[Freesurfer] Fwd: trouble in manual editing of pial surface
External Email - Use Caution -- Forwarded message - From: 박경일 Date: 2018년 12월 1일 (토) 오전 11:27 Subject: Re: [Freesurfer] trouble in manual editing of pial surface To: Freesurfer support list Thanks for you quick reply. I am uploading a compressed file to filedrop (example1.zip). Which email should be filled up in recipients's email to reach you? Kyung 2018년 11월 30일 (금) 오전 12:34, Bruce Fischl 님이 작성: > Hi Kyung > > it's impossible to tell what is going on from a single slice. Typically > the pial surface doesn't settle at the correct spot because the > underlying white is also off. If you tar and gzip the entire subject dir > and upload it to out ftp site together with a set of coordinates that you > think are incorrect we will take a look > > cheers > Bruce > On Thu, 29 Nov 2018, 박경일 wrote: > > > > > External Email - Use Caution > > > > Dear experts > > I met a problem during manual editing. My version is 5.3. > > Following FS tutorial, freeview process was run, which loaded T1, > brainmask and apar+aseg images. > > Then, I clicked 'voxel edit', checked 'recon-edit' and clicked a part of > image which had been excluded from > > cortex (outside the pial line). I saved it and also re-ran the recon-all > process. The saved images were as > > follows. I compared the values before and after editing, but, the > values of total cortical volume, e-TIV > > and the volume of temporal pole and sup temporal gyrus, were not changed. > > I have no idea whether some steps were skipped and why my editing did > not reflect the numerical values of > > this areas. > > > > Thanks always. > > > > Sincerely yours > > Kyung > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trouble in manual editing of pial surface
External Email - Use Caution Thanks for you quick reply. I am uploading a compressed file to filedrop (example1.zip). Which email should be filled up in recipients's email to reach you? Kyung 2018년 11월 30일 (금) 오전 12:34, Bruce Fischl 님이 작성: > Hi Kyung > > it's impossible to tell what is going on from a single slice. Typically > the pial surface doesn't settle at the correct spot because the > underlying white is also off. If you tar and gzip the entire subject dir > and upload it to out ftp site together with a set of coordinates that you > think are incorrect we will take a look > > cheers > Bruce > On Thu, 29 Nov 2018, 박경일 wrote: > > > > > External Email - Use Caution > > > > Dear experts > > I met a problem during manual editing. My version is 5.3. > > Following FS tutorial, freeview process was run, which loaded T1, > brainmask and apar+aseg images. > > Then, I clicked 'voxel edit', checked 'recon-edit' and clicked a part of > image which had been excluded from > > cortex (outside the pial line). I saved it and also re-ran the recon-all > process. The saved images were as > > follows. I compared the values before and after editing, but, the > values of total cortical volume, e-TIV > > and the volume of temporal pole and sup temporal gyrus, were not changed. > > I have no idea whether some steps were skipped and why my editing did > not reflect the numerical values of > > this areas. > > > > Thanks always. > > > > Sincerely yours > > Kyung > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.
Thanks, Bruce. >From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are different among subjects. As far as i understand, it is the subject space, not common space. is that right? If so, how can i get the thickness values in common space to compare the vertex data between subjects? (I'd already run recon-all and qcache process.) Kyung 2018-02-03 0:33 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Kyung > > you should look at the mris_convert help. It has an example of how to > convert a scalar overlay like a curv file to ascii: > > > Convert a scalar overlay file to ascii: > mris_convert -c lh.thickness lh.white lh.thickness.asc > > > it needs the surface as an input to do the conversion properly. > > cheers > Bruce > > > On Fri, 2 Feb 2018, 박경일 wrote: > > Hi Bruce >> I found a directory having a file with ".curv", open terminal and run >> following command. >> >> [root@localhost surf]# mris_convert rh.curv rh.curv.asc >> nquads=4587523, nvertices=476 >> ERROR: MRISread: file 'rh.curv' has many more faces than vertices! >> Probably trying to use a scalar data file as a surface! >> No such file or directory >> >> what is wrong? >> >> Thanks as always. >> >> Kyung >> >> 2018-01-31 0:04 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Kyung >> >> the thickness values are stored as "curvature" file format that you >> can load into matlab >> with read_curv.m. Alternatively, you can convert them to ascii with >> mris_convert and do >> what you want with them. For each index, you can look up its >> location on the white or >> pial (or whatever surface). That is, for the 2nd thickness value >> (index 1), you would go >> find vertex #1 on the other surface and read its location that way >> >> cheers >> Bruce >> On Tue, 30 Jan 2018, 박경일 wrote: >> >> Hi Bruce, I am very new for FS, so did not understand you >> comments >> completely. sorry.. >> >> For cortical thickness from each vertex in one subject, which >> scripts should >> follow "mris_convert"? >> And another question is how to recognize the location of each >> vertex in >> brain finally. >> >> thank you so much >> >> Kyung >> >> >> 2017-11-13 10:06 GMT+09:00 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu>: >> p.s. if you want the vertices to correspond, first run >> recon-all >> -qcache for each >> subject. That will generate a set of thickness maps in >> fsaverage space >> at predefined >> smoothing levels (so that the vertex numbers correspond >> across >> subjects) >> >> On Mon, 13 Nov 2017, 박경일 wrote: >> >> Hi Bruce,What I want is the values of cortical >> thickness in each >> vertex in >> each subject. Is that >> possible? >> Thanks so much. >> >> Kyung >> >> >> >> 2017-11-13 0:43 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi Kyung >> >> you can load them into matlab or convert >> them to ascii if >> you want >> Bruce >> On Sun, 12 Nov 2017, 박경일 wrote: >> >> Dear FS experts, >> I could get QDEC image comparing two >> groups. >> However, is there a way to get >> numerical values of >> cortical >> thickness in >> each vertex? >> >> Thank you >> >> Best, >> Kyung >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >>
Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.
