Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Re: [Freesurfer] Using mri_surf2surf to split files
by Douglas N. Greve 29 Jan '21

29 Jan '21

Sorry, can you include the previous correspondence so that I have context. Also, please remember to post to the list On 1/28/2021 12:07 PM, Karan Desai wrote: > > External Email - Use Caution > > My bad, I meant to say surfaces. Right now the files are downsampled on > fsaverage4 space and I need to now split it into the respective left/right > hemispheres. For context, these are .nii.gz files currently. Is there a way to > easily do this in Freesurfer? > > Best, > > Karan Desai > Morey Lab - Duke

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Fwd: SAMSEG longitudinal processing questions
by Douglas N. Greve 28 Jan '21

28 Jan '21

Forwarding Stefano's answers... -------- Forwarded Message -------- Subject: Re: [Freesurfer] SAMSEG longitudinal processing questions Date: Thu, 28 Jan 2021 16:45:39 +0000 From: Stefano Cerri <stce(a)dtu.dk> To: Douglas N. Greve <dgreve(a)mgh.harvard.edu> CC: Koen Van Leemput <leempko(a)gmail.com> External Email - Use Caution 1) SAMSEG long should compute more consistent longitudinal structural volumes than SAMSEG while detecting better volumetric group differences (cf. Table 1 and Fig 3 of https://arxiv.org/pdf/2008.05117.pdf) Yes, using SBTIV for correcting volume changes from different scanners would be beneficial and most probably necessary. 2) The lesion version of SAMSEG long is available in the development version. Enabling the lesion extension can be done by adding the same flag(s) as for the cross-sectional lesion version (--lesion, see the Wiki for details: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg) 3) We never conducted extensive experiments for the number of burn-in and samples for the MCMC scheme, but we found that 50 burn-in and 50 samples lead to robust and replicable lesion segmentation results. Increasing these two numbers might increase the lesion segmentation performance, although differences might be minimal and the overall computational cost high. We suggest to not decrease these two numbers as lesion performance could potentially decrease. Best, Stefano ------------------------------------------------------------------------ *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> *Sent:* 28 January 2021 16:30 *To:* Koen Van Leemput; Stefano Cerri *Subject:* Fwd: [Freesurfer] SAMSEG longitudinal processing questions -------- Forwarded Message -------- Subject: [Freesurfer] SAMSEG longitudinal processing questions Date: Thu, 28 Jan 2021 09:37:32 -0500 From: XY XY <kamsonmd(a)gmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu External Email - Use Caution Hi FreeSurfers, Thank you for sharing the new SAMSEG tool, which I consider a major breakthrough in image processing! I have a few questions about using SAMSEG vs SAMSEG_Long: 1. What volumetric differences should I expect between running SAMSEG on individual images, vs. using SAMSEG_Long for the longitudinal analysis? Could I use SBTIV to adjust differences between scans? (all images are FLAIRs preprocessed using mrI_robust_template) 2. Is there currently a way to integrate lesion segmentation into the SAMSEG_long’s longitudinal analysis? 3. What is the expected impact of increasing or decreasing -Burn-In and -Sample numbers for lesion segmentation? Thank you for all the help! Best, Dave Kamson _______________________________________________ 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.

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LME Univariate Analysis
by Boa Sorte Silva, Narlon 28 Jan '21

