Freesurfer

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Question for Multiple Sclerosis
by Manuel, Morganne 24 Jul '20

24 Jul '20

External Email - Use Caution Hey Freesurfer, I am new to Freesurfer. I wanting to use Freesurfer for measuring grey and white matter volumes in Multiple sclerosis. However I am wondering if there is a way to manually make a lesion mask for each individual and then use the mask to subtract the lesion volume from the white matter volume. We run recon we break it apart. So is there a certain recon set I can use to add the lesion mask to tell Freesurfer to subtract this volume from the white matter? Many thanks, Morganne

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PETSurfer questions part III
by Ferraro, Pilar 24 Jul '20

24 Jul '20

External Email - Use Caution Hi Douglas, All the analyses have been run with FS version 6 indeed. If you confirm the commands below are correct, I therefore assume I should rerun all the analyses using FS 7.1. I just have few remaining questions: 1. Are there any other ROIs more than the pons that you have changed from WM to GM in FS 7.1? 2. Is the same problem of WM/GM classification affecting MZ corrected uptake estimation? I suppose WM/GM classification should affect only MG since it’s a 3 compartment model, but I’m not sure. Many thanks, Pilar Commands: 1) With Muller-Gartner (MG): mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output Then: mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum MG_ROI.txt 2) With Meltzer (MZ): mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output Then: mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt > > On 7/20/2020 2:56 AM, Ferraro, Pilar wrote: >> >> ????????External Email - Use Caution >> >> Many thanks for the reply, >> >> Yep, unfortunately MG values are always much higher than SGTM ones (in >> all the ROIs). >> I wonder whether this might be related (for MG and MZ) to the absence >> of a normalization using the pons as a reference. >> >> Indeed, when I look at the file with mean values extracted for each >> modality, I see that the pons has always 1000 as mean uptake value for >> no PVC and SGTM, while for MG and MZ values in the pons range from >> -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ). > Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you > using? In version 6, pons was considered white matter, but I changed it > to gray matter in version 7. The bottom line on this is that you cannot > compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then > its value is bogus. >> >> Below are the commands I?ve used to obtain the MG and MZ values: >> >> 1) With Muller-Gartner (MG): >> >> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 >> --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output >> >> ?Then: >> >> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg >> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum >> MG_ROI.txt >> >> 2) With Meltzer (MZ): >> >> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 >> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o >> gtm_MZ.output >> >> Then: >> >> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg >> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum >> MZ_ROI.txt >> >> >> Do you recognize any errors in the commands? >> >> >> Many thanks, >> >> Pilar >> >> >> >> >> >>> >>> Message: 13 >>> Date: Thu, 16 Jul 2020 10:19:32 -0400 >>> From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu >>> <mailto:dgreve@mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] PETSurfer analysis question >>> To: <freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Message-ID: <d56acc7d-3273-4f40-ed17-570a893b26a3(a)mgh.harvard.edu >>> <mailto:d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edu>> >>> Content-Type: text/plain; charset="utf-8" >>> >>> >>> The NoPVC and SGTM values are reasonable. The MG value is pretty crazy. >>> I don't put stock in MZ. Is the MG value much higher than SGTM in other >>> ROIs? What is your mri_gtmpvc command? >>> >>> >>> On 7/16/2020 4:38 AM, Ferraro, Pilar wrote: >>>> >>>> ????????External Email - Use Caution >>>> >>>> Hi Freesurfer experts, >>>> >>>> I?ve run a PETSurfer analysis in order to compare mean?uptake values >>>> of ROIs obtained with different methods: No PVC, SGTM, MG and MZ. >>>> However, I?ve now extracted the mean values and they are extremely >>>> heterogeneous. >>>> As an example, the same ROI (lh banks of the superior temporal sulcus) >>>> has the following uptake values: >>>> >>>> No PVC= 1.709 >>>> SGTM= 2.495 >>>> MG= 23.847 >>>> MZ= 15.564 >>>> >>>> I?m particularly worried for the huge difference between noPVC - SGTM >>>> values and MG-MZ values. >>>> >>>> Any advice? I wonder whether this finding is normal or there is >>>> something I?ve missed. >>>> >>>> Many thanks, >>>> >>>> Pilar >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> Il giorno 15 lug 2020, alle ore 6:00 PM, >>>>> freesurfer-request(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer-request@nmr.mgh.harvard.edu> >>>>> <mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: >>>>> >>>>> Send Freesurfer mailing list submissions to >>>>> freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:freesurfer@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 >>>>> >>>>> When replying, please edit your Subject line so it is more specific >>>>> than "Re: Contents of Freesurfer digest..." >>>>> >>>>> >>>>> Today's Topics: >>>>> >>>>> ??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run >>>>> ?????for some subjects (Douglas N. Greve) >>>>> ??2. Re: mri_fieldsign error (Douglas N. Greve) >>>>> ??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Wed, 15 Jul 2020 11:12:21 -0400 >>>>> From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra >>>>> fails to run for some subjects >>>>> To: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <beb084b0-fe6b-c8a2-c0a5-e8bcc92769b6(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="windows-1252" >>>>> >>>>> Can you send the recon-all.log file for some of the failures? >>>>> >>>>> On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote: >>>>>> >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Dear list, >>>>>> >>>>>> As described by others on this list, recon-all with Freesurfer 7.1 on >>>>>> a Mac operating system seems to fail for around 10% of the subjects. >>>>>> >>>>>> The following solution was offered: >>>>>> >>>>>> sudo curl >>>>>> https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… >>>>>> ?-o rca-long-tp-init >>>>>> sudo chmod +x rca-long-tp-init >>>>>> However, this did not solve the problem for me. >>>>>> >>>>>> I re-ran recon-all for the same subjects, but it still failed, some of >>>>>> them at the following step: >>>>>> >>>>>> "####################################### >>>>>> GCADIR /Applications/freesurfer/average >>>>>> GCA RB_all_2020-01-02.gca >>>>>> GCASkull RB_all_withskull_2020_01_02.gca >>>>>> AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>>>>> GCSDIR /Applications/freesurfer/average >>>>>> GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>>>>> #######################################" >>>>>> >>>>>> It simply stopped running there. >>>>>> >>>>>> Others did finish running, but instead got a segmentation fault error. >>>>>> >>>>>> What could I do? I have Mac High Sierra. >>>>>> >>>>>> >>>>>> Annelies >>>>>> >>>>>> Annelies van't Westeinde?| PHD Candidate >>>>>> Department of Women's and Children's Health | Karolinska Institutet >>>>>> 171 77 Solna | Karolinskav?gen 37A >>>>>> +46 760967499 >>>>>> annelies.vant.westeinde(a)ki.se | ki.se <http://ki.se/en/startpage> >>>>>> ______________________________________ >>>>>> Karolinska Institutet ? a medical university >>>>>> >>>>>> >>>>>> >>>>>> /N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta >>>>>> att KI kommer att behandla dina personuppgifter. /H?r finns >>>>>> information om hur KI behandlar personuppgifter >>>>>> <https://ki.se/medarbetare/integritetsskyddspolicy>. >>>>>> >>>>>> >>>>>> /Sending email to Karolinska Institutet (KI) will result in KI >>>>>> processing your personal data./ You can read more about KI?s >>>>>> processing of personal data here >>>>>> <https://ki.se/en/staff/data-protection-policy>. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>>

