Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Begginer!
by Ash Rafea 01 May '13

01 May '13

Hi there, I am totally a begginer in the Neurodebian "world" so please be patient :( I installed FS but I don't know how to setup freesurfer? I don't know how to locate my FS home Simply, I'm stuck at this step: setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh any help?

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Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21
by Rotem Saar 30 Apr '13

30 Apr '13

Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual "The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA". All my values are above 0.4.... Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. Attached is the table again, Thanks Rotem > The values look about right in the table. Your pipeline looks ok, > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output > of mri_vol2vol (fa_FOLDER-NAME.nii). > doug > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > Hi all, > > I run into somthing that seems odd to me and wanted to consult - > > I run the following script for getting the FA values from my DTI > > scans: > > > > 1) dt_recon --i > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > 2) tkregister2 --s fsaverage --surf white --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > > -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > -fthresh 0.2 -fmax 1 > > 4) mri_vol2vol --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > FOLDER-NAME --interp nearest --o > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > 5) tkregister2 --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > 6) mri_segstats --seg > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > --sum > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > I got a table with all the FA values (see attached), for each > > segment, but I suspect a problem: I think that the values are too > > high (I set the threshold to 0.2-1), am I right ? > > Can u guide me regarding what I can do to solve the problem ? in > > addition I attached a figure of the corpus-callosum, in which I'm > > interested - i't seems that the green area in not big enough, is > > this fixable ? > > > > Thanks ! > > > > Rotem >

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R: Re: R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 30 Apr '13

30 Apr '13

Hi Anastasia, when I run the configuration file (which I'm attaching)ERROR: Could not find CVS template I apologize but which is the correct directory of CVS template? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 26-apr-2013 20.08 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts Hi Stefano - Just use the default for that, you don't need to specify the location. a.y On Sun, 21 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > I apologize but I do not find CVS template? Where it should be located? > > Thank you very much, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 9-apr-2013 17.50 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: incomplete tracts > > > Hi Stefano - Did you try CVS for the inter-subject registration? It > doesn't look like it from the configuration file. > > a.y > > On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > yes, I tried.I'm attacking the last configuration file that I used. > > > > Thanks, > > > > > > Stefano > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 9-apr-2013 1.42 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > What registration methods are you using for the intra-subject and > > inter-subject registration? Have you tried the different options? > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-apr-2013 18.57 > > > A: <stdp82(a)virgilio.it> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > > > > What you say "again" you mean with 5.2? > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia, > > > > yes, for some subject the low-b volume is in the end. > > > > Some subjects have again incomplete tracts. > > > > I'm attacking an example of configuration file that I'm using. > > > > I hope that you can check it please. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 18.45 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > > > volume in the end didn't run correctly, right? In that case, I didn't > > need > > > > to see anything, you were going to try running 5.2. > > > > > > > > a.y > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Hi Anastasia, > > > > > could I send you the data of a subject that I don't run correctly? > > > > > > > > > > I still have some subjects with tracts incomplete and I do not know if > > > it depends > > > > from > > > > > my analysis or whether the images are not good. > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 5-apr-2013 17.37 > > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > > > tractography initialization issue, I strongly recommend running 5.2 > > with > > > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > > > > > You can also upload an example data set with issues (include: dmri, > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > > > Hope this helps, > > > > > a.y > > > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > thanks for the help. There is also a line option in freeview. > > However > > > we still > > > > have > > > > > > brains with missing tracks, I rerun them with increasing the ncpts > > and > > > registering > > > > > to > > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > > confident that our > > > > > bvel > > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > > processed brains > > > > > where > > > > > > there are no missing tracts. Further sometimes only one tract is > > > missing, > > > > sometimes > > > > > it > > > > > > is more severe. We could not find any correlation with recon-all > > > problems or DTI > > > > raw > > > > > > data issues (all but one were without moving artefacts). Since we > > are > > > running > > > > > bedpostx > > > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > > > might it be an > > > > > issue > > > > > > that is solved with installing the 5.2. version? Would that run in > > > freesurfer > > > > 5.1.0? > > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > > > Kind regards > > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines > > in > > > the corpus > > > > > > callosum follow the curvature of the corpus callosum, and in a > > > sagittal > > > > > > view to see if the lines in the cingulum follow the curvature > > of > > > the > > > > > > cingulum. Does this make sense? > > > > > > > > > > > > a.y > > > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > > > our > > > > > > gradient table is wrong but I am not really sure how to > > analyse > > > > > > these informations. You wrote to Stefano the lines have to > > point > > > in > > > > > > the right direction and that the eigenvectors are not pointing > > > along > > > > > > his corpus callosum. Can you give me a more detailed > > description > > > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid > > on > > > > > > dtifit_FA. > > > > > > > > > > > > Thanks and kind regards > > > > > > Benjamin > > > > > > > > > > > > _______________________________________________ > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > http://gerit-orientation.blogspot.com > > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > 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 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. > > > > > > > >_______________________________________________ > 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. > > > >_______________________________________________ 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.