Hi Bruce I found a directory having a file with ".curv", open terminal and run following command. [root@localhost surf]# mris_convert rh.curv rh.curv.asc nquads=4587523, nvertices=476 ERROR: MRISread: file 'rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory what is wrong? Thanks as always. Kyung 2018-01-31 0:04 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Kyung > > the thickness values are stored as "curvature" file format that you can > load into matlab with read_curv.m. Alternatively, you can convert them to > ascii with mris_convert and do what you want with them. For each index, you > can look up its location on the white or pial (or whatever surface). That > is, for the 2nd thickness value (index 1), you would go find vertex #1 on > the other surface and read its location that way > > cheers > Bruce > > On Tue, 30 Jan 2018, 박경일 wrote: > > Hi Bruce, I am very new for FS, so did not understand you comments >> completely. sorry.. >> >> For cortical thickness from each vertex in one subject, which scripts >> should follow "mris_convert"? >> And another question is how to recognize the location of each vertex in >> brain finally. >> >> thank you so much >> >> Kyung >> >> >> 2017-11-13 10:06 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> p.s. if you want the vertices to correspond, first run recon-all >> -qcache for each >> subject. That will generate a set of thickness maps in fsaverage >> space at predefined >> smoothing levels (so that the vertex numbers correspond across >> subjects) >> >> On Mon, 13 Nov 2017, 박경일 wrote: >> >> Hi Bruce,What I want is the values of cortical thickness in >> each vertex in >> each subject. Is that >> possible? >> Thanks so much. >> >> Kyung >> >> >> >> 2017-11-13 0:43 GMT+09:00 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu>: >> Hi Kyung >> >> you can load them into matlab or convert them to ascii >> if you want >> Bruce >> On Sun, 12 Nov 2017, 박경일 wrote: >> >> Dear FS experts, >> I could get QDEC image comparing two groups. >> However, is there a way to get numerical values >> of cortical >> thickness in >> each vertex? >> >> Thank you >> >> Best, >> Kyung >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the >> e-mail >> contains patient information, please contact the Partners >> Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in >> error >> but does not contain patient information, please contact the >> sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> >> Kyung-Il Park, MD, PhD. >> >> Professor, >> >> Department of Neurology, Seoul National University >> Hospital; Seoul National >> University Hospital >> Healthcare System Gangnam Center. >> >> Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 >> >> Email: kip...@snuh.org / ideo...@gmail.com >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >>
Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.
Hi Bruce, I am very new for FS, so did not understand you comments completely. sorry.. For cortical thickness from each vertex in one subject, which scripts should follow "mris_convert"? And another question is how to recognize the location of each vertex in brain finally. thank you so much Kyung 2017-11-13 10:06 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > p.s. if you want the vertices to correspond, first run recon-all -qcache > for each subject. That will generate a set of thickness maps in fsaverage > space at predefined smoothing levels (so that the vertex numbers correspond > across subjects) > > On Mon, 13 Nov 2017, 박경일 wrote: > > Hi Bruce,What I want is the values of cortical thickness in each vertex in >> each subject. Is that >> >> possible? >> Thanks so much. >> >> Kyung >> >> >> >> 2017-11-13 0:43 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Kyung >> >> you can load them into matlab or convert them to ascii if you want >> Bruce >> On Sun, 12 Nov 2017, 박경일 wrote: >> >> Dear FS experts, >> I could get QDEC image comparing two groups. >> However, is there a way to get numerical values of cortical >> thickness in >> each vertex? >> >> Thank you >> >> Best, >> Kyung >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> >> Kyung-Il Park, MD, PhD. >> >> Professor, >> >> Department of Neurology, Seoul National University Hospital; Seoul >> National University Hospital >> Healthcare System Gangnam Center. >> >> Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 >> >> Email: kip...@snuh.org / ideo...@gmail.com >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Question about an error during recon-all process
Thanks. Douglas But, I've never performed each step of FS. Could you explain in detail how to check the registration and re-run with -no-talcheck? 2018-01-01 6:53 GMT+09:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > Probably not because of the voxel size. First, check the registration. If > it looks ok, then you can re-run with -no-talcheck. If it does, not look > good, then fix it and rerun. > > On 12/28/17 6:15 PM, 박경일 wrote: > > Dear experts, I am sorry for asking again. > > I have some problems in running recon-all. > Recon-all process was shut down with this error message > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0., pval=0. < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string." > > > I guess this is because of low resolution or small size of images. > > is it right? Thank you so much for you help in advance. > > > FYI, log file is attached. > > Kyung > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Question about an error during recon-all process
Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Question about an error during recon-all process
Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error in Talairach transformation
Dear experts, I have some problems in running recon-all. Recon-all process was stopped with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. Hopefully you can confirm why. Thank you so much for you help in advance. FYI, log file is attached. -- Kyung Mon Dec 18 17:25:10 KST 2017 /usr/local/freesurfer/subjects/p52 /usr/local/freesurfer/bin/recon-all -i p52.nii -s p52 -all subjid p52 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux localhost.localdomain 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 257168 total used free sharedbuffers cached Mem: 65863632 65452800 410832 50601284500 60079816 -/+ buffers/cache:4088484 61775148 Swap: 67108860 93000 67015860 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/18-08:25:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-642.11.1.el6.x86_64
[Freesurfer] covariates in Qdec
Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes. I just selected "diagnosis" and click "analyze". Is this a right way to remove effects by age and sex? Otherwise, do I need to check age and sex in nuisance factor box? Thank you so much. Park ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] contrasts mat file
Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files. FSTutorial shows only the example of two covariates. Thank you. Sincerely, Kyung___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] contrasts mat file
Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files. FSTutorial shows only the example of two covariates. Thank you. Sincerely, Kyung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] changing qdec path?
