Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] Problem about Surface-based Registration
by Bruce Fischl 19 Mar '14

19 Mar '14

Hi Yufeng can you remember to cc the list? And yes, if all you want is a common surface-based coordinate system for your subjects then there is no need for you to run mris_register yourself - it is done by recon-all. All you need to do is run mri_vol2surf for each individual, then map the resulting overlays to fsaverage with mri_surf2surf cheers Bruce On Wed, 19 Mar 2014, yufeng huang wrote: > Hi Bruce, > What does" rerun the registration - just use the ?h.sphere.reg files." mean? > Just using noting or using as follow code to produce new > ?h.sphere.reg.newtemplate? > > mris_register -curv surf/lh.sphere \ > $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ > surf/lh.sphere.reg.newtemplate > > > 2014-03-19 10:42 GMT-04:00 yufeng huang <trista.yfh(a)gmail.com>: > I want to do is map all the individual activation maps into a > common surface-based coordinate system. So I do not need to > follow the process of creating a registration template fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemp… > s) to do the surface-based registration. > 1If I just use the ?h.sphere.reg which produce by recon-all. But I > want to know : Who is the average subject at this time. The fsaverage? > 2 So at this time all I need to do is using mri_surf2surf onto > fsaverage surface? Or I should using mri_vol2surf first and do the > mri_surf2surf next? > Thanks very much! > > > > 2014-03-19 9:46 GMT-04:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Yufeng > > if all you want to do is map all the individual activation > maps into a common surface-based coordinate system,then > there is no need to create your own atlas and rerun the > registration - just use the ?h.sphere.reg files. > > > If there is some other reason you want to create your own > template/atlas, then you can check the results by using > make_average_subject to create a new version of > fsavverage, and mapping each subject's curvature file into > your new coordinate system using mri_surf2surf onto that > average subject's surface. Then see if they align. You > don't need to do anything about the inflated or other > surfaces. Use mri_vol2surf to map the data onto each > individual subject's surface, then mri_surf2surf with your > new registration file to map it to your new average > subject. > > cheers > Bruce > > > On Wed, 19 Mar 2014, yufeng huang wrote: > > Dear Burce, > I have 20 normal subjects, and I want to do > inter-subject surface-based > registration to all of them. So each one's > surface can align properly to the > other subject’s surface. After that I can put > the functional data onto the > surface which has aligned to each other > already. > And now I followed the process of creating a > registration templatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRe… > late > s) to do the surface-based registration. > Round 1, all reference subjects > data are registered to the initial template, > producing ?h.sphere.myreg0. > (I've coordinated the suffix numbers with the > template used to produce the > registration.) Using that registration, a new > template (mytemp1.tif) is made > using all reference subjects as input. Round 2 > is essentially a repeat of > Round 1, but produces an improved template > (mytemp2.tif) because Round 2's > initial registration step is based on a better > template than in Round 1. > I get the lh.sphere.reg.newtemplate1 and > rh.sphere.reg.newtemplate1 in > each subjects's surf folder. I do not know how > to check the result about if > every subject has aligned to each other > properly. And I do not know what > should I do next. > My question is : > 1 How can I check about the result as if every > one has aligned each other > properly? > 2 And what should I do next, I can not know if > the functional data can > aligned to the new surface properly. If I can > use mri_surf2surf or > mri_vol2surf can be used for this. > 3 The lh.sphere.reg.newtemplate1 and > rh.sphere.reg.newtemplate1is just for > sphere, and how about the inflate aligned to > each other? > Yours Yufeng > > > > > 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. > > > > >

2 2

Re: [Freesurfer] Problem about Surface-based Registration
by Bruce Fischl 19 Mar '14