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Fwd: recon-all -autorecon2 bug?
by Ioana Coman 30 Apr '13

30 Apr '13

Hi, I am facing the same error like Miklos Argyelan http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html and Jitesh Joshi http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28071.html I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 with the updated version of the bbregister script. Thank you, Ioana

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Re: [Freesurfer] Freesurfer Digest, Vol 110, Issue 20
by Rotem Saar 29 Apr '13

29 Apr '13

Dear Doug, I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:) Thanks for all your help !! Rotem ------------------------------ > > Message: 9 > Date: Thu, 11 Apr 2013 12:51:38 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] DTI: problems with (high) FA values > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5166EA1A.8000701(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > That is a good value, so the regis not the problem. If you upload your > dt_recon folder as well as your recon-all folder for that subject I'll > take a look. > doug > > On 04/11/2013 10:02 AM, Rotem Saar wrote: > > Hi Douge, > > > > In your last reply to my email (that contained questions regarding > > some really high FA values - see recent emails below), u asked me to > > write u the first value in register.dat.mincost - > > I'm copying the line I have: > > > > 0.280554 140.210312 156.795241 11.152485 > > > > Does this takes us one step further towards understanding the problem > > and its solution ? > > > > Thanks for your time, > > Rotem > > > > > > > > On 04/07/2013 06:48 AM, Rotem Saar wrote: > > > Hi Doug, > > > > > > Thanks for your answer. > > > I changed the last step as u suggested, but I think I need to clarify > > > my question: > > > Indeed values of the CC looks OK, but don't u think other values, like > > > the ventricles are too high ? > > *_yes, the ventricles look too high_* > > > > > > When I first run the script, I got all values and looked the the CC - > > > it looked fine. Then, I wanted to validate with some other regions, > > > just to show that I got the appropriate (low) FA values for regions I > > > don't expect to see high values in - and things looked odd (too high). > > > > > > I remember Bruce also writing me that the values seems a little high, > > > but we didn't further discuss. I read the following this link: > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual > > > > > > "The CC has an average FA of about 0.75, gyral parcellations are about > > > 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as > > > expected because the CC is highly directional with no crossing fibers > > > so we would expect the CC to have the highest FA. The gyral white > > > matter is also directional but has fibers crossing in them, so one > > > expects the FA to be lower than CC. The gray matter (putamen) is still > > > lower. The ventricle has no fibers, so we expect it to have the lowest > > > FA". > > > > > > All my values are above 0.4.... > > > > > > Additionally, if in the last step I'm writing --seg > > > /usr/local/freesurfer/ > > subjects/Rotem_try/mri/wmparc.mgz > > > > > > why do I get 182 regions ? in my wmparc.stats I have only 70... > > The wmparc includes all the subcortical and cortical regions too, but > > only the WM regions are reported in the wmparc.stats file. *_To only > > report the WM regions, add to mri_segstats --ctab > > $FREESURFER_HOME/_**_WMParcStatsLUT.txt_* > > > > > > I'm probably doing something wrong, but I can't really point to the > > > problem, thus asking for your help. > > _*I don't know either. If I had to guess, I'd say it is a registration > > problem. What is the first value in register.dat.mincost?