Re: [Freesurfer] Freesurfer skullstripping error

-- ------------------------------------------------ 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/1ADsfVKK3Kh87OVDYLZsPT1BgApEfEROyPNmisM7ZNiCDudM... -------------- 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/18YtCGuex1cbsFPLqZD5387KH1EoR7ZcSwB7RlG2qMTmSM4E... ------------------------------ Message: 5 Date: Tue, 1 Dec 2020 08:59:19 +0800 (GMT+08:00) From: ??? <mengjun@csu.edu.cn&gt; 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@nmr.mgh.harvard.edu&gt; Message-ID: <6d642f90.29e3.1761bcf9ccf.Coremail.mengjun@csu.edu.cn&gt; Content-Type: text/plain; charset="utf-8" &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Yes, what should I do if there is something wrong -----????----- ???:"Greve, Douglas N.,Ph.D." <DGREVE@MGH.HARVARD.EDU&gt; ????:2020-11-30 01:22:22 (???) ???: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu&gt; ??: ??: 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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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@MGH.HARVARD.EDU&gt; ????:2020-11-16 23:48:37 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; 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@MGH.HARVARD.EDU&gt; ????:2020-11-13 23:03:50 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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@MGH.HARVARD.EDU&gt; ????:2020-11-12 22:23:13 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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&nbsp; Index SegId NVertices Area_mm2&nbsp; StructName&nbsp; Mean&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; StdDev&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Min&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Max&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Range&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 161058&nbsp;&nbsp;&nbsp;&nbsp; 81037.1&nbsp;&nbsp; Seg0000&nbsp;&nbsp; 242940.3281&nbsp;&nbsp;&nbsp; 0.7312&nbsp;&nbsp;&nbsp;&nbsp; 0.0000&nbsp;&nbsp;&nbsp;&nbsp; 3.8885&nbsp;&nbsp;&nbsp;&nbsp; 3.8885 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2784&nbsp;&nbsp;&nbsp;&nbsp; 1182.3&nbsp;&nbsp;&nbsp; Seg0001&nbsp;&nbsp;&nbsp; 3760.6619&nbsp;&nbsp;&nbsp;&nbsp; 0.2525&nbsp;&nbsp;&nbsp;&nbsp; 0.7136&nbsp;&nbsp;&nbsp;&nbsp; 1.8140&nbsp;&nbsp;&nbsp;&nbsp; 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@MGH.HARVARD.EDU&gt; ????:2020-11-11 23:58:20 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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@MGH.HARVARD.EDU&gt; ????:2020-11-05 22:37:07 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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@mgh.harvard.edu&gt; ????:2020-11-02 23:36:14 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dear Professors:&nbsp; &nbsp; &nbsp; 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&nbsp; 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? &nbsp; (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@MGH.HARVARD.EDU&gt; ????:2020-10-30 23:40:30 (???) ???: freesurfer@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: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dear FreeSurfer Developers: &nbsp;&nbsp; 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@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4Y... _______________________________________________ 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_ooFbaO2RPlPXr9QF7bJuL7... ------------------------------ Message: 6 Date: Tue, 1 Dec 2020 09:24:44 +0800 From: " LIN, Yezhe " <yezhe.lin@foxmail.com&gt; Subject: [Freesurfer] Freesurfer skullstripping error To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu&gt; Message-ID: <tencent_98CA21CE342AD20E07070C068C2F226B7A07@qq.com&gt; Content-Type: text/plain; charset="utf-8" &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dear Freesurfer users, Hope this finds you well. I preprocessed our dataset with recon-all <subj&amp;gt; -s <subj&amp;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&amp;nbsp; (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee@gmail.com Twitter: @LinYezhe | LinkedIn&amp;nbsp;| Researchgate &amp;nbsp; -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1WaLSLli8-xxlWr0PLad30vFeAwS4XWtwf6rsb_V838ARzUl... -------------- 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-4VMkm3cl7RQPf... -------------- 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-g9SQMi5Ut2gpieVsrPT... -------------- 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-PGiUwLeuCDhLiqaQL8jj89UTj4H44s2dvuMXqXA... -------------- 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_c97r67acv1f... ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1z9iluK8C-0HIf0UFksBm0ZUhHli5Vc4eifBra2dUWisaOT... End of Freesurfer Digest, Vol 201, Issue 45 *******************************************