19 Mar '14

yes, fsaverage On Wed, 19 Mar 2014, yufeng huang wrote: > I want to do is map all the individual activation maps into a common > surface-based coordinate system. So I do not need to follow the process of > creating a registration template fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemp… > s) to do the surface-based registration. > 1If I just use the ?h.sphere.reg which produce by recon-all. But I want to > know : Who is the average subject at this time. The fsaverage? > 2 So at this time all I need to do is using mri_surf2surf onto fsaverage > surface? Or I should using mri_vol2surf first and do the mri_surf2surf next? > Thanks very much! > > > > 2014-03-19 9:46 GMT-04:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Yufeng > > if all you want to do is map all the individual activation maps > into a common surface-based coordinate system,then there is no > need to create your own atlas and rerun the registration - just > use the ?h.sphere.reg files. > > > If there is some other reason you want to create your own > template/atlas, then you can check the results by using > make_average_subject to create a new version of fsavverage, and > mapping each subject's curvature file into your new coordinate > system using mri_surf2surf onto that average subject's surface. > Then see if they align. You don't need to do anything about the > inflated or other surfaces. Use mri_vol2surf to map the data > onto each individual subject's surface, then mri_surf2surf with > your new registration file to map it to your new average > subject. > > cheers > Bruce > > > On Wed, 19 Mar 2014, yufeng huang wrote: > > Dear Burce, > I have 20 normal subjects, and I want to do > inter-subject surface-based > registration to all of them. So each one's surface > can align properly to the > other subject’s surface. After that I can put the > functional data onto the > surface which has aligned to each other already. > And now I followed the process of creating a > registration templatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRe… > late > s) to do the surface-based registration. Round 1, > all reference subjects > data are registered to the initial template, > producing ?h.sphere.myreg0. > (I've coordinated the suffix numbers with the > template used to produce the > registration.) Using that registration, a new > template (mytemp1.tif) is made > using all reference subjects as input. Round 2 is > essentially a repeat of > Round 1, but produces an improved template > (mytemp2.tif) because Round 2's > initial registration step is based on a better > template than in Round 1. > I get the lh.sphere.reg.newtemplate1 and > rh.sphere.reg.newtemplate1 in > each subjects's surf folder. I do not know how to > check the result about if > every subject has aligned to each other properly. > And I do not know what > should I do next. > My question is : > 1 How can I check about the result as if every one > has aligned each other > properly? > 2 And what should I do next, I can not know if the > functional data can > aligned to the new surface properly. If I can use > mri_surf2surf or > mri_vol2surf can be used for this. > 3 The lh.sphere.reg.newtemplate1 and > rh.sphere.reg.newtemplate1is just for > sphere, and how about the inflate aligned to each > other? > Yours Yufeng > > > > > 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. > > > >

1 0

Re: [Freesurfer] selxavg3-sess error]
by shahin＠nmr.mgh.harvard.edu 19 Mar '14

19 Mar '14

---------------------------- Original Message ---------------------------- Subject: Re: selxavg3-sess error From: shahin(a)nmr.mgh.harvard.edu Date: Wed, March 19, 2014 11:15 am To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- But this is a per-run analysis and preproc-sess is -per-run (in native space). I assumed that I have to change my mkanalysis-sess to this: mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 -paradigm Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color -per-run But using -mcprextreg flag generates an error. Is it a bug? > > There is not an mcextreg file there. There is mcprextreg file. I think > you need to run preproc with -per-session to get the mcextreg file > doug > > On 03/18/2014 02:34 PM, SHAHIN NASR wrote: >> Hi, >> When I run selxavg3-sess, I face this error: >> >> ERROR: cannot find volume matching >> /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg >> ERROR: loading nonpar reg >> /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg >> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> I repeated the preproc-sess from scratch and it worked fine, >> finished without any problem and I still get the same error. I even >> check the registration in this run and it fine. >> >> Now I am wondering why do I see this error for this subjects (and >> why I don't see it for the other subjects)? >> >> Regards >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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/ > > >