*_ > > doug > > > > > > Attached is the table again, > > > > > > Thanks > > > Rotem > > > > > > > > > The values look about right in the table. Your pipeline looks ok, > > > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the > > > output > > > of mri_vol2vol (fa_FOLDER-NAME.nii). > > > doug > > > > > > > > > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > > > > > Hi all, > > > > I run into somthing that seems odd to me and wanted to > > consult - > > > > I run the following script for getting the FA values from > > my DTI > > > > scans: > > > > > > > > 1) dt_recon --i > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > > > FOLDER-NAME --o > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > > > 2) tkregister2 --s fsaverage --surf white --reg > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > > > --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg > wmparc.mgz > > > > -reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > > -overlay > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > > > -fthresh 0.2 -fmax 1 > > > > 4) mri_vol2vol --mov > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > > > FOLDER-NAME --interp nearest --o > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > > --reg > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > > > 5) tkregister2 --mov > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > > > --targ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > > > --reg > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > > > 6) mri_segstats --seg > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > > > --sum > > > > > > > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > > > > > > > I got a table with all the FA values (see attached), for each > > > > segment, but I suspect a problem: I think that the values > > > are too > > > > high (I set the threshold to 0.2-1), am I right ? > > > > Can u guide me regarding what I can do to solve the > > problem ? in > > > > addition I attached a figure of the corpus-callosum, in > > > which I'm > > > > interested - i't seems that the green area in not big > > enough, is > > > > this fixable ? > > > > > > > > Thanks ! > > > > > > > > Rotem > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 10 > Date: Thu, 11 Apr 2013 17:47:14 +0000 > From: "Yang, Daniel" <yung-jui.yang(a)yale.edu> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and > 5.2.0 > To: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <CD8C6E39.1A7E1%yung-jui.yang(a)yale.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi PPJ and all, > > I found that the 5.2 ? 5.1 difference is primarily seen in the cortical > thickness, and much less so in the aseg.volume. > > Here, I picked right-amygdala volume as an example of aseg.volume and > rh_bankssts_thickness as an example of rh.aparc.thickness. > > While the correlation between the two versions of right-amygdala is r = > .92 (n = 161), that of the rh_bankssts_thickness is r = .45. > > Presumably I believe the correlation should be > .90 for a strong > continuity between the two versions? > > Do you have anything in the cortical thickness? > > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > From: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br > <mailto:ppj@netfilter.com.br>> > Date: Wednesday, April 10, 2013 11:07 AM > To: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu>> > Cc: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto: > fischl(a)nmr.mgh.harvard.edu>>, "freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > Ok, I'll try to put together a stat from aparc too. > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel <yung-jui.yang(a)yale.edu > <mailto:yung-jui.yang@yale.edu>> wrote: > Hi PPJ, > > Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any > chance you could also provide the cortical thickness of the 2009 atlas > (e.g., rh)? > > I will take a look into the aseg.volume in my data too. > > Best, > Daniel > > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454<tel:%28203%29%20737-5454> > > From: Pedro Paulo de Magalh?es Oliveira Junior <ppj(a)netfilter.com.br > <mailto:ppj@netfilter.com.br>> > Date: Wednesday, April 10, 2013 10:49 AM > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto: > fischl(a)nmr.mgh.harvard.edu>> > Cc: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu>>, " > freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" < > freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > You'll find attached some preliminary data of the comparison we did among > versions. > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi PPJ > That's exactly what we are doing. Good to hear its stable for you > Bruce > > > > On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalh?es Oliveira Junior< > ppj(a)netfilter.com.br<mailto:ppj@netfilter.com.br>> wrote: > > I have processed more that 600 brains with both versions in the last weeks > and the only difference I'm seeing