Freesurfer

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Recon-all error
by Courtney Haswell 02 Dec '20

02 Dec '20

External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS." I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening? I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?

2 1

Re: [Freesurfer] Freesurfer skullstripping error
by LIN, Yezhe 01 Dec '20

01 Dec '20

External Email - Use Caution Thank you so much for sharing the ideas, Bruce! ------------------ Best regards, Yezhe   ------------------ Original ------------------ From:  "freesurfer-request";<freesurfer-request(a)nmr.mgh.harvard.edu>; Date:  Dec 1, 2020 To:  "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>; Subject:  Freesurfer Digest, Vol 201, Issue 45 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1z9iluK8C-0HIf0UFksBm0ZUhHli5Vc4eifBra2dUWisaO… 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: Freesurfer skullstripping error (Fischl, Bruce)    2. Re: arguments to use after pial edits (Darko Komneni?)    3. Re: arguments to use after pial edits (Glasser, Matthew)    4. Fwd: Issue with custom label (Catherine Tallman)    5. Re: Extract he value of area and volume in the fsaverage for       every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}       {Disarmed} {Disarmed} {Disarmed} {Disarmed} (???)    6. Freesurfer skullstripping error ( LIN, Yezhe ) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Nov 2020 22:18:08 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer skullstripping error To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB66093563136717D2C5C0029BEFF50(a)BL0PR04MB6609.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hi Yezhe It depends a lot on what your resolution, read out direction, bandwidth and field strength are. We generally fix these with T2 or FLASH scans at the same resolution/geometry/readout as the T1. Otherwise they are pretty tough as the dura is close enough to the gray matter that you can?t see any space between them Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of LIN, Yezhe Sent: Monday, November 30, 2020 5:10 PM To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer skullstripping error         External Email - Use Caution Dear Freesurfer users, Hope this finds you well. I preprocessed our dataset with recon-all <subj> -s <subj> -all -qcache and found a number of our subjects had different levels of skullstrip errors. I tried fixing them by a couple of different approaches, such as -gcut and adjusted watershed threshold, but they both failed to fix the overlapping of dura mater (Fig1 and 2). I tried two methods on different subjects and received the same outcome. I wonder if you have any ideas to fix this error. At this point, for some who had less skullstripping, I can erase them manually and run -autorecon-pial or -make. But for the others with multiple locations of skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to them at a systemic level? Also I found the skullstripping error in over half of our subjects, is it normal that we have a such proportion? Thank you so much! ------------------ Best regards, Yezhe Yezhe Lin, MD MMed  (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee(a)gmail.com<mailto:yezhe.lin.bee@gmail.com> Twitter<https://secure-web.cisco.com/17wBDBOCFmouG2s48nVWmz-vtBr4ZdcKyF8LdUP3ubrRwD…: @LinYezhe | LinkedIn<https://secure-web.cisco.com/11z7MNr4cmxXqrne4KcsfCzlNqe69kxiyCzG4wHKz5Ap2h… | Researchgate<https://secure-web.cisco.com/1izwT1sMSoKIcMU2d5YWspFhUDtyiXLrkLArb2WuhXY_th…  IPlUPGjELGFQz8xsHlNuDNzKt-daYiJYAs1kgHgxtEF9vM-ssT2gYGaIzf2_qdHfnThVsbwdgrKCeQ/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FYezhe_Lin> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1f0DvXyGg-hMt-t89X5AELnPczD7CgpmxvOQ3mVYZuvrF9z… ------------------------------ Message: 2 Date: Tue, 1 Dec 2020 01:23:00 +0100 From: Darko Komneni? <komnenicd(a)gmail.com> Subject: Re: [Freesurfer] arguments to use after pial edits To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAL-_js1WYLPtgefg5A0NHLaaHcRv=eFJ4kxUAKtEWYP8P9O4kg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution        Thanks Matt! Should I also add the -autorecon3 flag, or does that get performed automatically if I put in "autorecon2"? Best, Darko > Message: 4 > Date: Mon, 30 Nov 2020 19:16:06 +0000 > From: "Glasser, Matthew" <glasserm(a)wustl.edu> > Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <274FD511-F94F-4BC1-AE0C-804F1A6A3A24(a)wustl.edu> > Content-Type: text/plain; charset="utf-8" > >         External Email - Use Caution > > I find the recon-all table to be helpful: > > > http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc… > > In this case, you probably need to run -autorecon2, as all subsequent > steps are affected by the brainmask.mgz file. > > Matt. