Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

ICV bias in CV measures
by Sahil Bajaj 03 Aug '18

03 Aug '18

External Email - Use Caution Dear FS experts, This paper was published in 2013: https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Di… I was just wondering if the current version of FreeSurfer can still introduce bias in cortical volume measures if ICV is used as an covariate or this has been fixed in the latest FS version. Specific to this issue, if nothing has been updated in FS (since 2013), would you still recommend to *ALWAYS* use ICV as a covariate while comparing CV? Thanks, Sahil

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SNA covariate in cortical thickness between groups analysis
by John Anderson 03 Aug '18

03 Aug '18

External Email - Use Caution Daer FS experts, I would like to inquire about including SNR as a covariate for the between groups cpmparison in cortical thickness. Is this procedure correct mathematically? Do I need to demean the SNA values before including it covariates? Finally, do you recommend any quality parameters other than SNR to be included covariate? I look forward to learn from your expertise, Thanks, John

2 1

Anterior / Posterior Partition in Hippocampus parcellation atlas
by Dev vasu 03 Aug '18

03 Aug '18

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/body/tail ) , on my subject pool the volumes that i have obtained for each subfield is very different from the volumes of corresponding subfields that i am getting when i have done subfield segmentation using freesurfer. I think algorithm does influence the segmentation procedure, if this is the case then i am getting different results for histology based segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and freesurfer. When i compare the subfield volumes between healthy and disease patients that i have obtained using first segmentation procedure using ANTS-MAGeT , i notice statistical significance in subfields like CA1,CA2-CA3 but when i do the same using freesurfer based algorithm i notice no statistical significance in these subfields. Do you think the algorithm has any influence on segmentation to such a level that we get completely different results on two occasions. Thanks Vasudev

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Re: [Freesurfer] Annotation question in freesurfer
by jahanvi patel 02 Aug '18

02 Aug '18

External Email - Use Caution Hi Bruce, Thanks a lot, here is the figure. We want to know the annotation of the red cluster. When we check the cache.th30.pos.sig.culster.summary, we got this cluster info. MNIX -8.8, MNIY -89.2, MNIZ 21.4 What are these coordinates? are they in MNI space? Cheers, Jahanvi > Date: Thu, 2 Aug 2018 10:23:02 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Annotation question in freesurfer > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1808021022090.1865(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > Hi Jahanvi > did you mean to attach a figure? If you did it did not make it. Definitely > > look at the annotation on the surface (inflated probably) if you want to > judge its accuracy > cheers > Bruce > On Thu, 2 Aug 2018, jahanvi patel wrote: > > > > ????????External Email - Use Caution???????? > > > > Dear List, > > > > We have a question about the annotation of this MNI coordinate (-8.8, > -89.2, 21.4). > > Freesurfer's report summary showed it is --?left superior parietal > lobule, while we see from the > > figure it seems not very much correct. It seems more occipital cortex. > Is there a chance to validate > > the annotation if possible? > > > > Best regards, > > Jahanvi > > >

2 1

Filling holes
by John Anderson 02 Aug '18

02 Aug '18

External Email - Use Caution Dear Freesurfer experts, I would like to inquire whether there is (are) any command(s) in FS6.0 that can help to fill holes in a brain mask without dilating it? I would appreciate any advice, John

2 3

recon-all did not create all files
by Ortal Nakash 02 Aug '18

02 Aug '18

External Email - Use Caution Hi, I tried to run the recon-all command on a single participant on a high memory cluster by typing: qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not. sincerely, Ortal Nakash

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Ex vivo segmentations
by Fotiadis, Panagiotis 02 Aug '18

02 Aug '18

Hi Bruce and Doug, I have processed a few ex vivo brains with the help of the ex vivo freesurfer pipeline (outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) and have extracted their cortical thickness. So far the range of the cortical thicknesses have been approximately between 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am asking because the typical cortical thickness that I would expect to find on an in vivo brain would be between 2.05 - 2.35 mm. Thanks in advance for any advice! Best, Panos Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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Annotation question in freesurfer
by jahanvi patel 02 Aug '18

02 Aug '18

External Email - Use Caution Dear List, We have a question about the annotation of this MNI coordinate (-8.8, -89.2, 21.4). Freesurfer's report summary showed it is -- left superior parietal lobule, while we see from the figure it seems not very much correct. It seems more occipital cortex. Is there a chance to validate the annotation if possible? Best regards, Jahanvi

2 1

PhD position avalaible in Torus, France : hisgh resolution Brainstem atlas
by Christophe Destrieux 02 Aug '18

02 Aug '18

External Email - Use Caution Dear all, we have an open 3-year position for a PhD student in our lab in Tours, France beginning 2018, oct 1st. This student will work on a brainstem atlas from 11.7T exvivo MRI data. Details are included here : https://ibrain.univ-tours.fr/actualites/scientifiques/offres-de-recrutement… <https://ibrain.univ-tours.fr/actualites/scientifiques/offres-de-recrutement…> Do not hesitate to distribute Christophe Destrieux, Unité iBrain UMRS INSERM U1253, Université de Tours http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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Problems associated segmentation results of hippocampal subfields
by Dev vasu 01 Aug '18

01 Aug '18

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