28 Jan '21

External Email - Use Caution Dear Freesurfer Experts, Hope this finds you well I am following the LME tutorial running LME Univariate analysis. I was wondering if someone would kindly check my steps below? I wanted to make sure specially that my matrix (X) and and contrast (C) were designed accordingly to assess group*time interaction. Study design: Two groups: 0 = control, 1 = intervention Time: 0 = baseline, 1 = 6-month follow-up Outcome of interest: Change in hippocampal volume Co-Variate: Estimated ICV Here are the steps I took in Matlab: # Loading into Matlab Qdec table with 7 columns in this exact order: fsid, fsid-base, time, group, Righ.Hipp, Left.Hipp, estimated_ICV: Qdec = fReadQdec('qdec-aseg.table.dat'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); Y = M(:,3:4); M = M(:,[1:2 5]); # Here I loaded estimated ICV already into M (as the third column), as it will be treated as a covariate later. # Sorting data according to time [M,Y,ni] = sortData(M,1,Y,sID); # Building design matrix X from M, for a simple time by group interaction. Note that here, I have the slope column as 1, then I add time and group columns via: M(:,1:2), then a column for group*time via: M(:,1).*M(:,2), and finally a column for estimated ICV, as the final column in the matrix via: M(:,3). I wonder if this is correct? X = [ones(length(M),1) [M(:, 1:2) M(:,1).*M(:,2) M(:,3)]]; # Determining model parameters, for total hippocampal volume, Left.Hipp, and Right.Hipp. Here, since my sample is small (N = 15), I am using 1 random effect only. hipp_vol_stats_tot = lme_fit_FS(X,[1],Y(:,1)+Y(:,2),ni); hipp_vol_stats_left = lme_fit_FS(X,[1],Y(:,1),ni); hipp_vol_stats_right = lme_fit_FS(X,[1],Y(:,2),ni); # Creating contrast (C) matrix for simple group*time interaction controlling for estimated ICV. Does this look correct, considering that the last 0 would control for estimated ICV? C = [ 0 0 0 1 0]; # Finally, F test for total, left and right hippocampal volumes F_C_tot = lme_F(hipp_vol_stats_tot,C); F_C_left = lme_F(hipp_vol_stats_left,C); F_C_right = lme_F(hipp_vol_stats_right,C); Thanks so much for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

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Re: [Freesurfer] Regarding the developer password.
by fsbuild 28 Jan '21

28 Jan '21

External Email - Use Caution Hello Anete, Sending the info to your email shortly. -R.On Jan 28, 2021, at 08:05, Anete Sneidere <anete.sneidere(a)gmail.com> wrote:        External Email - Use Caution         Hello!I have followed the Freesurfer installation guide with VB and Ubuntu but I have not been able to log in. It asks for a developers password and I was hoping maybe it would be possible for you to send it to me?I noticed many people were writing about this issue.Looking forward to hearing from you!Anete_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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help with labels
by Alberto Del Cerro Leon 28 Jan '21

28 Jan '21

External Email - Use Caution Hello Freesurfer team, I did an AAL atlas on the surface using mri_vol2surf, however when I look at this overlay there are many holes in the labels with vertices that don't belong to any label. Could u help me with this problem?

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ERROR: input(s) cannot have multiple frames!
by 南修司郎 28 Jan '21

28 Jan '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all a subject, but i got the following error. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames I checked mri_info, and the dimensions are 256 x 256 x 176 x 4. I asked the radiation technologist to change the dimensions to 256 x 256 x 176, but he told me it's impossible because of the multi echo sequence. I'd appreciate if someone help me out with this and resolve this error. Shujiro Minami M.D., Ph.D. Dpt. of Otolaryngology National Tokyo Medical Center 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan E-mail shujirominami(a)me.com 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1034-gcp x86_64) 3) uname -a: Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached User: shujirominami Machine: instance-1 Platform: Linux PlatformVersion: 5.4.0-1034-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/01/27-10:28:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: shujirominami Machine: instance-1 Platform: Linux PlatformVersion: 5.4.0-1034-gcp CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/shujirominami/freesurfer/subjects/todai_test mri_convert /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz mri_convert.bin /home/shujirominami/NIFTI/todai_test.nii.gz /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/shujirominami/NIFTI/todai_test.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Jan 27 10:29:57 UTC 2021 Found 1 runs /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux instance-1 5.4.0-1034-gcp #37~18.04.1-Ubuntu SMP Wed Jan 6 19:44:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s todai_test exited with ERRORS at Wed Jan 27 10:30:01 UTC 2021 To report a problem, see http://secure-web.cisco.com/1g-5Sw5A-mJK27f9rxSEw4DBgjmZ7KTng5JrfBIPRNQPlEH…

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Re: [Freesurfer] question on data quality - examples in appendix
by Douglas N. Greve 28 Jan '21

