Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

fcseedcor output
by Sara Jafakesh 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara

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Re: [Freesurfer] fsaverage6 FS6
by Sanfelici, Rachele 07 Dec '18

07 Dec '18

External Email - Use Caution Thanks Bruce, this is my command line (note that because of a different organization of the data, the subject dir is /Data/48/ and the subject is MRI_sMRI_fs_reconall_fs_reconall_gcv6s): mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --srcsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fsaverage6.mgh --trgsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --trgsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fwhm5.fsaverage6.mgh --surfreg sphere.reg --hemi lh --fwhm 5 so I could use the fsaverage6/surf/lh.sphere.reg for the --surfreg flag instead, right? But then I would need to copy and rename it in the subject folder, is that correct? Thanks a lot! Rachele ________________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Gesendet: Freitag, 7. Dezember 2018 19:14 An: Freesurfer support list Betreff: Re: [Freesurfer] fsaverage6 FS6 Hi Rachele what is your command line? The ?h.sphere.reg is in register with fsaverage, but it looks like your data has been mapped to the fsaverage6 subject (which has 40962), but you are specifying the individual subject surface. If that is the case, use the fsaverage6 surface instead cheers Bruce On Fri, 7 Dec 2018, Sanfelici, Rachele wrote: > External Email - Use Caution > > Many thanks Doug, that worked! > > Now that I resampled my data I'm having the next issue: smoothing. > I'm using mri_surf2surf specifying the same source and target subject (resampled to fsaverage6), but apparently to skip the registration I need to also specify the ?h.sphere.reg. I get this error: > > Reading source surface reg /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.sphere.reg > Loading source data > ERROR: dimension inconsistency in source data > Number of surface vertices = 151901 > Number of value vertices = 40962 > > Which I guess it's because the sphere is not "registered" to fsaverage6, right? > My solution would be to copy and rename fsaverage6 ?h.sphere.reg to the subject directory to bypass this problem. Can you please confirm that this approach is valid? Or otherwise would you have a better solution? > > Thanks a lot in advance! > Rachele > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > Gesendet: Donnerstag, 6. Dezember 2018 18:33 > An: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] fsaverage6 FS6 > > Try using mris_apply_reg. The command line is simpler (but otherwise > gives the same result). > > On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: >> >> External Email - Use Caution >> >> Dear FreeSurfer experts, >> >> >> I am encountering a problem when trying to downsample to fsaverage6 >> with FreeSurfer v.6.(see below): >> >> >> mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject >> fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> --sval >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> --sfmt curv --noreshape --cortex >> >> srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> srcval =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> srctype = curv >> trgsubject = fsaverage6 >> trgval = >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> trgtype = >> srcsurfreg = fsaverage6.sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = lh.cortex.label >> label-trg = lh.cortex.label >> OKToRevFaceOrder = 1 >> UseDualHemi = 0 >> Reading source surface reg >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg >> No such file or directory >> >> I guess it's because the naming of the sphere file is now different >> compared to v.5.3 (it was sufficient to run recon-all with the >> additional -qcache -target fsaverage6 flag), so it can't be found by >> mri_surf2surf. I tried to run mris_preproc instead of recon-all but I >> still get the same error. Could you please help me with the right command? >> >> Thank you very much in advance! >> >> Best >> Rachele >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] fsaverage6 FS6
by Sanfelici, Rachele 07 Dec '18

