Freesurfer

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Postdoc opportunity (2 years), C-Lab, Krakow (Poland)
by Renate Rutiku 22 Jul '20

22 Jul '20

External Email - Use Caution Dear all we are hiring a postdoc with strong experience in MRI data acquisition and analysis to collaborate on a large-scale international project ( https://skuldnet.org/) aimed at exploring the neural architecture of consciousness. For more information see: https://c-lab.pl/news/2020/07/09/post-doc-position.html Application deadline is August 9, starting date flexible this fall. If interested, please contact Prof. Michał Wierzchoń (michal.wierzchon at uj.edu.pl). Job ad in Polish: https://ncn.gov.pl/baza-ofert/?akcja=wyswietl&id=183286

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Re: [Freesurfer] mri_fieldsign error
by Douglas N. Greve 21 Jul '20

21 Jul '20

No, it does not. The only other problem I can think of is that it has something to do with WSL. Do you have a real linux box you can try it on? On 7/17/2020 5:24 PM, Xiaomin Yue wrote: > > External Email - Use Caution > > HI Doug, > > Sorry for the slow response. I got the same “segmentation fault (core > dumped)” error when running the left hemi. I tested it multiple > times. Does this function create a detailed log I can send to you? > > Thanks, > > Xiaomin > > *From: *Douglas N. Greve <mailto:dgreve@mgh.harvard.edu> > *Sent: *Friday, July 17, 2020 1:07 PM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > I was not able to replicate this on my CentOS7 linux box. You sent me > left hemi data, so I ran the command below > > mri_fieldsign --fs fieldsign.71.nii.gz --polar > LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz --eccen > LOO.ring.eccen.lh.real.nii.gz LOO.ring.eccen.lh.imag.nii.gz --s LOO > --hemi lh --sphere > > But I also noticed that the command that you gave below is for the > right hemi. Do you know if the left hemi works? > > > On 7/11/2020 1:43 PM, Xiaomin Yue wrote: > > * External Email - Use Caution * > > Hi Doug, > > I used FS 7.1 under WSL to analyze retinotopy data. Since the > ring and wedge were presented at a different frequency, the data > had to be analyzed separately for each condition. To get the > field sign, I had to use the mri_fieldsign function to combine > polar and eccen data. However, an error happened with running > mri_fieldsign: “Segmentation fault (core dumped)”. The > following is the command-line output. > > Thanks for your help! > > Xiaomin > > cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala > > cmdline mri_fieldsign --fs > LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar > LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > --s LOO --hemi rh --sphere > > sysname Linux > > hostname DESKTOP-SVDQE4Q > > machine x86_64 > > user xiaominyue > > eccen real > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > > eccen imag > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > > polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > > polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz > > patch (null) > > subject LOO > > hemi rh > > fwhm -1.000000 > > nsmooth -1 > > fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz > > usenew 1 > > Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere > > Using spherical coordinates > > Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) > > Complex > > Ripping Zeros > > Rot (rad): 0 0 > > surfer: compute_fieldsign2() > > dthresh = 1.5 > > shape = 1 > > nvertices = 153801 > > 0 0 45452 0.03 33.2224 > > 1018 1000 39160 21.33 -18.3959 > > 2055 2000 44734 43.26 33.0783 > > 3148 3000 49793 65.38 0.653687 > > 4344 4000 38626 88.16 16.7555 > > 5529 5000 54149 110.12 -4.90118 > > 6706 6000 61599 133.36 -5.74607 > > 7971 7000 50134 155.88 -17.5589 > > 9165 8000 34182 178.05 -18.9387 > > 10591 9000 59682 200.70 -4.60514 > > 12034 10000 63856 223.18 -4.4884 > > 13297 11000 41007 245.62 27.3489 > > 14938 12000 27365 267.70 -1.40077 > > 16684 13000 23615 289.10 -0.518007 > > 18048 14000 47088 309.37 18.7017 > > 19798 15000 21060 330.11 15.9458 > > 21681 16000 33067 350.27 -11.1953 > > 23173 17000 28744 371.48 -6.18747 > > 25112 18000 27738 392.41 -6.93845 > > 26953 19000 20538 414.47 2.99349 > > 28903 20000 80583 435.98 -0.338512 > > 30319 21000 16251 459.83 -45.2313 > > 32174 22000 17139 483.36 -2.31642 > > 34093 23000 13307 507.02 19.1461 > > 36170 24000 17826 530.65 -10.7575 > > 37683 25000 69324 555.78 -6.17011 > > 39666 26000 14043 583.29 -10.5151 > > 41746 27000 76017 609.92 -0.0112556 > > 43986 28000 84646 636.28 1.24722 > > 46088 29000 9763 664.26 12.7035 > > 48326 30000 92161 694.30 2.03416 > > 50431 31000 99884 724.91 1.20525 > > ./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation > fault (core dumped) mri_fieldsign --fs > $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz > --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz > $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz > --s $subjname --hemi $hemi --sphere > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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PETSurfer questions - Part II
by Ferraro, Pilar 21 Jul '20

