Freesurfer

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30066 discussions

BBRegister + partial FoV fail
by Paul Glad Mihai 13 Jul '17

13 Jul '17

Dear List, I've been quite frustrated with the BBRegister results when trying to register a partial field of view EPI mean functional image to a T1 scan. I've tried different init arguments (fsl, spm, header) and none really work. I've found that the initial registration is causing the problem, since the T1 and mean EPi are in reasonable alignment, but not perfect. As soon as it passes the initial alignment it's totally off and obviously fails in the BBR step. I have no full head EPI, unfortunately. I have a full head scout which seems to be a T1 image with really poor contrast. If I try to register this to the T1 through BBRegister it works. But if I use it as an intermediate file it still fails. What can I do? How does the intermediate file come into play? Will it get registered to the T1 initially and then the resulting matrix is used further? I also tried to feed the resulting registration matrix as init-reg but that didn't work either. Is there a way to skip the initial registration? Can I mask the T1 image with the FoV of the functional scan if they are initially in reasonable alignment? Would that work? Would that mean that I have to re-run ReconAll with the masked T1? Would love to hear back from someone. Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: mihai(a)cbs.mpg.de

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How to edit Fsgdf4G2V about the group.effect.mtx
by haidong wang 12 Jul '17

12 Jul '17

Hello FS expert, I have four groups and two covariables. The groups are MCI_P,MCI_S,MCI_R,NC and the covariables are age and education. I want to test the thickness differences of the groups regressing out age and education.My group.effect.mtx is as following with the feedback of error. 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 1 0 0 -1 0 0 0 0 0 0 0 0 Thanks! I am looking forward for your prompt reply. Yours, Haidong

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TAR fs files
by Schumman Resonance 12 Jul '17

12 Jul '17

Hi freesurfers, I'm compressing FS files for storage, and while runnig TAR I got this message for all the files in the directory I'm compressing: "tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z.inv.y.mgz: file changed as we read it" Any thoughts on whether this message is making any changes on those tailrace files so that when I decompress the file I do not get the original information in those files. Thanks for your help/advice, Kev

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smoothing data
by Tamara Tavares 12 Jul '17

12 Jul '17

Hi All, I was hoping someone can help me with two naive questions I have: I have read on the Freesufer wiki that you should smooth surface data before analyzing. Should I smooth the data only after I have ran recon-all and have made edits? Also, should volumetric data be smoothed or is this limited to surface data? Thank you in advance for your help. Best, Tamara

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Simple math with freesurfer surfaces
by Van Der Deijl, Rosanne 12 Jul '17

12 Jul '17

Dear Freesurfer team, Is it possible to add/subtract/compute the average of freesurfer surface .mgh files? And how would I do this? Thank you in advance. Kind regards, Rose

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Re: [Freesurfer] GLM question
by Yann Ying Chye 12 Jul '17

12 Jul '17

Thanks for your reply, I have a follow up on my first question - if however I was not looking for a main effect of gender, but for the main effect of something else (e.g. diagnosis), will it then be ok to include the unbalanced group (i.e. A-male), to control for gender? Thanks! Regards Yann On 7 July 2017 at 18:34, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > On 7/7/17 1:58 PM, Yann Ying Chye wrote: > > Dear FreeSurfer mailing list, > > > > I've got two questions regarding the freesurfer GLM analysis. > > > > 1. I am trying to run mri_glmfit on the cortical thickness of a > > dataset that has a few interacting factors of unequal levels. > > For example, my dataset may have groups A, B, C, and D. Within the > > groups, subjects are further divided by gender - male and female. > > However, group A only has males, such that the classes in my FSGD file > > = A-male, B-male, B-female, C-male, C-female, D-male, and D-female. > > Will this design be a problem? Will it be statistically sound? > > Additionally if I was looking for an effect of gender, how would I > > weigh my contrast? I was thinking 0.25 0.25 -0.33 0.25 -0.33 0.25 > > -0.33. Would that be valid? > I think I would lean against including A-male. Otherwise, what is the > null hypothesis? Without A-male, it would be that males and females > differ when regeressing out the effect of group, but you can't say that > if you include A-male. Eg, if there were no difference between A-male > and A-female but A tended to be larger than the other groups, then > including A-male and not A-female would create a confound making males > look bigger than females. > > 2. Does mri_glmfit have a limit to the number of subjects it can run > > with? If I have say upwards of a few thousand subjects, will this be > > possible to run/how long would that take? > I don't think it has a limit. > > > > Thanks for your help! > > > > Regards > > Yann > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 161, Issue 17 > ******************************************* >

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Subject with missing fMRI data
by Sadie Marvel 12 Jul '17

12 Jul '17

Hi List, I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically? Thanks.

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mkbrainmask-sess: couldn't find register.dof6.lta
by Li Guo 12 Jul '17

12 Jul '17

Dear freesurfer developers, I’d like to ask about an error I encountered in Freesurfer v6.0 with mkbrainmask-sess. I am using macOS Sierra. Here is the error: error:"ERROR: cannot find /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you might need to run register-sess” The error goes away if I run register-sess before mkbrainmask-sess. However, my lab mates use v5.3 and ran the exact same preprocess pipeline without this error. The order for them is mkbrainmask-sess first and register-sess later. I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess now depends on register-sess to generate the register.dof6.lta file? Or how should I interpret this? Does running registration and masks have some fixed order at all or it doesn’t matter? Best, Li

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petsurfer stats for multiple segmentations
by Lu Zhao 12 Jul '17

12 Jul '17

Dear freesurfer support, I am using the PetSurfer to process our PET data. But by default, it would only generate stats for the segmentation with the aparc atlas. However, I want to obtain the stats for different freesurfer atlases, like in the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, ?h.aparc.DKTatlas.stats, etc.) How should I set the ‘gtmseg' to make it produce segmentations for the GTM with different freesurfer atlases? I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation can be set using --ctx-annot --wm-annot. However, I still don’t know how exactly these should be set. I will be very grateful if you could give me some suggestions and detailed guidance to help me obtain the PetSurfer stats for different freesurfer segmentations. Best regards, Lu

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Pial surface editing
by Michelle VanTieghem 12 Jul '17

12 Jul '17

Hello, We have assessed freesurfer output for 160+ brains, and about 50% have poor segmentation of pial matter that includes too much skull. Manual edits and re-running does work to improve the problem, but is very time/labor intensive for so many scans. I saw on the freesurfer wiki that you can include T2 or Flair images to improve the segmentation for this problem. However, we do not have these extra scans. What do you recommend to do otherwise? Thank you! -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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