Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30079 discussions

Re: [Freesurfer] Rookie question
by Addison, Reuben 17 Jul '22

17 Jul '22

I have a rookie question regarding free surfer after going through the excellent course on youtube First time I know the free surfer does the reconstruction on the anatomical scan (eg., T1t1_mprage_sag_p2_iso.nii) I see 3 other files in my data that were never used in the tutorials (SpinEchoFieldMap_AP/PA.nii, AHead_Scout_32ch-head-coil.nii, Phoenix_Document.nii). I am wondering when they were needed. I read about them just never saw them used. Thanks, Reuben N. Addison Postdoctoral Fellow Brain Recovery Lab MGH Institute of Health Professions<https://www.mghihp.edu/> Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129 p. 225-439-5354 | raddison(a)mghihp.edu<mailto:raddison@mghihp.edu>

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Problem with labels
by Alberto Del Cerro Leon 17 Jul '22

17 Jul '22

External Email - Use Caution Hello Freesurfer Team, I am trying to use a ROI to create a label into fsaverage. Once I registered my ROI to the fsaverage space I performed a mri_vol2surf and mri_cor2label to obtain a label of the ROI on the fsaverage surface. However, this label has several holes and irregularities. I know how to edit manually with tksurfer but, is there a method to fill the holes and smooth the borders of the label automatically?

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recon-all finished without error but no results
by Zixuan Lin 17 Jul '22

17 Jul '22

External Email - Use Caution Hello! I am trying to run recon-all but it only converted the original image to .mgz and finished without error. I checked all other folders and it's empty. Attached please find the recon-all.log. The command line I used is recon-all -i hc01.nii -s hc01 -sd /home/zlin/Documents/MDD_CVR/control Could you please help me check what happens here? Thanks a lot, Zixuan.

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FW: recon-all error on brain with abnormality
by Gumenyuk, Valentina 17 Jul '22

17 Jul '22

External Email - Use Caution Dear Freesurfer team, I was trying to run recon - all of the brain ( see below) with large hemorrhage in the right hemisphere. Recon all finished with the an error ( log is attached) . Please advise what can be done to complete the recon all on this type of the brain abnormality. Thank you , Valia [cid:image001.png@01D89616.87353E10] The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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How should I use fslreoient2std?
by Arman Avesta 17 Jul '22

17 Jul '22

External Email - Use Caution Hi gang, I want to use fslreorient2std to reorient my NIfTI files in the standard MNI format. I tried: fslreorient2std T1.mgzfslreorient2std -file T1.mgzfslreorient2std --file T1.mgz but none of them worked. And I cannot find any documentation online that explains how I can use this command. I would appreciate your help for telling me how I can use this command. Best,Arman

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Surface-based vertex-wise analysis of two imaging outcomes
by Silva Rudberg, Jason 17 Jul '22

17 Jul '22

External Email - Use Caution Hello Freesurfers, I am trying to conduct a vertex-wise comparison of diffusion MRI and PET data. I know how to do group vertex-wise comparisons for one imaging outcome (ie. vertex-wise comparison of a diffusion MRI outcome between two groups). Is this type of analysis comparing the vertex values of multiple imaging outcomes possible in Freesurfer? Thank you! Jason

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CC mask in ASEG calculations
by Ramtilak Gattu 17 Jul '22

17 Jul '22

External Email - Use Caution Hello all, We built a CC mask with 3 segments ( Genu, body and Splenium) and made it a part of the existing ASEG.mgz in "fsaverage" folder. Would like to incorporate this shown Corpus Callosum (CC) mask into aseg calculations replacing the existing inbuilt CC 5 segments. What is the best way to do it? We replaced the original aseg.mgz in fsaverage folder with our aseg.mgz that has whole CC with 3 segments and re-ran the recon-all but still we got the same old results. We even tried the mri_cc (mri_cc -aseg aseg.mgz -o aseg.auto_CCseg.mgz sub_01) where aseg.mgz is the aseg.mgz with new CC but still we got the same old results. Does this new aseg.mgz should be a part of labels file in "rb_xxx_xx.gca" ? If so can it be done by extracting the old "rb_xxx_xx.gca" file with mriconvert and add this aseg_CC and rebuild a new .gca file? Can mriconvert create a gca file? Please advice. Thanks Regards Tilak