between version 5.2.0 and 5.1, besides > the obvious new features, is processing time. > > Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. > > Besides that there's no visible difference in terms of cortical thickness, > volumes, etc. > > If you have access to computer resources to spare you can run recon-all of > both versions in some well known database of images and do a more formal > test. > > > > > > > --------------------------------------------------------------------- > Pedro Paulo de Magalh?es Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br<http://www.netfilter.com.br> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel <yung-jui.yang(a)yale.edu > <mailto:yung-jui.yang@yale.edu>> wrote: > Dear FreeSurfer Experts and Users, > > Did anyone find similar things using FS 5.2 (please see my previous post > below)? That is, FS 5.2 is including more non-cortical "black spaces" > within pial surfaces, compared to FS 5.1? > > I'm not interested in nitpicking but I feel this is a rather serious > issue, so I would like to raise it again before it's completely forgotten. > > At the meantime I keep receiving Emails from people asking me this issue. > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454<tel:%28203%29%20737-5454> > > > > > > > On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.yang(a)yale.edu<mailto: > yung-jui.yang(a)yale.edu>> wrote: > > > > >Posting one of the brains. > > > >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn > > > > > >It seems to me that neither version is perfect; however, 5.2.0 is > >capturing more "black spaces" in the region I'm looking at. > > > >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). > > > >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the > >region I examined with my samples, it's not a systematic "predictable" > >bias. > > > >Any solution? > > > >-- > >Yung-Jui "Daniel" Yang, PhD > >Postdoctoral Researcher > >Yale Child Study Center > >New Haven, CT > >(203) 737-5454<tel:%28203%29%20737-5454> > > > > > > > > > > > > > >On 3/18/13 6:27 PM, "Matt Glasser" <matt(a)ma-tea.com<mailto: > matt(a)ma-tea.com>> wrote: > > > >>Do the surfaces look correct in these regions? You might post some > >>screenshots of subjects who have a big difference between 5.1 and 5.2 > >>with > >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight > >>the difference. Without this kind of info, its hard to know which was > >>more correct, 5.1 or 5.2. > >> > >>Peace, > >> > >>Matt. > >> > >>On 3/18/13 5:13 PM, "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu > <mailto:ridatta@mail.med.upenn.edu>> wrote: > >> > >>>I concur. I have seen similar results in primary visual cortex from ~40 > >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to > >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. > >>> > >>>Ritobrato Datta, Ph.D. > >>>Post Doctoral Researcher > >>>Department of Neurology > >>>University of Pennsylvania School of Medicine > >>>3rd Floor, Room 312 > >>>3710 Hamilton Walk (Goddard Laboratories) > >>>Philadelphia, PA 19104-6241 > >>>email - ridatta(a)mail.med.upenn.edu<mailto:ridatta@mail.med.upenn.edu> > >>> > >>> > >>>----- Original Message ----- > >>>From: Daniel Yang <yung-jui.yang(a)yale.edu<mailto:yung-jui.yang@yale.edu > >> > >>>To: freesurfer(a)nmr.mgh.harvard.edu<mailto: > freesurfer(a)nmr.mgh.harvard.edu> > >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) > >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > >>> > >>>Dear FreeSurfer Experts, > >>> > >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 > >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in > >>>particular. > >>> > >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in > >>>5.2.0. They are significantly different, t(160) = 56.71. > >>> > >>>The correlation between the two versions is r = .33 > >>> > >>>Is this something possible?? I can't see what went wrong in my > >>>procedures. > >>> > >>>Thanks! > >>>Daniel > >>> > >>>-- > >>>Yung-Jui "Daniel" Yang, PhD > >>>Postdoctoral Researcher > >>>Yale Child Study Center > >>>New Haven, CT > >>>(203) 737-5454<tel:%28203%29%20737-5454> > >>> > >>>_______________________________________________ > >>>Freesurfer mailing list > >>>Freesurfer(a)nmr.mgh.harvard.edu<mailto: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 mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