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1JC9bGmfD8ICPWLEYWuztA9d0Bavk-ouMj0Eb9TYCm3uUqZ… ------------------------------ Message: 3 Date: Tue, 1 Dec 2020 00:25:57 +0000 From: "Glasser, Matthew" <glasserm(a)wustl.edu> Subject: Re: [Freesurfer] arguments to use after pial edits To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <C985CC68-34CB-4788-81EB-7B912105AD3F(a)wustl.edu> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution        I think so. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Darko Komneni? <komnenicd(a)gmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, November 30, 2020 at 6:23 PM To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] arguments to use after pial edits         External Email - Use Caution Thanks Matt! Should I also add the -autorecon3 flag, or does that get performed automatically if I put in "autorecon2"? Best, Darko Message: 4 Date: Mon, 30 Nov 2020 19:16:06 +0000 From: "Glasser, Matthew" <glasserm(a)wustl.edu<mailto:glasserm@wustl.edu>> Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed} To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <274FD511-F94F-4BC1-AE0C-804F1A6A3A24(a)wustl.edu<mailto:274FD511-F94F-4BC1-AE0C-804F1A6A3A24@wustl.edu>> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution I find the recon-all table to be helpful: http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc… In this case, you probably need to run -autorecon2, as all subsequent steps are affected by the brainmask.mgz file. Matt. ________________________________ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1UWwFkBGY57eHrVJmdzlE9t0-f_sYBqRvDMW4W5WqqYu13J… ------------------------------ Message: 4 Date: Mon, 30 Nov 2020 16:28:07 -0800 From: Catherine Tallman <ctallman(a)ucsd.edu> Subject: [Freesurfer] Fwd: Issue with custom label To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CA+obyhmiXyGfYsdBrB+kqtCb6DGowgCLF0wB=UNDG7ACiv3MFA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution        Hello, I was wondering if there were any updates on this question? Thank you, Catherine ---------- Forwarded message --------- From: Catherine Tallman <ctallman(a)ucsd.edu> Date: Thu, Nov 19, 2020 at 8:57 AM Subject: Issue with custom label To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hello, After running mri_vol2label I created a custom label named test.label. When I try to load the label onto lh.pial, I receive the following error: "Could not load label from <path>". The file is saved within the path folder itself. Within the terminal I receive the warning "label has not been mapped to surface". I was wondering what might be causing this issue? Attached is the label file. mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.test.label Thank you, Catherine -- ------------------------------------------------ Catherine Tallman, M.A. Graduate Student CNS Laboratory of Memory and Brain University of California, San Diego -- ------------------------------------------------ Catherine Tallman, M.A. Graduate Student CNS Laboratory of Memory and Brain University of California, San Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1ADsfVKK3Kh87OVDYLZsPT1BgApEfEROyPNmisM7ZNiCDud… -------------- next part -------------- A non-text attachment was scrubbed... Name: test.label Type: application/octet-stream Size: 95213 bytes Desc: not available Url : http://secure-web.cisco.com/18YtCGuex1cbsFPLqZD5387KH1EoR7ZcSwB7RlG2qMTmSM4… ------------------------------ Message: 5 Date: Tue, 1 Dec 2020 08:59:19 +0800 (GMT+08:00) From: ??? <mengjun(a)csu.edu.cn> Subject: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6d642f90.29e3.1761bcf9ccf.Coremail.mengjun(a)csu.edu.cn> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution        Yes, what should I do if there is something wrong -----????----- ???:"Greve, Douglas N.,Ph.D." <DGREVE(a)MGH.HARVARD.EDU> ????:2020-11-30 01:22:22 (???) ???: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong On 11/17/2020 8:08 PM, ??? wrote:         External Email - Use Caution        I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct? -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-16 23:48:37 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average. On 11/14/2020 5:24 AM, ??? wrote:         External Email - Use Caution          I am sorry for that my presentation was not that good, the lh_areapial.sum and lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file with the following command. mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0 My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects. -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-13 23:03:50 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} sorry, I don't know what you are asking On 11/12/2020 8:30 PM, ??? wrote:         External Email - Use Caution        Thanks! I get only one area value in the lh_areapial.sum file with this command: mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0 (1)Should I extract the area and volume one by one with the following command for each subject: mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0 -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-12 22:23:13 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0 On 11/12/2020 5:39 