1 0

Fwd: Problem about Surface-based Registration
by yufeng huang 19 Mar '14

19 Mar '14

Hi Bruce, I want to do is map all the individual activation maps into a common surface-based coordinate system. So I do not need to follow the process of creating a registration template from scratch(GW)( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based registration. 1If I just use the ?h.sphere.reg which produce by recon-all. But I want to know : Who is the average subject at this time. The fsaverage? 2 So at this time all I need to do is using mri_surf2surf onto fsaverage surface? Or I should do the mri_vol2surf first and do the mri_surf2surf next? Thanks very much! 2014-03-19 9:46 GMT-04:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: Hi Yufeng > > if all you want to do is map all the individual activation maps into a > common surface-based coordinate system,then there is no need to create your > own atlas and rerun the registration - just use the ?h.sphere.reg files. > > > If there is some other reason you want to create your own template/atlas, > then you can check the results by using make_average_subject to create a > new version of fsavverage, and mapping each subject's curvature file into > your new coordinate system using mri_surf2surf onto that average subject's > surface. Then see if they align. You don't need to do anything about the > inflated or other surfaces. Use mri_vol2surf to map the data onto each > individual subject's surface, then mri_surf2surf with your new registration > file to map it to your new average subject. > > cheers > Bruce > > > > On Wed, 19 Mar 2014, yufeng huang wrote: > > Dear Burce, >> I have 20 normal subjects, and I want to do inter-subject surface-based >> registration to all of them. So each one's surface can align properly to >> the >> other subject's surface. After that I can put the functional data onto the >> surface which has aligned to each other already. >> And now I followed the process of creating a registration template >> fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/ >> fswiki/SurfaceRegAndTemplate >> s) to do the surface-based registration. Round 1, all reference subjects >> data are registered to the initial template, producing ?h.sphere.myreg0. >> (I've coordinated the suffix numbers with the template used to produce the >> registration.) Using that registration, a new template (mytemp1.tif) is >> made >> using all reference subjects as input. Round 2 is essentially a repeat of >> Round 1, but produces an improved template (mytemp2.tif) because Round 2's >> initial registration step is based on a better template than in Round 1. >> I get the lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1 in >> each subjects's surf folder. I do not know how to check the result about >> if >> every subject has aligned to each other properly. And I do not know what >> should I do next. >> My question is : >> 1 How can I check about the result as if every one has aligned each other >> properly? >> 2 And what should I do next, I can not know if the functional data can >> aligned to the new surface properly. If I can use mri_surf2surf or >> mri_vol2surf can be used for this. >> 3 The lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1is just for >> sphere, and how about the inflate aligned to each other? >> Yours Yufeng >> >> >> > > 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. >

1 0

(no subject)
by Charnjit Sidhu 19 Mar '14

19 Mar '14

Dear freesurfers, This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster. We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag: recon-all -subjid $i -localGI I know this requires matlab which we have installed on the cluster however we cannot submit matlab within a working node which the submitted node is trying to do, we get the following error: denied: host "hostname" is no submit host this message is given when the make_outer_surface script matlab script is submitted within the submitted job. We have a script that allows matlab to run from within the cluster and have tried to add this as an environment variable to the script: matlab=matlab_cluster ; export matlab source $matlab But when we add this it still fails with the same error, Do you know how I can make changed to the script allowing us to run the above script when matlab is called? Or are we missing something from our script? I have attached the relevant scripts and output sent to me by the user. Can you help me. Thanks Charnjit

2 1

selxavg3-sess error
by SHAHIN NASR 19 Mar '14

19 Mar '14

Hi, When I run selxavg3-sess, I face this error: ERROR: cannot find volume matching /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg ERROR: loading nonpar reg /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg ------------------------------------------ ERROR: fast_selxavg3() failed\n I repeated the preproc-sess from scratch and it worked fine, finished without any problem and I still get the same error. I even check the registration in this run and it fine. Now I am wondering why do I see this error for this subjects (and why I don't see it for the other subjects)? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

bug in surface-based area and volume, and use of total brain volume as a covariate
by Narly Golestani 19 Mar '14