2 2

convert labels to volumetric masks
by limengsecret 29 Apr '13

29 Apr '13

Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng

2 1

how to register my surface label to the epi volume
by limeilingcheng 29 Apr '13

29 Apr '13

Hi all, Now I got some results by freesurfer, finally I selected two vertexs which the coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were left superiortemporal and right superiortemporal. In the following step, I want to make the left and right superiortemporal as ROIs and observe the functional connectivity between the ROIs and the voxels in the whol brain. However, it is difficult for me to understand how to register this surface label to the epi volume. and how to created the masks in FSL using the labels and Harvard-Oxford atlas to ensure the correct anatomical location. 2013-04-29 limeilingcheng

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Re: [Freesurfer] adding grey matter
by Claudia Dacquino 29 Apr '13

29 Apr '13

The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Claudia > > can you describe the problems? And cc the list so that others can help? > thanks > > Bruce > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? >> >> I'm trying to upload data, but I've problems with your server. >> Cheers, >> Claudia >> >> >> 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Claudia >> >> it really depends on the individual case and what's causing the >> exclusion. Does the wm.mgz look accurate? If so, you may have a >> topological defect that is being fixed incorrectly. Usually we >> focus on fixing the white boundary and that will also correct >> the pial. You can set the expected gray matter intensities in >> the xopts file, but that is rarely necessary and only if your >> gray matter looks very different than the sequences we are used >> to. >> >> If you can't sort it out feel free to upload you data. >> >> cheers >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Hi Freesurfers,I have a question about pial editing. >> I have some reconructions in which there's a lot of >> grey matter excluded, >> and consequently white metter too. I did correct >> these images manually by >> control points editing, and then autorecon2-cp >> autorecon3, but some cortical >> grey matter continues to not be included in the pial >> surface, and I have >> white matter areas that are still not included in >> either the pial or white >> matter boundaries. >> Is there anyother ethods for adding grey matter in >> the pial surfeces other >> than editing control points (such as by editing >> voxels to add grey matter), >> or something like that? >> Thanks for your help. >> Claudia >> >> >> >> >> 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<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 12

Trouble with flip angle map when computing T1 maps
by Johannes Klein 29 Apr '13

29 Apr '13

Dear all, I've had some trouble feeding a flip angle map into mri_ms_fitparms. If I don't provide it, the estimates look fine; with the FA map however, all brain voxels in the resultant T1.mgz are set to 50000. I've checked that all images are registered, and the nominal values in the FA map look good to me. I'm running Freesurfer 5.1.0 Here's the output: johannes$ mri_ms_fitparms -afi B1Map_in_degrees.mgz DESPOT_FA_18.mgz DESPOT_FA_4.mgz t1_fs using flip angle map DESPOT1HIFI_B1Map_in_degrees.mgz with nominal value 60.0 degrees reading DESPOT_FA_18.mgz...TE = 3.70, TR = 8.00, flip angle = 18.00 reading DESPOT_FA_4.mgz...TE = 3.70, TR = 8.00, flip angle = 4.00 using 2 FLASH volumes to estimate tissue parameters. parameter rms = 77.083 non-equal flip_angle found for the volume 1. Flip_angle is set to zero. TR = 8.00, TE = 3.70, Flip_angle = 0.00 are used writing PD estimates to t1_fs/PD.mgz... writing T1 estimates to t1_fs/T1.mgz... writing residual sse to t1_fs/sse.mgz... writing faf map to t1_fs/faf.mgz... writing synthetic images to t1_fs/flash18.mgz... writing registration matrix to t1_fs/flash18.lta... writing synthetic images to t1_fs/flash4.mgz... writing registration matrix to t1_fs/flash4.lta... parameter estimation took 1 minutes and 18 seconds. Any thoughts on what I'm doing wrong? Thanks for your help, Johannes

1 0

Re: [Freesurfer] adding grey matter
by Claudia Dacquino 29 Apr '13

29 Apr '13

Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Claudia Dacquino <claudia.dacquino(a)gmail.com> > Hi Bruce, > I think wm.mgz it's accurate enough, but what you mean? > I'm trying to upload data, but I've problems with your server. > Cheers, > Claudia > > > 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Claudia >> >> it really depends on the individual case and what's causing the >> exclusion. Does the wm.mgz look accurate? If so, you may have a topological >> defect that is being fixed incorrectly. Usually we focus on fixing the >> white boundary and that will also correct the pial. You can set the >> expected gray matter intensities in the xopts file, but that is rarely >> necessary and only if your gray matter looks very different than the >> sequences we are used to. >> >> If you can't sort it out feel free to upload you data. >> >> cheers >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Hi Freesurfers,I have a question about pial editing. >>> >>> I have some reconructions in which there's a lot of grey matter excluded, >>> and consequently white metter too. I did correct these images manually by >>> control points editing, and then autorecon2-cp autorecon3, but some >>> cortical >>> grey matter continues to not be included in the pial surface, and I have >>> white matter areas that are still not included in either the pial or >>> white >>> matter boundaries. >>> Is there anyother ethods for adding grey matter in the pial surfeces >>> other >>> than editing control points (such as by editing voxels to add grey >>> matter), >>> or something like that? >>> Thanks for your help. >>> Claudia >>> >>> >>> >> >> 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<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. >> > >

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