28 Jan '21

On 1/27/2021 1:34 PM, Nils B. wrote: > > External Email - Use Caution > > Hello and thank you for you answer, > > to the first point: Freesurfer is recognizing this area as Gray > Matter. Can I just delete this part manually and see if the WM/GM > pials are correct or would this lead to other problems? You can do this. It is essentially a skull stripping error, though it is really hard to remove because it is between two bits of brain. > > To the second point: I mean the tool, which enables me to do manual > edits like deleting areas. It's the 4th tool from the left in the top > bar of the Freesurfer GUI. What editing did you do there? I don't think they look that unusual; sometimes you need to look in all 3 dims. > > Best regards, > > Nils > > Am Mi., 27. Jan. 2021 um 00:41 Uhr schrieb Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>: > > > > On 1/26/2021 3:18 PM, Nils B. wrote: >> >> External Email - Use Caution >> >> Hello everyone, >> >> I'm analyzing 1,5T scans and I've two problems with the data >> quality of my participants, where I hope you can help me. >> >> 1. In two of my scans the participants have blurry areas near the >> cerebellum, which makes it nearly impossible for Freesurfer >> (Version 7.1) to set the pials correctly (see Appendix: Scan 1). >> Is this problem caused by movement while scanning or is there >> something i can do? > This looks like it could be the transverse sinus vein and not > brain tissue. >> >> 2. Sometimes when I'm using the manual tool "recon-edit" for >> manual skullstrips the pials look weird after another recon (see >> Appendix: Scan 2, green box). > I'm not sure what you did here. What is the "recon-edit" tool? >> >> I hope you can help me with this. >> >> Best regards, >> >> Nils >> -- >> >> Nils Böer >> Research Assistant with Bachelor Degree (WHB) >> *Psychology and Movement* >> University of Paderborn >> Department of Sports and Health >> Warburger Str. 100 >> 33098 Paderborn >> Room: Sp 1.401 >> >> Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de >> <mailto:nils.tobias94@gmail.com> >> Web: *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ >> <https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytx…> >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://sug.uni-paderborn.de/department/it/ >> <https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytx…> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ebaicrtMvX86fCQuDMZFMWOkJ4vM6dRUCWNDuwB1kTnIA…> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://secure-web.cisco.com/1ebaicrtMvX86fCQuDMZFMWOkJ4vM6dRUCWNDuwB1kTnIA…> > > > > -- > > Nils Böer > Research Assistant with Bachelor Degree (WHB) > *Psychology and Movement* > University of Paderborn > Department of Sports and Health > Warburger Str. 100 > 33098 Paderborn > Room: Sp 1.401 > > Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de > <mailto:nils.tobias94@gmail.com> > Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ > <https://secure-web.cisco.com/12L5BzXRxn0U_MtVCIYPpF_vPrWZBaleUFS-W6WNhqJUYQ…> > https://sug.uni-paderborn.de/department/it/ > <https://secure-web.cisco.com/12L5BzXRxn0U_MtVCIYPpF_vPrWZBaleUFS-W6WNhqJUYQ…>

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SAMSEG longitudinal processing questions
by XY XY 28 Jan '21

28 Jan '21

External Email - Use Caution Hi FreeSurfers, Thank you for sharing the new SAMSEG tool, which I consider a major breakthrough in image processing! I have a few questions about using SAMSEG vs SAMSEG_Long: 1. What volumetric differences should I expect between running SAMSEG on individual images, vs. using SAMSEG_Long for the longitudinal analysis? Could I use SBTIV to adjust differences between scans? (all images are FLAIRs preprocessed using mrI_robust_template) 2. Is there currently a way to integrate lesion segmentation into the SAMSEG_long’s longitudinal analysis? 3. What is the expected impact of increasing or decreasing -Burn-In and -Sample numbers for lesion segmentation? Thank you for all the help! Best, Dave Kamson

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Regarding the developer password.
by Anete Sneidere 28 Jan '21

28 Jan '21

External Email - Use Caution Hello! I have followed the Freesurfer installation guide with VB and Ubuntu but I have not been able to log in. It asks for a developers password and I was hoping maybe it would be possible for you to send it to me? I noticed many people were writing about this issue. Looking forward to hearing from you! Anete

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Using mri_surf2surf to split files
by Karan Desai 27 Jan '21

27 Jan '21

External Email - Use Caution Hi FreeSurfer developers, I have preprocessed files in single niftis and would like to split the data for each file into left and right hemispheres to run it through a specific toolbox. It seems like there should be a way to run mri_surf2surf or another command to just split it into 2 hemispheres, what would you all recommend for this? Thanks.

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Freesurfer January 2021