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Fwd: Re: Segmentation with FreeSurfer 7.1
by Sara PONTICORVO 24 Jul '20

24 Jul '20

External Email - Use Caution Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1 Message-ID <d7c325ac-e3a9-41a6-3cf0-17c35e0b4749(a)mgh.harvard.edu> Hi, thanks a lot. What do you mean for topological default? We have checked our data, and there aren't any visible artifacts (if you were referring to this kind of things). Actually we have seen these problems in about 50% of the already acquired data. If it can be useful for you we can also send you the raw DICOM images to check yourself. It is possible that there are some default settings in the 7.1 recon-all pipeline that we can adjust? Thanks again, Sara -- Sara Ponticorvo PhD Student Departement of Medicine Surgery and Dentistry, University of Salerno

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mesh referential
by TACONNE Marion (INTERN) 24 Jul '20

24 Jul '20

External Email - Use Caution Hello, I would like to know in which referential is the meshes ( lh.smoothwm for example). Is it RAS ? If not, how can we change the mesh referential in this referential. Thank you in advance for your time and answer. Best regards, Marion Taconné This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) you should not read, disclose, or copy it, (ii) please notify sender of your receipt by reply email and delete this email and all attachments, (iii) Dassault Systèmes does not accept or assume any liability or responsibility for any use of or reliance on this email. Please be informed that your personal data are processed according to our data privacy policy as described on our website. Should you have any questions related to personal data protection, please contact 3DS Data Protection Officer at 3DS.compliance-privacy(a)3ds.com<mailto:3DS.compliance-privacy@3ds.com> For other languages, go to https://www.3ds.com/terms/email-disclaimer

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Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password
by fsbuild 24 Jul '20

24 Jul '20

External Email - Use Caution Hello Nuri, I am sending the password directly to your email. -R. On Jul 24, 2020, at 09:30, Choi, Nuri <nuri.choi(a)wustl.edu> wrote:        External Email - Use Caution        Hi,I followed the given instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email - may I request the password as well? Sorry if this is quite redundant on your end...Thank you very much,-Nuri_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Extract the cerebellum
by Camargo, Aldo 24 Jul '20