AM, ??? wrote:         External Email - Use Caution        Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject? (2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2?Blue color). Is this correct? ColHeaders  Index SegId NVertices Area_mm2  StructName  Mean          StdDev      Min        Max       Range                1   0    161058     81037.1   Seg0000   242940.3281    0.7312     0.0000     3.8885     3.8885               2   1      2784     1182.3    Seg0001    3760.6619     0.2525     0.7136     1.8140     1.1005 Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-11 23:58:20 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} Sorry, try this mri_segstats --i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) On 11/5/2020 10:26 PM, ??? wrote:         External Email - Use Caution        I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-11-05 22:37:07 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} Try --slabel fsaverage lh /path/to/lh.areapial.label On 11/2/2020 10:24 PM, ??? wrote:         External Email - Use Caution        Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) I did not get a text file including the areas of all subjects. Is this code correct? -----????----- ???:"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> ????:2020-11-02 23:36:14 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you input) all your subjects for that label. On 10/30/2020 10:37 PM, ??? wrote:         External Email - Use Caution        Dear Professors:      I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview  Then the value of the label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions: (1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values?   (2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects Best wishes Mengjun Li -----????----- ???:"Douglas N. Greve" <dgreve(a)MGH.HARVARD.EDU> ????:2020-10-30 23:40:30 (???) ???: freesurfer(a)nmr.mgh.harvard.edu ??: ??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology. On 10/29/2020 9:51 PM, ??? wrote:         External Email - Use Caution        Dear FreeSurfer Developers:    I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4… _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1xBvUCYKavZVolKahDBlsMBn8_ooFbaO2RPlPXr9QF7bJuL… ------------------------------ Message: 6 Date: Tue, 1 Dec 2020 09:24:44 +0800 From: " LIN, Yezhe " <yezhe.lin(a)foxmail.com> Subject: [Freesurfer] Freesurfer skullstripping error To: " freesurfer " <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <tencent_98CA21CE342AD20E07070C068C2F226B7A07(a)qq.com> Content-Type: text/plain; charset="utf-8"         External Email - Use Caution        Dear Freesurfer users, Hope this finds you well. I preprocessed our dataset with recon-all <subj&gt; -s <subj&gt; -all -qcache and found a number of our subjects had different levels of skullstrip errors. I tried fixing them by a couple of different approaches, such as -gcut and adjusted watershed threshold, but they both failed to fix the overlapping of dura mater (Fig1 and 2). I tried two methods on different subjects and received the same outcome. I wonder if you have any ideas to fix this error. At this point, for some who had less skullstripping, I can erase them manually and run -autorecon-pial or -make. But for the others with multiple locations of skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to them at a systemic level? Also I found the skullstripping error in over half of our subjects, is it normal that we have a such proportion? ? Thank you so much!? ------------------ Best regards, Yezhe Yezhe Lin, MD MMed&nbsp; (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee(a)gmail.com Twitter: @LinYezhe | LinkedIn&nbsp;| Researchgate &nbsp; -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1WaLSLli8-xxlWr0PLad30vFeAwS4XWtwf6rsb_V838ARzU… -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig.2 After running recon-all -skullstrip -clean-bm -gcut -s subj.png Type: application/octet-stream Size: 115736 bytes Desc: not available Url : http://secure-web.cisco.com/1xPithPGi6qFor7IcbrAXJILT6reMdb7Uz-4VMkm3cl7RQP… -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig 3. Another subject before ?gcut.png Type: application/octet-stream Size: 166493 bytes Desc: not available Url : http://secure-web.cisco.com/1_8e4pPmg-UyONGCtsGyB8WGWoB6-g9SQMi5Ut2gpieVsrP… -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig 4. Another subject after ?gcut.png Type: application/octet-stream Size: 179439 bytes Desc: not available Url : http://secure-web.cisco.com/17typU6f-PGiUwLeuCDhLiqaQL8jj89UTj4H44s2dvuMXqX… -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig.1 skullstrip error after recon-all.png Type: application/octet-stream Size: 45526 bytes Desc: not available Url : http://secure-web.cisco.com/1q-rKUt7oCl8SURwLDABTHJ-uCdwRQGlGrgV_c97r67acv1… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1z9iluK8C-0HIf0UFksBm0ZUhHli5Vc4eifBra2dUWisaO… End of Freesurfer Digest, Vol 201, Issue 45 *******************************************