07 Dec '18

External Email - Use Caution Many thanks Doug, that worked! Now that I resampled my data I'm having the next issue: smoothing. I'm using mri_surf2surf specifying the same source and target subject (resampled to fsaverage6), but apparently to skip the registration I need to also specify the ?h.sphere.reg. I get this error: Reading source surface reg /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 151901 Number of value vertices = 40962 Which I guess it's because the sphere is not "registered" to fsaverage6, right? My solution would be to copy and rename fsaverage6 ?h.sphere.reg to the subject directory to bypass this problem. Can you please confirm that this approach is valid? Or otherwise would you have a better solution? Thanks a lot in advance! Rachele ________________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Gesendet: Donnerstag, 6. Dezember 2018 18:33 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] fsaverage6 FS6 Try using mris_apply_reg. The command line is simpler (but otherwise gives the same result). On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > > I am encountering a problem when trying to downsample to fsaverage6 > with FreeSurfer v.6.(see below): > > > mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s > --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject > fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval > ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh > --sval > /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi > --sfmt curv --noreshape --cortex > > srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s > srcval =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi > srctype = curv > trgsubject = fsaverage6 > trgval = > ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh > trgtype = > srcsurfreg = fsaverage6.sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = lh.cortex.label > label-trg = lh.cortex.label > OKToRevFaceOrder = 1 > UseDualHemi = 0 > Reading source surface reg > /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg > No such file or directory > > I guess it's because the naming of the sphere file is now different > compared to v.5.3 (it was sufficient to run recon-all with the > additional -qcache -target fsaverage6 flag), so it can't be found by > mri_surf2surf. I tried to run mris_preproc instead of recon-all but I > still get the same error. Could you please help me with the right command? > > Thank you very much in advance! > > Best > Rachele > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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gray intensity
by 1013364183 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Bruce, I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yujunjie

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Help with Data
by T and LS 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Help Desk - I have a few basic questions about freesurfer. I am retired military bomb technician working on a blast TBI initiative and not a research so please bear with me. We are looking at a long term study of bomb technicians and I am curious about the following before moving forward. 1. Total number of images processed by freesurver? Is this in the thousands or millions? 2. Cohart group data is this from each organization or is there a central pool. e.g. I had a 3D volumetric MRI done with DTI at Washington University in St Louis and am 49yrs old is this only from their pool or larger data base? Any idea number of images in that data base? 3. Standard Deviations, Patient Annual Volume Change and Group Annual Volume change; are these organizations specific or a larger data base. 4. How accurate are the volumes from a 3T MRI and is there a huge fluctuation if scans are done on the same exact MRI system? e.g. in my scan some of the thicknesses were down to .0013mm and volumes down to .9mm3 = is there a lot of error in those numbers. Thanks for any information you can provide! It seems there will be a DVBIC site open soon where our school is and I would like to be able to provide some input on this. Thanks, Todd Sheckley

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mri_segstats - different results with --ctab
by Winkelbeiner, Stephanie A 07 Dec '18

07 Dec '18

External Email - Use Caution Hi freesurfer experts, I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation volume (parc2502dwi.nii.gz) and the corresponding color table with: for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ # extract FA mri_segstats \ --seg mri/parc2502dwi.nii.gz \ --ctab colortable.txt \ --i $dtipath/$subj/dti_FA.nii.gz \ --excludeid 0 \ --sum ../FA/${subj}_fa.stats cd ../ fi done The color table has 297 parcels specified but the summary statistics file only includes 38 regions. This is due to zero values in the other regions, I assume. Both (dti_FA and parc2502dwi) are perfectly co-registered. Not providing a color table results in 1234 regions being read out. Am I missing an argument in my command? Or is there anything else that is obviously wrong? I would be very glad for some hints! Thanks, Steph The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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When segmentation went perfect but some pial is remaining: looking for advice
by Rosalia Dacosta Aguayo 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Free Surfer team, I am checking my group of HCs. I have seen that GM and WM segmentation is nearly perfect (for now) but, there are some point in which I can see more pial, but pial has not been considered in the segmentation. I have the believe, maybe biased, that the best for Free Surfer is that every participant has to be very well skull stripped (even pial) as then Free Surfer works very well in all the other steps. I wonder if the fact the GM and WM were very good and pial surface was not considered in the segmentation, I should edit pial and then control points, or, on the contrary, just I should see if there is any control point to add and then, run -autorecon2-cp and -autorecon3. Yours sincerely, Rosalia