Hi, Dr Greve I tried following command setenv SUBJECTS_DIR /mnt/data2 (data2 is a mounted disk) the result is bash: setenv: command not found what is wrong? Kyung 2017-11-16 4:57 GMT+09:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > You can just > > setenv SUBJECTS_DIR /path/to/your/big/disk > > > > > On 11/15/2017 04:06 AM, 박경일 wrote: > > Dear experts, > > Based on my knowledge, all image folders should be within subject_dir > > for qdec process. > > But, my data are so huge to be included in this directory in my > > default setting. > > Do you have any idea to change qdec path by which qdec can import > > image files in external hard drive or other bigger directory, > > excepting hard formatting? > > Thank you as always > > > > > > Kyung > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] changing qdec path?
Dear experts, Based on my knowledge, all image folders should be within subject_dir for qdec process. But, my data are so huge to be included in this directory in my default setting. Do you have any idea to change qdec path by which qdec can import image files in external hard drive or other bigger directory, excepting hard formatting? Thank you as always Kyung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.
Hi Bruce, What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung 2017-11-13 0:43 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Kyung > > you can load them into matlab or convert them to ascii if you want > Bruce > > On Sun, 12 Nov 2017, 박경일 wrote: > > Dear FS experts, >> I could get QDEC image comparing two groups. >> However, is there a way to get numerical values of cortical thickness in >> each vertex? >> >> Thank you >> >> Best, >> Kyung >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.
Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec image considering multiple variables
So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > You can't run it with missing variables > > On 10/9/17 12:40 AM, 박경일 wrote: > > Dear FS developer, > I am a FS beginner and trying to make QDEC images of cortical thickness > difference (color-coded inflated brain) between groups. > No problem when fsid, diagnosis, age, and sex were only included in > qdec.table.dat file. However, adding any other factors such as > hypertension, diabetes... etc. made error messages in a terminal window. I > guess this error came from the some blank data, because some subjects do > not have any information regarding hypertension or diabetes. > Is there a way to make a figure showing a results of multivariate > analysis? > > Thanks a lot in advance. > > Kyung Il Park, MD > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kip...@snuh.org / ideo...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] [freesurfer] Qdec image considering multiple variables
Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension, diabetes... etc. made error messages in a terminal window. I guess this error came from the some blank data, because some subjects do not have any information regarding hypertension or diabetes. Is there a way to make a figure showing a results of multivariate analysis? Thanks a lot in advance. Kyung Il Park, MD 전달된 메시지 시작: > 보낸 사람: 박경일 <ideo...@gmail.com> > 날짜: 2017년 10월 9일 오후 1시 40분 36초 GMT+9 > 받는 사람: freesurfer@nmr.mgh.harvard.edu > 제목: Qdec image considering multiple variables > > Dear FS developer, > I am a FS beginner and trying to make QDEC images of cortical thickness > difference (color-coded inflated brain) between groups. > No problem when fsid, diagnosis, age, and sex were only included in > qdec.table.dat file. However, adding any other factors such as hypertension, > diabetes... etc. made error messages in a terminal window. I guess this error > came from the some blank data, because some subjects do not have any > information regarding hypertension or diabetes. > Is there a way to make a figure showing a results of multivariate analysis? > > Thanks a lot in advance. > Kyung Il Park, MD > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec image considering multiple variables
Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension, diabetes... etc. made error messages in a terminal window. I guess this error came from the some blank data, because some subjects do not have any information regarding hypertension or diabetes. Is there a way to make a figure showing a results of multivariate analysis? Thanks a lot in advance. Kyung Il Park, MD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