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mri_vol2surf error
by Rachel Wagner 17 Jul '22

17 Jul '22

External Email - Use Caution Hello everyone, I am trying to display my lesion map I created in Matlab on a cortical surface, and am getting the following error: developer@developer-VirtualBox:~$ mri_vol2surf --mov rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject fsaverage --hemi lhrh --out lh_spm.mgh --projfrac-max 0 1 .1 srcvol = rReslice_Combined_roi_meanRD.nii srcreg = /usr/local/freesurfer/7.2.0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lhrh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 0.99753 -0.00732 0.01760 0.95709; -0.01296 -0.00926 0.99706 -17.81596; -0.01460 -1.00094 0.00244 -18.54964; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /usr/home//fsaverage/surf/lhrh.white error: No such file or directory error: MRISread(/usr/home//fsaverage/surf/lhrh.white): could not open file error: No such file or directory error: mri_vol2surf: could not read surface /usr/home//fsaverage/surf/lhrh.white Could anyone help me fix this? I am very new to this software and need to have this results ready for my supervisor if possible! Thank you, Rachel

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Re: [Freesurfer] FW: How to project SPM image
by Douglas N. Greve 17 Jul '22

17 Jul '22

First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is you lesion map, then it is not the right input to BBR. I can't remember, but if the AAL is in the MNI152 space, then it will be easier to just run recon-all on the MNI152 ( or whatever the atnatomical reference is for the AAL). You can then just run mri_vol2surf using --regheader and skip BBR. You may have to play with some of the options (eg, projection fraction) On 7/5/2022 2:08 PM, Rachel Wagner wrote: > > External Email - Use Caution > > Hello Dr. Greve, > > I hope this finds you well! I am currently working on displaying my > SPM overlay on a 3D brain volume in FreeSurfer (email below). Dr. > Fischl mentioned you may know the command line to do so – I hope this > isn’t a bother, I know you must be quite busy – totally understood if > you don’t have the time. > > So far, I have the following: > > bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated > -overlay --s fsaverage \ --init-rr --lta register.lta > > I am hoping to smooth out the surface and change the coloring to > ultimately export a heatmap image from FreeSurfer that looks something > like this. > <https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXS…> > > Would you have any suggestions for how I should alter my code? > > Thank you very much in advance – no problem again if you don’t have > the time! > > > Kind Regards, > > Rachel Wagner > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *July 5, 2022 9:34 AM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Hi Rachel > > I’ll leave bbreg command lines to others (Doug?), but in general you > don’t want to base the registration on the inflated since it doesn’t > have a meaningful location within the volume. I would use the standard > bbreg command, then use mri_vol2surf to paint what you want onto the > surface. Once it is on any surface for a subject you should be able to > display it on any other surface for that same subject (and same > hemisphere). > > Cheers > > Bruce > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Tuesday, July 5, 2022 12:17 AM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you, that would work very well! I’m trying this code without > success, am I missing a component to display on an inflated surface? > > bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated > -overlay --s fsaverage \ --init-rr --lta register.lta > > *From: *Fischl, Bruce <mailto:BFISCHL@MGH.HARVARD.EDU> > *Sent: *July 4, 2022 3:45 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Well you can display it on inflated surfaces instead of white ones, > which will remove most of the folds. Then you can smooth the surface > overlay however you like (the colors on the surface) in freeview > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Monday, July 4, 2022 3:27 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you, noted! > > I think I am on the right track, but I’d like to smooth the surface > out (particularly the coloring and the sulci, which are quite deep) > considerably – is there any way for me to do that? > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *July 3, 2022 7:44 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > I see, and what’s wrong with the screen shot you have? (and “Bruce” is > fine). > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Sunday, July 3, 2022 7:41 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Hi Dr. Fischl, > > My apologies, I don’t have much of a background in software generally! > > For the SPM image, I used the AAL atlas to label lesioned brain > regions and colored by frequency to generate the heatmap. Image > dimensions: 1x1x1, Image Size [91 109 91], Pixel Dimensions [2 2 2], > Bits Per Pixel: 32. I will map onto fsaverage! > > I’m hoping to display it as a heatmap on an average surface, to look > something like this: *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* | Decreased > functional connectivity from Wernicke's area homologue in... | > Download Scientific Diagram (researchgate.net) > <https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXS…> > > This is a screenshot of what I currently have within FreeSurfer: > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://drive.google.com/file/d/150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD/view?usp=… > <https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_…> > > Thank you very much again for your help! > > Rachel > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Fischl, Bruce > <BFISCHL(a)mgh.harvard.edu> > *Sent:* Sunday, July 3, 2022 6:37:42 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > Can you give us more details? How did you create the > rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are > you trying to display it? On an average surface? Why are you mapping > it to bert and not fsaverage? > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Sunday, July 3, 2022 6:26 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Hello Dr. Fischl, thank you for your reply, it is much appreciated. > > I am trying to cortically project my spm lesion location/frequency > map, according to instructions linked here: > AnalyzingData/MNE_SPM2Freesurfer - Meg Wiki (cam.ac.uk) > <https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1i…> > > I have used the following code: bbregister --mov > rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta > register.lta > > However, my results still look very grainy. Is there a better way to > do this? > > Thank you again, > > Rachel Wagner > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *June 30, 2022 9:09 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Can you summarize what you are trying to do? What kind of overlay are > you trying to visualize and what exactly do you mean by a “3D image”? > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Thursday, June 30, 2022 2:48 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you so much for your response – I’m a master’s student and am > really struggling - I’ve been stuck trying to do this for about 2 > weeks now, so the help is so appreciated! > > My results look very grainy in mricron so my supervisor wants me to > keep trying in FreeSurfer unfortunately for me. > > I uploaded a the brain.mgz volume in freeview, but I’m not sure how to > add an overlay and project as a 3D image. Would you happen to have any > ideas? > > Thank you so, so much again, > > Rachel Wagner > > *From: *niels.foit(a)gmx.de > *Sent: *June 30, 2022 2:35 PM > *To: *'Freesurfer support list' <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > > > > You don't often get email from niels.foit(a)gmx.de > <mailto:niels.foit@gmx.de>. Learn why this is important > <https://secure-web.cisco.com/1IGyjHfcGxatghbnnU4QrmkjiCFhtGpKgDShLha5LYdEXD…> > > > > Sure is, through freeview, however if you already have spm format > files, it is much easier to use mricron > > *Von:*freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *Im Auftrag von > *Rachel Wagner > *Gesendet:* Donnerstag, 30. Juni 2022 18:18 > *An:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > *Betreff:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thanks very much, I will absolutely do so! Just so I know – is there > not any way of generating such figures in Freesurfer? > > *From: *niels.foit(a)gmx.de > *Sent: *June 30, 2022 4:47 AM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > > > > You don't often get email from niels.foit(a)gmx.de > <mailto:niels.foit@gmx.de>. Learn why this is important > <https://secure-web.cisco.com/1i1UJeVjwlumrCAM-yAFlTcIKRz-AyoK3nEvXbthMrwntc…> > > > > * External Email - Use Caution * > > Rachel, these figures were likely created with a software called > mricron, not freesurfer. Check it out :) > > Holen Sie sich Outlook für Android > <https://secure-web.cisco.com/1XvY3sA4-dRCvGWfgKiNWJHfOTGrrzAnDZB_-8JrFkF7ZC…> >

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Help with FreeSurfer Tutorial FsFast Group Level
by Tchir, Sophia Mae 17 Jul '22

17 Jul '22

Hello, I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu)<https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLev…>, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system: My issue is with step 3.2: Correcting for Multiple Comparisons. [cid:8a8a9d8a-afaf-420d-8092-2525282e7e16] When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized. [cid:e82f076f-dc27-4767-90c9-8c4fc2603831] Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information. Do you have any recommendations for what to do? Is it an issue with my version of freesurfer? Thank you, Sophia Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University

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