Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

Re: [Freesurfer] Edits to Aseg in the Longitudinal Stream
by Antonin Skoch 30 Jan '17

30 Jan '17

Dear Tamara, I presume that you edited your reconstruction in "Long" (=3rd) stage of longitudinal stream (recon-all -long )?. If this is the case, I think that you can use recon-all -long tpN1 templateID -autorecon2-wm -autorecon3 or recon-all -long tpN1 templateID -autorecon2-noaseg -autorecon3 (effectively both commands are equivalent, they run the same steps). where tpN1 is name of your directory defining cross-sectional recon (1st stage) and templateID is name of directory of your base (created in stage 2). See https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#RerunningEditsC… Regards, Antonin Skoch Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes:recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

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Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3
by Antonin Skoch 30 Jan '17

30 Jan '17

Dear Matthieu, your issue is discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html and indirectly also here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51111.html I think that with V6.0 you maybe could get slightly better results (some bugs have been fixed and some tools improved), but definitelly it would require to re-inspect your data after reprocessing. Antonin Skoch Dear experts, Does anybody could answer my last request ?Best, Matthieu 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...(a)gmail.com>: > Dear FS's experts, > > I have run all my cross with v5.3 and hesitate to run all longitudinal > process with v6. Does that make sense and will improve the process or would > it be risky to do this ? > > Many thanks for your lights ! > > Best regards, > Matthieu

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Fw: Issue with creating inflated surface - poor surface registration?
by Saltzman, David 30 Jan '17

30 Jan '17

Hello FreeSurfer Developers, We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent. 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OS 10.12 3) recon-all.log: see attached 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels] Any help would be tremendously appreciated! Thanks, David Saltzman Lab Manager Language and Brain Laboratory Department of Speech, Language, & Hearing Sciences University of Connecticut

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problem with qdec
by Eva Wiedemann 30 Jan '17

30 Jan '17

Dear freesurfer-users, I want to run a qdec analysis, comparing cortical thickness between two groups and using age and gender as nuisance factors. those factors are included in my data.table but when i want to chose the design i can only select gender as a discrete factor and not as a nuisance factor (see images attached). The second problem I have is, when displaying the results, I can't change the threshold. I can mark them but not change them. All the other buttons in the window work though. Thanks for your help in advance! Yours sincerely, Eva Wiedemann PS: I'm using freesurfer v.5.3.0 on Ubuntu 15.10.

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Edits to White Matter
by Gundel, Tristan J 30 Jan '17

30 Jan '17

Hello, I work in a lab that is currently using the Freesurfer algorithm to collect data from MRI images of individuals with Multiple Sclerosis. In order to increase the precision of our white matter masks we have combined your algorithm with ANTS, hoping to achieve more accurate surface volumes and aparc+aseg masks. Unfortunately we have had some issues when we edit our ANTS white matter mask (using value of 255) and then put it through freesurfer again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w <subID>). Our wm_surface and aparc+aseg mask do not change based on the edits we have made, and do not follow the white matter volume surface volume. How can we be sure that our white matter mask, and the edits we make to it, are considered in the creation of wm_surface and aparc+aseg mask? Please let me know if any of this is unclear and I will explain it in more detail. Thank you, Tristan

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Time Series Revision in FS-Fast
by pfannmoelj＠uni-greifswald.de 30 Jan '17

30 Jan '17

Dear Experts, I have a question concerning the evaluation of the time series in the FS-Fast stream. There is one time series for each vertex of a brain. Can single time points or series of time points be excluded from the analysis in the following way: Remove time point 10 from the time series of vertex 220 and time point 550 from vertex 42. This means a time point exclude file can not be used in my case. Can I achieve this removal by setting the value of the time points to not-a-number or something similar? Yours pfannmoe

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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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