzi 14 Dec '18

14 Dec '18

External Email - Use Caution Dear FreeSurfer Experts, I have some baseline and follow-up MRI scans that I would like to process through the longitudinal stream. Some of the baseline images were originally in Analyze format (LAS orientation) and were converted into nifti (keeping the LAS orientation) and then processed through the recon-all stream (and edited). A few other baseline images were instead in nifti format (RAS orientation). The follow-up images were all in nifti format (RAS orientation) and were as well processed through the recon-all stream and edited. For all the images that were originally in Analyze format at baseline and converted in nifti, the within subject template (base) failed, i.e., the surfaces clearly do not properly follow the WM and GM boundaries. Instead, for the baseline images that were in nifti format the template looks fine. Given that the problem arose only with the Analyze images, could the different orientation (LAS and RAS) explain the issue? If so, is it possible to flip the orientation after the preprocessing, keeping the edits that were made on the pial of the baseline images? Apologies if any of these questions was already asked but I couldn’t find an answer. Thank you very much, Elena

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Longitudinal Stream - LONG step
by Figueiro Longo, Maria Gabriela 14 Dec '18

14 Dec '18

Hello FreeSurfer Developers, I'm attempting to run the longitudinal stream, but in the [LONG] step of one time-point of on of my subjects, I have the following error: MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone have any thoughts on how to trouble-shoot this one? I attached the recon-all.log. FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8 Thanks, Gabriela

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Longitudinal processing and paralllel flag
by Erik O'Hanlon 14 Dec '18

14 Dec '18

External Email - Use Caution Hi FS experts, I'm running a longitudinal process with three time points per subject and was wondering if you can advise on the typical time to process? Can the -parallel flag be added to the base and long steps? I'm running this on a cluster that has 16 core nodes with 32gigs of ram so it might give me a good tme saving if these steps can be parallelized. Thanks and regards Erik Postdoctoral Research Fellow Dept. Of Psychiatry Royal College of Surgeons in Ireland ERC Building Beaumont Hospital Dublin & Dept. Of Psychiatry Trinity College Institute of Neuroscience The Llyod Institute Trinity College Dublin D2 Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png]

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longitudinal analyses after lesion segmentation
by kathleen Gerbino 14 Dec '18

14 Dec '18

External Email - Use Caution Hi FreeSurfer experts: I hope you are well. I need to segment quite a few longitudinal T1 scans from patients with multiple sclerosis. A colleague has applied an automated lesion segmentation algorithm to segment and fill the lesions. During this process, the follow-up scans were registered to the baseline scan. My question is whether I could still apply the Freesurfer longitudinal pipeline to these images or whether your had any recommendations on the appropriate steps to take if this is not appropriate. Kind regards, Kathleen

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