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Freesurfer skullstripping error
by LIN, Yezhe 30 Nov '20

30 Nov '20

External Email - Use Caution Dear Freesurfer users, Hope this finds you well. I preprocessed our dataset with recon-all <subj> -s <subj> -all -qcache and found a number of our subjects had different levels of skullstrip errors. I tried fixing them by a couple of different approaches, such as -gcut and adjusted watershed threshold, but they both failed to fix the overlapping of dura mater (Fig1 and 2). I tried two methods on different subjects and received the same outcome. I wonder if you have any ideas to fix this error. At this point, for some who had less skullstripping, I can erase them manually and run -autorecon-pial or -make. But for the others with multiple locations of skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to them at a systemic level? Also I found the skullstripping error in over half of our subjects, is it normal that we have a such proportion? Thank you so much! ------------------ Best regards, Yezhe Yezhe Lin, MD MMed  (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee(a)gmail.com Twitter: @LinYezhe | LinkedIn | Researchgate  

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Re: [Freesurfer] arguments to use after pial edits
by Darko Komnenić 30 Nov '20

30 Nov '20

External Email - Use Caution Thanks Matt! Should I also add the -autorecon3 flag, or does that get performed automatically if I put in "autorecon2"? Best, Darko > Message: 4 > Date: Mon, 30 Nov 2020 19:16:06 +0000 > From: "Glasser, Matthew" <glasserm(a)wustl.edu> > Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <274FD511-F94F-4BC1-AE0C-804F1A6A3A24(a)wustl.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > I find the recon-all table to be helpful: > > > http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc… > > In this case, you probably need to run -autorecon2, as all subsequent > steps are affected by the brainmask.mgz file. > > Matt. > > >

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Freesurfer skullstripping error
by LIN, Yezhe 30 Nov '20

30 Nov '20

2 1

arguments to use after pial edits {Disarmed}
by Darko Komnenić 30 Nov '20

30 Nov '20

External Email - Use Caution Dear Freesurfer experts, I am using Human Connectone Project pipelines to calculate cortical myelin levels. These pipelines use Freesurfer 6. Since certain subjects' brain surfaces had some chunks and spikes sticking out, I edited the brainmask.mgz file for those subjects as described in this tutorial. https://secure-web.cisco.com/134OA5xpyRuAJ4raLibeAZDGkJ8VFvtiCm69m7hXhYD442… To get the myelin maps again, I got the instruction from the HCP mailing list that I should call again the FreeSurferPipeline script, but add the --existing-subject and --extra-reconall-arg flags. If I understood correctly, after --extra-reconall-arg flag, there should be an equal sign, and then keywords that specify which recon-all stages I want to run. Could you please tell me what those stages are, i.e. what keywords I should use after the equal sign? I want to keep the brainmask.mgz file that I edited, and then repeat all the steps that happen after braimask.mgz is generated. I was referred to the FS tutorials/wiki at the HCP mailing list, but I would like to double-check with someone here. Based on the tutorial link above, it seems this should be "-autorecon-pial -subjid pial_edits_before", but I'm not sure if this would be applicable in this case. Thanks in advance and I hope my question wasn't too confusing. Best, Darko

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Sources Sought: Octave/MATLAB programmer {Disarmed}
by Anderson M. Winkler 30 Nov '20

30 Nov '20

External Email - Use Caution Dear all, The NIMH/NIH is looking for a skilled Octave/MATLAB programmer, with knowledge of multivariate statistics, to implement inference for canonical correlation analysis (CCA) using permutations, as described in the recent paper (https://secure-web.cisco.com/1OvbxEv9_JHQute8AUV1-CRpI494R210wv39uPXMnlrig7…) together with other features that have already been published and which are part of PALM, as described in the "Sources Sought" notice linked below: https://secure-web.cisco.com/1fHXlDSQEyeCMPT25xy9Gg_S11v-upDxypVxM2AtRSYwhk… Note: - The search is open to persons or businesses. - The search is not limited to US citizens or to vendors based in the US. - The prospective vendor must have a Data Universal Numbering System (DUNS) number and an NATO Commercial and Government Entity Code (NCAGE code). - The prospective vendor must have either a Social Security Number (SSN) or a Tax Identification Number (TIN). - This is not employment or scholarship, but provision of a specific service to the US government. Please, read thoroughly the Sources Sought page in the link above. If you have availability and capability to perform this potential requirement, please contact Mr. Thien Nguyen (thien.nguyen2(a)nih.gov, +1-301-827-0914). All the best, Anderson

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Multiple regression analysis
by Marina Fernández 30 Nov '20

30 Nov '20

External Email - Use Caution Dear all, I am doing a multiple regression analysis with 3 covariates of interest. I know that for testing two-way and three-way interactions I must create new variables by multiplying the covariates of interest. As Freesurfer transforms continuous variables to z score before applying statistic, is it correct to transform to z score the result of the previous multiplication? I am asking this because the result of multiplying two z transformed variables would be different. Thanks a lot in advance. Marina

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mri_surf2surf Cannot allocate memory
by 1248742467 30 Nov '20

30 Nov '20

External Email - Use Caution Hello,Fs When I used mri_surf2surf command to template the lh.thickness to fsaverage5 space, the error appeared: Command: mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/thickness --trg_type curv --hemi lh Error message: Reading source surface reg /home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/surf/lh.sphere.reg TAGskip: tag=1601402226, failed to calloc 1931488256 bytes! Do you know how to salve it? The memory is : tj@bme01:~/application/freesurfer/subjects$ free               total        used        free      shared  buff/cache   available Mem:      131673804     1398160    79091688        2416    51183956   129212776 Swap:       8388604      169108     8219496 Looking forward to your reply.

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what command can be used to template .vtk file to fsaverage5 space?
by 1248742467 30 Nov '20

30 Nov '20

External Email - Use Caution Hello, what command can map VTK file to fsaverage5 space? I want its vertex number to be 10242. If you know, please give me an example. Looking forward to your reply

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