21 Jul '20

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). 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/0… ------------------------------ Message: 2 Date: Wed, 15 Jul 2020 11:14:53 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_fieldsign error To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41c91(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I don't know what is going wrong here. One simple thing to check is to make sure that all the input files have the same number of vertices as the surface. If that is the case, then upload the subject and input files using the instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 7/15/2020 11:07 AM, Xiaomin Yue wrote: ????????External Email - Use Caution Hi All, Just in case the below poster was missed. Thanks, Xiaomin *From: *Xiaomin Yue <mailto:yuexm@hotmail.com> *Sent: *Saturday, July 11, 2020 1:43 PM *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] mri_fieldsign error *????????External Email - Use Caution * Hi Doug, I used FS 7.1 under WSL to analyze retinotopy data.? Since the ring and wedge were presented at a different frequency, the data had to be analyzed separately for each condition.? To get the field sign, I had to use the mri_fieldsign function to combine polar and eccen data. However, an error happened with running mri_fieldsign: ?Segmentation fault????? (core dumped)?.? The following is the command-line output. Thanks for your help! Xiaomin cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala cmdline mri_fieldsign --fs LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO --hemi rh --sphere sysname? Linux hostname DESKTOP-SVDQE4Q machine? x86_64 user???? xiaominyue eccen real ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz eccen imag ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz patch???? (null) subject???? LOO hemi??????? rh fwhm??????? -1.000000 nsmooth???? -1 fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz usenew????? 1 Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere Using spherical coordinates Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Complex Ripping Zeros Rot (rad): 0 0 surfer: compute_fieldsign2() dthresh = 1.5 shape = 1 nvertices = 153801 ??? 0???? 0 45452?? 0.03? 33.2224 1018? 1000 39160? 21.33? -18.3959 2055? 2000 44734? 43.26? 33.0783 3148? 3000 49793? 65.38? 0.653687 4344? 4000 38626? 88.16? 16.7555 5529? 5000 54149 110.12? -4.90118 6706? 6000 61599 133.36? -5.74607 7971? 7000 50134 155.88? -17.5589 9165? 8000 34182 178.05? -18.9387 10591? 9000 59682 200.70? -4.60514 12034 10000 63856 223.18? -4.4884 13297 11000 41007 245.62? 27.3489 14938 12000 27365 267.70? -1.40077 16684 13000 23615 289.10? -0.518007 18048 14000 47088 309.37? 18.7017 19798 15000 21060 330.11? 15.9458 21681 16000 33067 350.27? -11.1953 23173 17000 28744 371.48? -6.18747 25112 18000 27738 392.41? -6.93845 26953 19000 20538 414.47? 2.99349 28903 20000 80583 435.98? -0.338512 30319 21000 16251 459.83? -45.2313 32174 22000 17139 483.36? -2.31642 34093 23000 13307 507.02? 19.1461 36170 24000 17826 530.65? -10.7575 37683 25000 69324 555.78? -6.17011 39666 26000 14043 583.29? -10.5151 41746 27000 76017 609.92? -0.0112556 43986 28000 84646 636.28? 1.24722 46088 29000 9763 664.26? 12.7035 48326 30000 92161 694.30? 2.03416 50431 31000 99884 724.91? 1.20525 ./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault????? (core dumped) mri_fieldsign --fs $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s $subjname --hemi $hemi --sphere _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/e… ------------------------------ Message: 3 Date: Wed, 15 Jul 2020 15:39:08 +0000 From: "O'Dell, Ryan" <ryan.odell(a)yale.edu> Subject: [Freesurfer] Extracting PET Binding Values from Inflated Surface To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BN8PR08MB5825811A87A2758B0DDC2D25F57E0(a)BN8PR08MB5825.namprd08.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" ???????External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the cortical ribbon), and then displayed on the inflated hemisphere surfaces. We would like to extract the average binding values from the cortical surface ROIs using the Desikan-Killiany atlas, but are unsure how to go about this. Is there a simple way to use aparcstats2table or a similar command to extract average values from surface ROIs as defined by the ?h.aparc.annot file? Thanks! Ryan O'Dell MD/PhD PGY4 Psychiatry Resident, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/5… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 197, Issue 33 ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200716/4… ------------------------------ Message: 14 Date: Thu, 16 Jul 2020 17:57:28 +0200 From: Knut J Bjuland <knutjorgen(a)outlook.com<mailto:knutjorgen@outlook.com>> Subject: Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>, "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Message-ID: <DB6PR05MB3494D92A68AF36388DFFCF6EC37F0(a)DB6PR05MB3494.eurprd05.prod.outlook.com<mailto:DB6PR05MB3494D92A68AF36388DFFCF6EC37F0@DB6PR05MB3494.eurprd05.prod.outlook.com>> Content-Type: text/plain; charset="windows-1252" External Email - Use Caution Thanks Sure, Here is the log file. Knut J?rgen On 16/07/2020 16:12, Douglas N. Greve wrote: Can you send the log file? On 7/15/2020 1:51 PM, Knut J Bjuland wrote: ????????External Email - Use Caution Dear freesurfer experts I was able to run the same subects on the longitudinal stream using FS 6 , but when I use FS7.1 I got this error RROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! ERROR: @#@FSTIME ?2020:07:15:18:43:31 longmc N 5 e 1.75 S 0.47 U 0.15 P 35% M 2444 F 88 R 26962 W 0 c 321 w 33906 I 19328 O 14 L 31.52 31.63 31.62 @#@FSLOADPOST 2020:07:15:18:43:33 longmc N 5 31.55 31.64 31.63 Linux c5-31 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 007_Run1.long.007_Run1_base exited with ERRORS at Wed Jul 15 18:43:33 CEST 2020 Knut J?rgen Bjuland _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200716/1… -------------- next part -------------- A non-text attachment was scrubbed... Name: recon-all.log Type: text/x-log Size: 67529 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200716/1… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 197, Issue 34 *******************************************