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(no subject)
by Sara Jafakesh 07 Dec '18

07 Dec '18

External Email - Use Caution Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > ????????External Email - Use Caution > > > > > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fseed-sess , I used fcseedcor. the command > that I trying to run is as follow: > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat > but the output of fcseedcor is not? .dat file ( the > connectivity matrix for my result 2*2 matrix)? as it has been > explained in the fcssedcor help. the output is just the .log > file named? seedcor2.dat.log. although it has been done > without error. > I really dont know what is the problem. > I would be grateful if you could help me. > best regards, > sara thank you for your reply my full terminal output is: [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done

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Re: [Freesurfer] Direction of significant group comparison
by Backhausen, Lea 07 Dec '18

07 Dec '18

External Email - Use Caution Hey Doug, thanks so much for your answer! Do you mean the "Max" column? This is the only one that changes signs in all my results. I used abs in the analyses. So if the order in my FSGD file is subjects of the groups ADHD, Comorbid and Typically developing; my contras matrix looks like this: 1 0 -1 and the output for e.g. volume is this: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.086 143615 165.54 34.0 -10.4 -34.8 0.84806 0.84310 0.85285 273 fusiform ... does this mean there is decreased volume in the ADHD group compared to the typically developing group? Am I interpreting it right? Best Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, December 06, 2018 6:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 178, Issue 7 Send Freesurfer mailing list submissions to freesurfer(a)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. visual cortex {Disarmed} (???) 2. Longitudinal processing and paralllel flag (Erik O'Hanlon) 3. Re: visual cortex {Disarmed} (Bruce Fischl) 4. Re: [PETsurfer] Use of MGX and RBV partial volume correction (Greve, Douglas N.,Ph.D.) 5. Re: Fwd: Overall maxima is high and still no significant cluster (Greve, Douglas N.,Ph.D.) 6. Re: mris_preproc paired diff outputs 0 values (Greve, Douglas N.,Ph.D.) 7. fsaverage6 FS6 (Sanfelici, Rachele) 8. Re: Direction of significant group comparison (Greve, Douglas N.,Ph.D.) 9. Re: Extracting ROI from atlases (Greve, Douglas N.,Ph.D.) ---------------------------------------------------------------------- Message: 1 Date: Thu, 6 Dec 2018 16:58:32 +0800 (GMT+08:00) From: ??? <zhengfenglian0105(a)163.com> Subject: [Freesurfer] visual cortex {Disarmed} To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1cd7a499.10465.16782bd7046.Coremail.zhengfenglian0105(a)163.com> Content-Type: text/plain; charset="gbk" External Email - Use Caution Hi experts, I want to do some research on the cortical thickness of visual cortex using FS 6.0. Is there specified or associated cortex model for the segmentation of visual cortex? Thanks for your reply in advance. I need your help. Sincerely, Zheng | | ??? | | ???zhengfenglian0105(a)163.com | ??? ?????? ??

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How to use FIR to get HRF shape
by Lauri Tuominen 06 Dec '18

06 Dec '18

External Email - Use Caution Hi there, I would like to know if a condition leads to a delayed HRF peaking. To device an experiment to answer this, I collected finger tapping pilot data with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, TR=1.6. The trials are not TR locked because I thought I’d sample different portions of the HRF during each trial. I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. My problem is that the resulting ces.nii.gz has only 16 volumes, which correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time resolution for peak detection would be 1.6, which is not what I would like it to be. This is obviously less than ideal for answering my research question. How could I get the FIR fit to each timepoint so I could reconstruct the HRF myself? Or would there be some other workaround / analysis? Or do I need to collect the data in some other way, i.e somehow sliding the TR-event locking? Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, iminsig.nii.gz and minsig.nii.gz? Thanks so much again for the help Lauri Tuominen

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Freesurfer December 2018