Freesurfer

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30131 discussions

Annotation File to ROI Volume Estimate
by Jacoby, John 22 Feb '22

22 Feb '22

Hi all, We were sent a FreeSurfer annotation file that denotes some ROIs we're interested in. What's the proper way to map this annotation to the cortical ribbon volume and get an estimate of that volume for each ROI? I've already registered the annotations to the subject from fsaverage space using mri_surf2surf. I'm thinking something like: mri_label2vol --annot {registered_annotation_file} --temp {$SUBJECT/mri/orig.mgz} --o {output_volume_segmentation_file} --subject {$SUBJECT} --hemi {lh,rh} --identity --proj frac 0 1 0.01 And then run mri_segstats on the output_volume_segmentation_file This seems to do what I need, but I want to confirm that I'm not missing import details. I'm also not entirely sure what the 'delta' parameter of the --proj flag is doing. I gather that it's some kind of step size, but will it have a big impact on the resulting ribbon volume? Thanks for any help! Best, John

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Re: [Freesurfer] Subject ID error with bbregister
by Tisdall, Dylan 22 Feb '22

22 Feb '22

External Email - Use Caution Hi Doug and Matt, I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for recon-all on this subject and the files seem to be in the right place; wee below: [mtisdall@ftdc-gpu01 126346]$ echo $SUBJECTS_DIR /home/mtisdall/Research/7TAnalysis/subjects [mtisdall@ftdc-gpu01 126346]$ ls $SUBJECTS_DIR/126346 label mri scripts stats surf tmp touch trash I don't see a blank subject line in the lta file. I tried to make the initial transform manually in Freeview by just loading the two volumes, using `Transform Volume` until they were close, and then saving the resulting transform. I then re-loaded my 7T data, using the option in FreeView to apply the transform on load, and it looks right. See the file contents below: [mtisdall@scisub 126346]$ cat 7Tto3Tinit.lta type = 1 # LINEAR_RAS_TO_RAS nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 1.0000 1 4 4 9.961947798728943e-01 8.715574443340302e-02 4.656613983300417e-10 -1.702789425849915e+00 -8.682409673929214e-02 9.924039244651794e-01 -8.715574443340302e-02 -7.269048690795898e+00 -7.596124429255724e-03 8.682409673929214e-02 9.961947798728943e-01 1.319813346862793e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii volume = 208 240 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 cras = 5.000000000000000e-01 1.455932617187500e+01 -1.323728942871094e+01 dst volume info valid = 1 # volume info valid filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii volume = 208 240 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 cras = 5.000000000000000e-01 1.455932617187500e+01 -1.323728942871094e+01 fscale 0.100000 Note that, when I move the --s flag to the end of the command line, it runs slightly further, but ultimately fails searching for `subject-unknown` within my subjects directory: [mtisdall@scisub 126346]$ bbregister --mov mgz/7T_MEMPRAGE.mgz --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 --s 126346 ... Loading mov error: mghRead(/home/mtisdall/Research/7TAnalysis/subjects/subject-unknown/mri/orig.mgz, -1): could not open file Any other suggestions on what I'm doing wrong here? Thanks again, Dylan > Date: Mon, 21 Feb 2022 16:58:22 -0500 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Subject ID error with bbregister > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <6f0565c8-c4f3-8289-d41b-0558a1fb69f9(a)mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Is there a blank subject line in the lta file? If so, it is probably > trying to get the subject from there. You can try putting the --s after > the --lta > > On 2/21/2022 3:43 PM, Tisdall, Dylan wrote: >> External Email - Use Caution >> >> Hi all, >> >> Quick question on a puzzling error with bbregister version 7.1.1. When I run: >> >> bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 >> >> I get the error: >> >> ERROR: must spec a subject id >> >> which I thought I'd done with the --s flag. What am I missing? >> >> Even more odd, if I just move the to the end of the command, bbregister will run, but eventually fails with: >> >> error: mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, -1): could not open file >> >> Is there something obvious I'm doing wrong with these two command lines that cause these behaviors? >> >> >> Thanks, >> Dylan >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/12zXL_eM4ShAKwlFflhqDPeh22njZyomMazJzeiBX6fxvF… >

