Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

FLAIR in hippocampus subfield segmentation
by tulu 30 Jan '17

30 Jan '17

Dear Freesurfer experts Under Freesurfer V6 version, could the hippocampus subfield segmentation use high resolution FLAIR image ? if yes, is the command line -hippocampal-subfields-T1T2 ? Thanks JLH

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Re: [Freesurfer] freesurfer 6.0 with some of the analyses
by Antonin Skoch 29 Jan '17

29 Jan '17

Dear Batool, just small remark: If you did not manually modified talairach registration in your v5.3 subjects, I think it could be maybe beneficial to add -clean-tal to reinvoke talairach registration. The registration atlas has been updated in V6 but without -clean-tal option the registration will not be run again. And, also, if you do T2 or FLAIR adjustment of surfaces, it could be maybe beneficial to add -clean-T2 (-clean-FLAIR) to reinvoke T2/FLAIR registration to T1. There is new implementation of initial registration method (mri_coreg) for bbregister. Regards, Antonin Skoch You are correct that the former is true. Run recon-all -all on your existing subject directories after moving them to a new v6 directory (with the new fsaverage, etc.) -- it will rerun all the commands and use your brainmask.mgz deleted voxels, and your wm.mgz 255 voxels to correct the surfaces.You will still need to open your subjects up in tkmedit or freeview and inspect the surfaces for errors. On Fri, Jan 27, 2017 at 11:13 AM Rizvi, Batool <br2...(a)cumc.columbia.edu> wrote: > > > > > > > > > > > > > Thanks for your responses! > > > > > > > Sorry for the naive question, but I'm wondering which commands I'd use to > re-process all the data from 5.3. Can I run recon-all -all, and it will go > through all the steps that it would if I ran it from the start? Or would it > skip certain steps if it finds > > certain files existing already. I'm pretty sure the former is true, but > just wanted to confirm. > > > > > > > > Thanks again! > > > > > > > > Batool > > > > > > > ------------------------------ > > > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu [ > freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, > Eugenio [e.igles...(a)ucl.ac.uk] > > > *Sent:* Thursday, January 26, 2017 11:01 AM > > > *To:* Freesurfer support list > > > *Subject:* Re: [Freesurfer] freesurfer 6.0 with some of the analyses > > > > > > > > > > Dear Batool, > > Sorry for missing your message. > > > And dear Adam: > > > Thanks for covering me! That’s exactly my standard answer to that question > ;-) > > > > > > > > > > > > > > Juan Eugenio Iglesias > > > > > ERC Senior Research Fellow > > > Translational Imaging Group > > > University College London > > > http://www.jeiglesias.com > > > http://cmictig.cs.ucl.ac.uk/ > > > > > > > > > > > > > > > > > > > > > On 26 Jan 2017, at 15:55, Adam Martersteck <acmar...(a)gmail.com> wrote: > > > > > > > > I believe Dr. Iglesias previous responses on this exact question have > been, "yes it's possible, but your results may be harder to > > reproduce" > > > e.g. If someone wanted to replicate your study they may have a harder time > having to download 2 different versions of freesurfer > > to achieve comparable results with your study. > > > > > > > > I think the general consensus is "how many subjects do you have?" -- if > it's less than 50, you may want to just rerun > > v6 on your subjects as it should preserve the edits -- but it's > recommended you still open them up and double check. > > > > > > > > -Adam > > > > > > > > On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2...(a)cumc.columbia.edu> > wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi, > > > > > > Can anyone comment on my question below? > > > > > > > > > I think the FAQ page mentions that the same version should be used to > process all cases within a dataset, but my question is whether I can have > the same dataset used for two different versions for separate analyses? > This is considering > > that I've already > > > > > > processed all my data with 5.3, but am interested in getting hippocampal > subfields through 6.0. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Thanks so much! > > > > > > > > > Batool > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > > *From:* Rizvi, Batool > > > > > > > > > *Sent:* Wednesday, January 25, 2017 12:54 PM > > > > > > > > > *To:* > > freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > *Subject:* freesurfer 6.0 with some of the analyses > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > I'm wondering if it's okay to run some of the analyses within one study > on v.5.3 and > > the other hippocampal analyses on 6.0? > > > > > > Or do you recommend us starting over for the analyses we've already done > in 5.3 for that study? > > > > > > > > > > > > > > > > > > > > > > > Thank you! > > > > > > > > > Batool > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > > > > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > > > > > contains patient information, please contact the Partners Compliance > HelpLine at > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > > > > > > but does not contain patient information, please contact the sender and > properly > > > > > > dispose of the e-mail. > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > > contains patient information, please contact the Partners Compliance > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > > > but does not contain patient information, please contact the sender and > properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview command line options
by peng 29 Jan '17