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recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects
by Annelies Vant Westeinde 21 Jul '20

21 Jul '20

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 | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här 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>.

2 3

How to do permutation for multiple comparison correction?
by Xiaojiang Yang 21 Jul '20

21 Jul '20

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 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. 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? 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? Thank you! Xiao

2 1

FsAverage4 vertex coordinates
by Walsh, Shane W. 21 Jul '20

21 Jul '20

Hi FreeSurfer developers, I'm looking for the xyz coordinate table for the vertices of the FsAverage4 atlas. I have fMRI data that has been sampled to the FsAverage4 space and it would be helpful if I could understand where a given vertex is located in the brain in terms of coordinates. Does anyone on the list know where I could find this information? I imagine it may be in the subjects directory that comes with the FreeSurfer software, but I haven't been able to locate it. Thank you for your help, Shane

2 1

T2 or FLAIR data to improve pial surfaces
by Batra, Vinita R. 21 Jul '20

21 Jul '20

External Email - Use Caution Dear FreeSurfer experts, I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1]. My questions are: 1) In general, should I prefer FLAIR over T2, or the other way around? 2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images so I wanted to hear your opinion. Best, VB

2 1

Flag(s) for parallel processing
by Billah, Tashrif 21 Jul '20

21 Jul '20

Hi Douglas, You asked a good question which prompted me to do an experiment with just "-threads 8 -itkthreads 8". The run time has been quite slower (~8 hours) compared to ~5 hours it took with "-parallel -openmp 8". I agree with you about the underestimation of run time with the latter flags in that page. Though the page stipulates 3 hours, I have never been able to get a freesurfer done in less than 5 hours. Maybe it is related to the resolution of my data? -Tashrif . -parallel -openmp 4 should run things with 4 processors and parallelize across hemi where it can The run time on that page is probably not accurate. But is it faster when you use those options? On 7/16/2020 11:47 PM, Billah, Tashrif wrote: This <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>says "-openmp <num> after -parallel", this <https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures> says "export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2", while this <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_coreg> says "--threads nthreads" for parallel processing. I want to run recon-all and want all processes under recon-all to be parallelized. Which one(s) of the above flags should I provide with recon-all? Please note that the values are not my interest, the flags are. I know the proper values I should choose for the flags on my machines. So far I have been trying "-parallel -openmp 4" option only but my run time stays over 5 hours contrary to less than 3 hours stipulated in the documentation. -Tashrif . _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

HCP-MMP1 Parcellation to individual brain for stats
by Alina Rojas 20 Jul '20

20 Jul '20

External Email - Use Caution Hello Freesurfer support list, I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my subjects to get the values of the parcellation, like aparc.stats but aparc being HCP-MMP1. The aim ist to compare the cortical thickness of the Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the archive and didn’t find the solution. It would be so great if you could help me! Thank you and regards, Alina Rojas

3 9

Error for version 7.1.0 when run the recon-all
by Yang Molly 20 Jul '20

20 Jul '20

External Email - Use Caution Hi list, I tried to run the latest version Freesurfer (7.1.0) on the Ubantu 18.04 system. I downloaded the “freesurfer-linux-centos7_x86_64-7.1.0.tar.gz” and successfully installed. I tried to run "recon-all -s bert -autorecon1" and the terminal replied as "recon-all -s bert finished without error ". However, when I tried to run the recon-all use the common" recon-all -i /home/molly/FStry/preA063/preA063.nii -s sub063 -all", the terminal replied "Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in <module> file.write(arg + '\n') UnicodeEncodeError: 'ascii' codec can't encode character '\udc87' in position 12: ordinal not in range(128) ERROR: could not configure recon-all parameters" I did not retrieve a similar question in the previous mailing list and hope to get your help. Thank you Molly

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