24 Jul '20

External Email - Use Caution Hi Freesurfer experts, I am trying to extract only the cerebellum and then save it to nii file. How can I do it with freesurfer ? Thanks a lot and have a nice day, Aldo

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FreeSurfer 7.1.0 VirtualBox Installation password
by Choi, Nuri 24 Jul '20

24 Jul '20

External Email - Use Caution Hi, I followed the given instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README file to find the password to log in to the developer account. I've seen that other users in the archive received the password privately via email - may I request the password as well? Sorry if this is quite redundant on your end... Thank you very much, -Nuri

1 0

Re: [Freesurfer] How to do permutation for multiple comparison correction?
by Xiaojiang Yang 23 Jul '20

23 Jul '20

External Email - Use Caution Hi Doug, For the first question, you answered "It is unusual, though it should work". Could you please briefly describe the way FS used to permute (based on my notation v0, v1, ... vn)? Or, the usual way to permute? The way I described seems to be the only way I can think of. Looking forward to your help here. Thanks a lot! Xiao Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 23 Jul 2020 07:37:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> On 7/21/2020 11:45 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space." By "In the ROI", I mean for all vertices listed in the label file. Here, I am talking about a test subject and n control subjects, they are all considered in the same reference subject space - fsaverage. A ROI is defined by a label file for the subject fsaverage. So, I am comparing the test subject and control group on the same ROI region, vertex by vertex. I want to permute points in the test subject and points in all subjects in control groups. I am not talking about permuting vertex locations; I am talking about permuting values (thickness in my case) from subjects on each vertex. For example, for vertex i, I have one value (v0) from test subject, and n values (v1, v2,...vn) from control subjects: test subject control subjects v0 v1, v2, ...... vn One way of permutation would be: test subject control subjects v1 v0, v2, ...... vn Is this a reasonable way to do permutation? It is unusual, though it should work. 2. "Not sure. You cannot discriminate between the groups when you are doing permutation" By doing the permutation many (say 1000) times, I want to get the probability distribution of the sampling (observed or test) data inside the ROI area, so that I can decide if I should reject or accept null hypothesis based on cluster-wise significance level. What problems do you think I have in this idea? That should work. I'm not sure what my original concern was Thanks a lot! On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how mri_glmfit-sim does the permutation. The link here http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has <http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm%C2%A0has> a simple description for how to do permutation, but I don't quite understand the 1st step: Permute the design matrix. To me, permute the design matrix means permute the matrix rows here, but still hard to understand why permuting matrix rows does the trick. This is pretty standard in permutation. I think Tom Nichols has some basic tutorials on how permutations work. Anyway, I will not use any design matrix in my customized implementation, so it does not matter for now. My problem can be described as follows: if I have a ROI (a label file) on fsaverage, and I have a test subject and a group of control subjects whose thickness values on every vertex in this label are all known. (The test subject and control subjects are all using fsaverage reference space). I want to compare this test subject's thickness within the ROI to a control group of subjects (within the same ROI). This is a multiple-comparison problem, so I want to use permutation to get less FP rate. My question is: How do I permute the test subject's points and control subjects' points in ROI? Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space. My understanding is that: for each point in the label, I randomly re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is the number of subjects in control group). And when all points in the label are done, this is only 1 permutation. I will need at least 1000 times of permutation to get the comparison statistics. Is my understanding right? Not sure. You cannot discriminate between the groups when you are doing permutation Thank you! Xiao _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

nu_correct error
by Bahrani, Ahmed A. 23 Jul '20

23 Jul '20

External Email - Use Caution Hello Freesurfer experts, I have a question related to the singularity container to run a bash script that contains a freesurfer's commend "nu_correct". The singularity container only runs as a root user login and gives error as shown below with a general user login. ================================================================================== ---Error message--- evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running evaluate_field (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) -------------------------------------------------------------------- ---Error message--- ncvarput: ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running minccalc (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) -------------------------------------------------------------------- Would you advise, please? Thanks, Ahmed

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Cortical Parcellations in FreeDurger 7
by Al Qadi, Ameen 23 Jul '20

23 Jul '20

External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: - Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROIs, but got empty ROI files. - Given that Freesurfer version 7 contains segmentations not previously generated in recon-all (i.e. hippocampal subfields), is it possible to extract these ROIs using aparc+aseg images generated using previous versions of Freesurfer? Or do we need to repeat the cortical parcellations (i.e. rerun recon-all) using FS7? I’d highly appreciate your time and feedback on this matter. Thank you. Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

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