Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results
by Bruce Fischl 15 Dec '18

15 Dec '18

when you bring it up in freeview does it properly show left and right? If it ever went through analyze as a format you will have lost the information that lets us distinguish left from right cheers Bruce On Fri, 14 Dec 2018, Geha, Paul wrote: > It is NIFTI format. > —————————————————— > 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 14, 2018, at 10:53 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > 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 (https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.cts… > bel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c > bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN > MMSLiAGyXq734%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.cts… > abel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8 > cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM > NMMSLiAGyXq734%3D&reserved=0>). 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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mri_surf2vol: has many more faces than vertices
by Winkelbeiner, Stephanie A 14 Dec '18

14 Dec '18

External Email - Use Caution Hi Freesurfers, I'm trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_surf2vol \ --o FA/annot2FA.nii.gz \ --subject $subj \ --so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz cd ../ fi done However, I get ERROR: MRISread: file '$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot' has more faces than vertices! How can I solve this? Thanks, Stephanie Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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mri_segstats reporting more decimals
by Winkelbeiner, Stephanie A 14 Dec '18

14 Dec '18

External Email - Use Caution Hi Freesurfers, Is there an option to write out more decimals when using the mri_segstats command? I'm extracting mean diffusivity values and would need at least 5 decimals to make sense of them. Thanks for your help! Cheers Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Power analysis
by Laura Ferrero 14 Dec '18

14 Dec '18

External Email - Use Caution I performed a two tailed t-test analysis using stats data and after the analysis, results were corrected for multiple comparisons using FDR. Now, I want to perform a power analysis and I have some doubts: 1. Gammavar is the variance or the standard deviation (i.e., effect size should be gamma/gammavar or gamma/sqrt(gammavar)). 2. The alpha value to be used should be the original alpha (0,05) or the new one obtained after FDR. Thank you, Laura

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FreeSurfer Stats files: format of 'Measure' lines
by ts+ml＠rcmd.org 14 Dec '18

14 Dec '18

External Email - Use Caution Dear FreeSurfer experts, I'm parsing data from FreeSurfer stats files, e.g., <subject>/stats/lh.aparc.stats and aseg.stats. My question: when parsing measure lines, which combination of fields are guaranteed to uniquely identify a measure? Here are two example lines (from aparc.stats): # Measure Cortex, NumVert, Number of Vertices, 140843, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 94426.8, mm^2 If you ignore the line header part '# Measure ', each line consists of 5 fields. Is it, for example, safe to assume that the combination of the first 2 fields ("Cortex" + "NumVert" for the first example line) is unique? Thanks in advance, 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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NormMean information
by Keith Harenski 14 Dec '18

14 Dec '18

External Email - Use Caution Hello, What would local, individual differences in normMean voxel intensities signify? Is this related to any physical properties of the brain, or is the more of a QA measure for the white matter segmentation? Thank you, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski(a)mrn.org | www.mrn.org | www.lrri.org

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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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