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Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
by Fischl, Bruce 21 Feb '22

21 Feb '22

Hi Edan It’s hard for me to see what’s going on in those images. What is the intensity of the white matter in the middle of the occipital strands in the brain.mgz and the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably want some control points in the occipital lobe. Cheers Bruce From: Edan Daniel <edand(a)princeton.edu> Sent: Friday, February 18, 2022 12:15 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) External Email - Use Caution Hi Bruce! We are focusing on the occipital lobe where the white matter boundary is often too far into the gray matter, and we need those voxels to record visual signals. Attaching a few images for reference - notice how much 'thicker' the wm segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this sort were accepted when we were using the same pipeline with v6 (separate datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd be happy to provide more information or images. Many thanks!!! Edan @ PrincetonBrainDevLab On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> wrote: Hi Edan Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two? Cheers Bruce From: freesurfer-bounces(a)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>> On Behalf Of Edan Daniel Sent: Thursday, February 17, 2022 6:51 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0) External Email - Use Caution * Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness? Many thanks! Edan @ Princeton BrainDevLab On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts. When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote: External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on? Would love to hear your thoughts about this. Many thanks!! Edan, Braindevlab@Princeton _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL…> _______________________________________________ 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/12WGi9fwMNRKoc7g0UsFngq4QzxkPkp8uUBbbPuKzCH_q-…>

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Contrasts 3 groups 4 covariates
by fernanda rohrsetzer 21 Feb '22

21 Feb '22

External Email - Use Caution Hi guys, I'm a beginner in Freesurfer and I want to perform an analysis of the difference between 3 groups in cortical thickness,volume and area having age, mean thickness and etiv as covariate. my design matrix for 3 groups comparison as "1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 (LR-HR) 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 (LR-MDD) 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 (HR-MDD) If possible, I would like to know how my contrasts change when I wish to test the change in thickness with age, after removing the group effects. Another question I have is how can I create contrasts to control etiv between groups, like 2x2 comparison. I'm sorry if I was not clear... thanks Fernanda my FSGD file is GroupDescriptorFile 1 Title MyStudy Class LR Class HR Class MDD Variables age meanThick totalarea eTIV Input Sub001 LR 14.3 1350519.71 1954527.71 1552459.71 Input Sub002 MDD 15.7 1558515.86 1689767.98 1809809.87

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GLM analysis - volume and surface area
by Laura Willers de Souza 21 Feb '22

21 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!? I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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vertex indices in EPI space - mri_surf2vol registration issues
by Gomez, Daniel 21 Feb '22

21 Feb '22

Dear FS users, I’m trying to get surface indices from surfaces generated with recon-all into a volume in native functional/EPI space. I’m using mri_surf2vol for that, though if there is a better alternative solution, I’m happy to take it. My issue is that the output index volume (vtxvol) I get from mri_surf2vol does not seem to ever be properly aligned/registered with the target space. Here's the command I run (I'm interesting in vtxvol.nii.gz) mri_surf2vol --reg anat2epi.dat --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template epi.nii.gz --mkmask Upon further investigation, I learn I can’t get the projection to work properly even if I try projecting the surface onto the native anatomical space. As in: mri_surf2vol --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template ../mri/orig.mgz --mkmask --identity sub-01 Given the output vtxvol doesn't even have the same dimensions as the template specified in the command line, it makes me think I’m doing something wrong: > nib-ls vtxvol.nii.gz ../mri/orig.mgz vtxvol.nii.gz float32 [320, 320, 320] 1.00x1.00x1.00 sform ../mri/orig.mgz uint8 [320, 320, 320] 0.75x0.75x0.75 What is the proper way to get vertex indices in EPI space? Thank you, Daniel -- Daniel Gomez, Ph.D. MR Physics and Instrumentation Group A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 USA dgomez1(a)mgh.harvard.edu

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Confusing Permissions Error
by Jacoby, John 21 Feb '22

21 Feb '22

Hi all, I have a recon that looks like it ran (almost) to completion, but then threw a permissions error in the stdout and directed me to the log. I can't determine what the issue might have been. I've attached the .log file as well as .error and .done files. I'll also paste the end of the stdout below because for some reason the permissions error was not captured by the log file. I appreciate any insight anyone can give. Best, John end of stdout: tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied setting seed for random number generator to 1234 total integrated curvature = 26.759*4pi (336.266) --> -26 handles ICI = 173.9, FI = 1548.0, variation=24893.111 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2022:02:17:09:34:06 mris_curvature N 4 e 1.41 S 0.03 U 1.30 P 94% M 157860 F 0 R 20801 W 0 c 20 w 53 I 0 O 2176 L 1.29 1.25 1.20 @#@FSLOADPOST 2022:02:17:09:34:07 mris_curvature N 4 1.29 1.25 1.20 Linux erso.nmr.mgh.harvard.edu 4.18.0-365.el8.x86_64 #1 SMP Thu Feb 10 16:11:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied recon-all -s sub-LALM61_ses-LALM61 exited with ERRORS at Thu Feb 17 09:34:08 EST 2022 tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied For more details, see the log file /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting BugReporting - Free Surfer Wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> top. Bug Reporting. Submitting a request for help . When submitting a request for help with your problems please be aware that the developers will try and repeat your ... surfer.nmr.mgh.harvard.edu

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Subject ID error with bbregister
by Tisdall, Dylan 21 Feb '22

21 Feb '22

External Email - Use Caution Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject id which I thought I'd done with the --s flag. What am I missing? Even more odd, if I just move the to the end of the command, bbregister will run, but eventually fails with: error: mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, -1): could not open file Is there something obvious I'm doing wrong with these two command lines that cause these behaviors? Thanks, Dylan

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Re: [Freesurfer] Subject ID error with bbregister
by Glasser, Matt 21 Feb '22

21 Feb '22

External Email - Use Caution Hi Dylan, I call bbregister with --s in the same place you have it. Is it possible there is something wrong with $SUBJECTS_DIR when you are calling bbregister? Matt. On 2/21/22, 2:43 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Tisdall, Dylan" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of mtisdall(a)pennmedicine.upenn.edu> wrote: Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject id which I thought I'd done with the --s flag. What am I missing? Even more odd, if I just move the to the end of the command, bbregister will run, but eventually fails with: error: mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, -1): could not open file Is there something obvious I'm doing wrong with these two command lines that cause these behaviors? Thanks, Dylan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1wND93MoprFSyHH-F94sUpXKmf26HHTyp_vwiNVZHarL9o… ________________________________ 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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Re: [Freesurfer] Question glm analysis g4v0
by Laura Willers de Souza 21 Feb '22

21 Feb '22

External Email - Use Caution Got it! The 4 groups I'm testing are: CU cortisol low; CU cortisol high; CI cortisol low; CI cortisol high. So if I found a significant cluster for this contrast, can I interpret that the cortical thickness of this region of the cluster is affected by both the diagnosis and cortisol levels? In this case I made the correction of multiple comparisons with positive direction. That means that the worse the diagnosis and the cortisol levels (CI cortisol high) the more the cortical thickness of this region of the cluster will be affected, or to draw this conclusion would I need the results of the other contrasts as well? Thanks so much for all the help! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil ________________________________ De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: quinta-feira, 17 de fevereiro de 2022 20:25 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Assunto: Re: [Freesurfer] Question glm analysis g4v0 No, that was only for interactions between the covariates and the groups On 2/17/2022 10:05 AM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1U3sqGZa-FRgmgKfJEevEk2EOd_uv7vQJWJjf_LYazWAn4…<https://secure-web.cisco.com/1VuhMA49mKmIDKH_rGPy4c67MdbjL6bNv2i_WwNDwvMA5-…> In a previous analysis (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RhFqzblDwAITsckPrr706fDxu-1VP5A0p_2Z1L_dV6eBL…<https://secure-web.cisco.com/1qw-8Oc7vg0Tc3_ilXhnADw1_lWmUuUCQVr-MNNAiNRRR1…>), Dr Douglas had told me that before any analysis I should test whether the interaction is significant or not. I would like to know if this also applies to this case, the interaction being tested by contrast number 7 of the wiki. Thanks in advance! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1opnu8lzUFtpkWbHA-714sXrzRJWxeI-j3CsFLaYe-LC2A…

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