19 Mar '14

Dear all, Related to the bug that was reported in 2011 (see http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html) with the way that surface-based volumes and areas were calculated in Freesurfer versions 5.1 and earlier, I’d like to confirm that region-of-interest measures obtained using those earlier versions (e.g. when exporting the volume / surface area to tables using aparcstats2table) were unaffected by this bug (i.e. rerunning qcache should not change ROI-based results). 2. I’d like to also confirm that otherwise, for vertex-based analyses, it should be sufficient to run ‘recon-all subject –qcache’ using a more recent version of freesurfer in order to obtain accurate measures for data that was originally processed using 'recon-all –all' with an earlier version of freesurfer (I have data that was originally processed with version 4.4 and other data that was processed with version 5.1 that I would like to now examine in a surface-based manner). 3. The bug was related to how the measures were converted to standard space - I’d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses). Many thanks, and all the best, Narly.

3 5

bug in surface-based area and volume, and use of total brain volume as a covariate
by Narly Golestani 19 Mar '14

19 Mar '14

>> why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? >The vertex-based measures are computed in individual space, not standard >space >doug Dear Doug, I would like to know at what stage the measures computed in individual space are normalised, if at all, in order to make comparisons of data across participants (e.g. in qdec) meaningful. Differences in the relative position of a particular structure across participants will make it difficult if not impossible to examine effects at the group level. If the vertex-wise data is in individual space, then I’m not sure that I understand how using total brain volume as a covariate would solve the above problem. I would greatly appreciate any clarifications that you might have. Best wishes, Narly.

2 1

Problem about Surface-based Registration
by yufeng huang 19 Mar '14

19 Mar '14

Dear Burce, I have 20 normal subjects, and I want to do inter-subject surface-based registration to all of them. So each one's surface can align properly to the other subject's surface. After that I can put the functional data onto the surface which has aligned to each other already. And now I followed the process of creating a registration template from scratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplate… to do the surface-based registration. Round 1, all reference subjects data are registered to the initial template, producing ?h.sphere.myreg0. (I've coordinated the suffix numbers with the template used to produce the registration.) Using that registration, a new template (mytemp1.tif) is made using all reference subjects as input. Round 2 is essentially a repeat of Round 1, but produces an improved template (mytemp2.tif) because Round 2's initial registration step is based on a better template than in Round 1. I get the lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1 in each subjects's surf folder. I do not know how to check the result about if every subject has aligned to each other properly. And I do not know what should I do next. My question is : 1 How can I check about the result as if every one has aligned each other properly? 2 And what should I do next, I can not know if the functional data can aligned to the new surface properly. If I can use mri_surf2surf or mri_vol2surf can be used for this. 3 The lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1is just for sphere, and how about the inflate aligned to each other? Yours Yufeng

2 1

Fwd: FW: bug in surface-based area and volume, and use of total brain volume as a covariate
by _andreia_＠sapo.pt 19 Mar '14

19 Mar '14

Hi all, just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures? Thanks, Andreia Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>> why would one control for total brain volume in doing vertex-based > analyses when the vertex-based measures are computed in standard space? > > The vertex-based measures are computed in individual space, not standard > space > doug > > > On 03/17/2014 05:12 PM, Narly Golestani wrote: >> Dear Doug, >> >> Many thanks for your answers. >> >> > 3. The bug was related to how the measures were converted to standard >> > space - I?d like to therefore confirm that when doing >> > surface/vertex-based analyses, it is not necessary to use total brain >> > volume as a covariate (whereas it is for ROI-based analyses). >> > >> This question has nothing to do with the bug. People generally use ICV >> or total brain volume when exploring cortical volume or surface area, >> but it is inappropriate for thicknss studies >> doug >> > >> >> Regarding the last point (which indeed has nothing to do with the bug, >> sorry for having given the impression that I thought that it did), why >> would one control for total brain volume in doing vertex-based >> analyses when the vertex-based measures are computed in standard >> space? I realize that this has to be done for ROI analyses since these >> measures are in native space. >> >> Thanks again, and best, >> Narly. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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.

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer