On 7/24/2020 10:27 AM, Ferraro, Pilar wrote: > 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? Ventral Diencephalon (VentralDC) is now GM. > > 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. It should not > > 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" <dgr...@mgh.harvard.edu >>>> <mailto:dgr...@mgh.harvard.edu>> >>>> Subject: Re: [Freesurfer] PETSurfer analysis question >>>> To: <freesurfer@nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> Message-ID: <d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu >>>> <mailto:d56acc7d-3273-4f40-ed17-570a893b2...@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-requ...@nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> ha scritto: >>>>>> >>>>>> Send Freesurfer mailing list submissions to >>>>>> freesurfer@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-requ...@nmr.mgh.harvard.edu >>>>>> >>>>>> You can reach the person managing the list at >>>>>> freesurfer-ow...@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" <dgr...@mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra >>>>>> fails to run for some subjects >>>>>> To: <freesurfer@nmr.mgh.harvard.edu> >>>>>> Message-ID: <beb084b0-fe6b-c8a2-c0a5-e8bcc9276...@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-long-tp-init >>>>>>> ?-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.westei...@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@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/20200715/0c660d36/attachment-0001.html >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 2 >>>>>> Date: Wed, 15 Jul 2020 11:14:53 -0400 >>>>>> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] mri_fieldsign error >>>>>> To: <freesurfer@nmr.mgh.harvard.edu> >>>>>> Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41...@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:yu...@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@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/e047416d/attachment-0001.html >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 3 >>>>>> Date: Wed, 15 Jul 2020 15:39:08 +0000 >>>>>> From: "O'Dell, Ryan" <ryan.od...@yale.edu> >>>>>> Subject: [Freesurfer] Extracting PET Binding Values from Inflated >>>>>> Surface >>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>>>>> Message-ID: >>>>>> <bn8pr08mb5825811a87a2758b0ddc2d25f5...@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/20200715/570ee5fa/attachment-0001.html >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@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@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/20200716/41e10c32/attachment-0001.html >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 14 >>>> Date: Thu, 16 Jul 2020 17:57:28 +0200 >>>> From: Knut J Bjuland <knutjor...@outlook.com >>>> <mailto:knutjor...@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@nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>>,"Douglas >>>> N. Greve" <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> >>>> Message-ID: >>>> <db6pr05mb3494d92a68af36388dffcf6ec3...@db6pr05mb3494.eurprd05.prod.outlook.com >>>> <mailto:db6pr05mb3494d92a68af36388dffcf6ec3...@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@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@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/20200716/173f9ccd/attachment.html >>>> >>>> -------------- 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/20200716/173f9ccd/attachment.bin >>>> >>>> >>>> ------------------------------ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@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 >>>> ******************************************* >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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/20200721/ae900158/attachment-0001.html >> >> ------------------------------ >> >> Message: 10 >> Date: Tue, 21 Jul 2020 10:45:26 -0500 >> From: Xiaojiang Yang <xjyan...@gmail.com> >> Subject: Re: [Freesurfer] How to do permutation for multiple >> comparison correction? >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAPg=14ykgyijhytdqb_xv08bunhsdbhogbua5tuvznnka-7...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> 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? >> >> 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? >> >> >> 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 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200721/39c1a255/attachment-0001.html >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> End of Freesurfer Digest, Vol 197, Issue 41 >> ******************************************* > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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