29 Jan '17

Dear Freesurfer experts, When I use Freeview GUI to show overlays on a surface, I can click on the button "Configure", and then check the box "Enable" in the smooth section (upper right of the pop-out window), to smooth it. Is there any options to do similar stuff in the command line of freeview? e.g. when I want to generate a lot of screenshots by the -ss option. Thank you in advance! best Peng

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freesurfer 6.0 with some of the analyses
by Rizvi, Batool 29 Jan '17

29 Jan '17

Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study? Thank you! Batool

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Re: [Freesurfer] Ghosting Artifact
by Harms, Michael 27 Jan '17

27 Jan '17

That subjects looks like a candidate for exclusion, because the SNR anteriorly is much less than posteriorly. It looks to me like there is either a problem with your head coil, or the anterior coil elements were not active. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fotiadis, Panagiotis" <PFOTIADIS(a)mgh.harvard.edu<mailto:PFOTIADIS@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, January 27, 2017 at 12:30 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Ghosting Artifact Hello, I have a T1 weighted scan with a semi-severe ghosting artifact, and recon-all is not able to complete the reconstruction process (according to recon-all log, it tries to fix 237 defects and at defect 209 the recon stops). Is there anything that I can do to recover the scan so I can reconstruct it successfully? (I have attached a few pics indicating the artifact). Thanks in advance for your time! Best, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Ghosting Artifact
by Fotiadis, Panagiotis 27 Jan '17

27 Jan '17

Hello, I have a T1 weighted scan with a semi-severe ghosting artifact, and recon-all is not able to complete the reconstruction process (according to recon-all log, it tries to fix 237 defects and at defect 209 the recon stops). Is there anything that I can do to recover the scan so I can reconstruct it successfully? (I have attached a few pics indicating the artifact). Thanks in advance for your time! Best, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869

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White matter probability map.
by miracooloz＠gmail.com 27 Jan '17

27 Jan '17

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Cortical volume from masked region
by Eli Johnson 27 Jan '17

27 Jan '17

Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli

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PETsurf - point-spread function in ADNI
by Eduard Vilaplana Martinez 27 Jan '17

27 Jan '17

Dear Freesurfer experts, I'm processing ADNI PET data (AV45 and AV1451) in a surface-based approach following your guidelines (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) Do you guys have any experience with ADNI data? I would like to apply partial volume correction but I don't know which is the FWHM of the point-spread function. I'm taking the most pre-processed images (i.e. co-reg, avg, std image and vox siz, uniform resolution), and ADNI say that "Each image set is filtered with a scanner-specific filter function (can be a non-isotropic filter) to produce images of a uniform isotropic resolution of 8 mm FWHM, the approximate resolution of the lowest resolution scanners used in ADNI." Would using a 8mm FWHM for the PV correction be a correct approach? Any help would be greatly appreciated. Thanks in advance Edu V.

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find surface coordinates in MNI space
by Jacobs H (NP) 27 Jan '17

27 Jan '17

Dear FreeSurfers, I am trying to locate certain regions from the Desikan atlas on a MNI surface (Brainnet-viewer) . How can I convert coordinates in surface space to MNI coordinates and are these the regular coordinates (RAS)? Many thanks. Heidi

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Freesurfer January 2017