Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Re: [Freesurfer] Total White matter and CSF value Calculation
by M Janani 09 Aug '17

09 Aug '17

Hi Douglas, Thanks for your support. From the below conclusion, can I say Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle + 5th Ventricle + CSF. Also Is it correct to compute Total CSF using the below mentioned formula Total CSF = Intracranial Volume - (Total white matter + Total Gray matter) Regards, Janani ---------------------------------------------------------------------------------------------------------------------------------------------------- Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 31 Jul 2017 07:48:02 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> On 7/31/17 3:12 AM, M Janani wrote: Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1.Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter looks right, though some times people will include brainstem as part of WM 2.Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle There is a 5th ventricle (which I think is basically the aqueduct). There is also a segment called "CSF" (24) but can't remember what gets labeled as "CSF" Thanks for your support. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ---------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume
by Lucette Cysique 09 Aug '17

09 Aug '17

Hello all FYI I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my healthy young sample It is probably due to the cerebellum computation changes (presented in released notes for 6.0) Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar (all was checked by simple correlations) Could people who have good knowledge of cerebellum studies comment on the reliability of freesurfer 5.3 in assessing size of the cerebellum versus manual tracing? This may need to be redone for version 6.0. Regards Lucette Lucette A. Cysique, Ph.D. NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017 NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA Senior Lecturer SoMs, UNSW Medicine Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit Postal Address: Neuroscience Research Australia PO Box 1165 (Street Address: 139 Barker Street) Randwick NSW 2031 Australia Office Ph: +61 2 9399 1880 Mobile Ph: (+61) (0)431 576 710 (text preferred) Emails: lcysique(a)unsw.edu.au (primary) Lucette.Cysique(a)svha.org.au (St. Vincent's Hospital Sydney, related project) lcysique(a)ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project) Twitter: @Lucette_C http://www.neura.edu.au/research/themes/cysique-group

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Urgent help with stats in FreeSurfer
by Martin Juneja 08 Aug '17

08 Aug '17

Hi, One of my papers is under review showing significant differences in cortical surface area between healthy controls and patients. In this paper, regarding statistical results, for multiple comparison correction, I ran Monte Carlo simulations using following command: mri_glmfit-sim \ --cache 4 neg \ --cwp 0.05\ --2spaces In the paper, I reported that multiple comparisons were corrected at p < 0.05 using Monte Carlo simulations. I also reported cluster sizes (number of voxels) of all clusters which survived multiple comparison correction. I checked literature and found that that's how people report cluster results after running analysis in FreeSurfer. One of the reviewers asked- Did you consider any constraints on findings (specifically cluster size) before considering the finding significant? Could you please help me in understanding this question and how can this be answered? In this paper: http://onlinelibrary.wiley.com/store/10.1002/pbc.25386/asset/pbc25386.pdf?v…, authors reported that - "The data were tested against an empirical null distribution of maximum cluster size across 10,000 iterations using Z Monte Carlo simulations as implemented in FreeSurfer [31,32] synthesized with a cluster-forming threshold of P < 0.05 (two-sided), yielding clusters fully corrected for multiple comparisons across the surfaces. Clusterwise corrected P < 0.05 (two-sided) was regarded significant." I assume that that's what reviewer is demanding me to report in my paper. I would really appreciate any help.

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Open position at Lausanne University Hospital: research and development engineer (fwd)
by Lilla Zollei 08 Aug '17

08 Aug '17

FYI ---------- Forwarded message ---------- Date: Mon, 7 Aug 2017 12:54:29 +0000 From: Meritxell Bach Cuadra <Meritxell.BachCuadra(a)unil.ch> To: Meritxell Bach Cuadra <Meritxell.BachCuadra(a)unil.ch> Subject: Open position at Lausanne University Hospital: research and development engineer Dear colleague, we are looking for a research and development engineer, for a one year position (extension of additional 6 months possible) at the Lausanne University Hospital, together with the Radiology and the Psychiatric Departments. The position is related to diffusion and functional MRI analysis and Connectome studies. Details and requirements are in the pdf attached. I would really appreciate if you could forward it to whom might be interested. Best regards, Meri Meritxell Bach Cuadra, PhD, M.E.R. Medical Image Analysis Laboratory (MIAL) - http://www.unil.ch/mial/ Department of Radiology, CIBM- Signal Processing Core - CHUV Unit University Hospital Center (CHUV) and University of Lausanne (UNIL) Rue du Bugnon 46, CH-1011 Lausanne, Switzerland Office BH 08-079, Phone: +41-21-314-67-75

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Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation
by Tabassum, Ruchira 07 Aug '17

07 Aug '17

Can anyone provide me the link of freesurfer version 5.3 vdi file? I was trying to install it in windows 10 using virtual box, but its not working. Thanks Ruchira From: Tabassum, Ruchira Sent: Saturday, August 5, 2017 1:22 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: Need Urgent Help!! Regarding FreeSurfer Installation Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum

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tracula problem
by Lin, Yizhi 07 Aug '17

07 Aug '17

I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Aug 6 23:37:59 EDT 2017 I am sure that I have the aparc+aseg file in the right directory but it showed that the files are missing..... I would be really appreciated if anyone could please help!!! Thanks so much!!! Sincerely, Ariel

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TRACULA ERROR!!
by Lin, Yizhi 07 Aug '17

07 Aug '17

Dear fellow researchers, I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Aug 6 23:37:59 EDT 2017 I am sure that I have the aparc+aseg file in the right directory but it showed that the files are missing..... I would be really appreciated if anyone could please help!!! Thanks so much!!! PS: I attached trac-all.log as an attachment. Thanks Sincerely, Ariel

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Thalamus ROI
by saraizad＠alumni.ubc.ca 07 Aug '17

07 Aug '17

Hi Freesurfer team, Is it possible to extract Thalamus as an ROI from aseg.mgz to be used for tractography in FSL. If so, what command I have to use to extract it. Can I use the LUT table to extract thalamus? Thanks, Sara

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pineal gland
by Rotem Saar 07 Aug '17

07 Aug '17

Dear Bruce and Doug, Thank u for your replay saying that it is possible to manually draw the pineal gland using freeview and extract stats for it. Can u please refer me to a link on wiki that explain how to do it? I'm not familiar with this procedure and although Doug explain it in brief I feel I need to follow some manual...is there something on the net? If not - can u please specify the steps I need to go through? Also, I have a full recon-all for the subjects I want to extract the volume of the pineal gland (using freesurfer version 3 something...). If I want to extract the volume of a specific ROI today using and advance freesurfer version (5+) - Do I need to run recon-all again with the newer version? Many thanks ! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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Updating FreeSurfer v5.1 statistics to FreeSurfer v5.3
by Hatton, Sean 07 Aug '17

07 Aug '17

Hello FreeSurfer experts, I have many FS5.1 edited-subjects that I want to use in an application that only takes FS5.3 formatted statistics. I ran 20 subjects in FS51 and FS53. I took the FS51 subjects and reran recon-all -segstats (in FS53) and it updated aseg.stats closer to the values for FS53 native. I reran recon-all -parcstats but that didn't change the parcellation statistics. Correlations between FS51 updated and FS53 were ~r=0.91. It this a fair approach to take? Is there a fundamental difference between FS51 and FS53 that requires that I rerun/edit everything? Regards, Sean Hatton, PhD Postdoctoral Scholar, Department of Psychiatry UCSD

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Freesurfer August 2017