Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

asegstat values pre and post editing
by Claudia Dacquino 24 Jul '13

24 Jul '13

Dear Freesurfers, we recently processed a sample of adult patients and then we reran autorecon-2 and autorecon-3 after editing contol points, white matter and pial surface. We exported the asegstat table both pre and post editing, and we got different volumes for most of the subjects. How is that possible, given that the kind of editing we performed is not supposed to affect subcortical segmentation? Thanks a lot. Claudia

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Average cortical diffusion
by Afaf Elsarraj 24 Jul '13

24 Jul '13

Hi, I've registered the mean diffusivity (MD) values on the cortical surface. Can you please tell me how to get the average cortical MD of the whole hemisphere for each subject, rather than the regional cortical MD. Kind regards, Afaf This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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a second "subjcts" folder...
by Gonzalo Rojas Costa 24 Jul '13

24 Jul '13

Hi: I has a "subjects" folder in one physical harddisk... How can I continue processing more images in another "subjects" folder in a new physical harddisk without erasing the first one ?... Sincerely Gonzalo Rojas Vosta -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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qdec -- confused by glm output for custom ROIs
by Maria Kharitonova 24 Jul '13

24 Jul '13

Hello, I have a question regarding the interpretation qdec's output for the custom ROI's thickness estimates. I ran an analysis comparing cortical thickness in children with and without ADHD (categorical variable), controlling for age and demeaned ICV, using 5.0. After controlling for multiple comparisons with the monte-carlo simulation, there were 2 ROIs in the right hemisphere that were significantly different across groups: a regions near parstriangularis and near medial orbital cortex. I then created custom ROIs for these regions, and extracted thickness estimates for each participant for each of these ROIs. I then decided to do a "sanity check" of the data -- run a linear regression on these extracted thickness estimates to see if the mean thickness in each region differed as a function of diagnosis (again controlling for age and demeaned ICV). By logic, I should see differences in thickness estimates for these 2 ROIs across the 2 groups, because that's how these ROIs were defined, right? But in reality, there is no difference at all between groups, with p-values around .9! I tried saving the ROIs by both manually tracing and with the mri_surfcluster command -- I get very similar estimates of thickness (correlation coefficients of .9 across 32 subjects). So that's not the cause of error. Both manual and automatic extraction fails to find differences across subjects that I described above. What am I missing? is the original GLM in QDEC that finds differences between groups doings something other than looking for differences in each voxel/region across groups? Thanks in advance for the help! Maria ******************************* Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital Division of Developmental Medicine Harvard Medical School

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Re: [Freesurfer] error with fast_selxavg3
by Leila Reddy 24 Jul '13

24 Jul '13

Hi Doug, Thanks for your reply. Yes, it does work with a longer -refeventdur. In fact, I had tried that yesterday before posting my original message but I'd forgotten to make the corresponding changes to the 3rd column of the paradigm file and so kept getting the error message. The shortest I can bring -refeventdur down to is 0.05. Anything smaller causes the same error as before. In the end it's not a huge problem for us if we have to set an event duration of 50ms instead of 16.6 ms but I'd like to understand what is going on. So, I wondered if the error had anything to do with the fact that when I run mkcontrast-sess the script automatically sets -TER to 0.05. I re-ran the analysis and set -TER and -refeventdur to 0.016 in mkanalysis-sess. The analysis runs with no error for selxavg-sess and visually (with tksurfer) the results look the same as with -TER and -refeventdur set to 0.05. Since the help for mkanalysis-sess -TER says " It is best to know what you are doing if you are going to change this.", I'd like to know if it makes sense to change the TER like I have. What does the TER achieve (if that's not too complicated a question)? Thanks again, Leila

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Re: [Freesurfer] infant atlas segmentation
by Mark Plantz 24 Jul '13

24 Jul '13

Finally got the registration to work. However, it looks like the out of bounds regions (in red) are still present (even though the regions are well within our boundaries). Is that expected since they were labeled in the original segmentation volume? Is there anyway to correct those? Thanks for all of the help! - Mark p.s. I attached a picture of the original brain.mgz file viewed with the corrected segmentation volume On Wed, Jul 24, 2013 at 12:22 PM, Mark Plantz < markplantz2016(a)u.northwestern.edu> wrote: > Finally got the registration to work. However, it looks like the out of > bound regions (in red) are still prevalent. Is that expected since they > were present in the original segmentation volume? Would there be anyway to > correct those? > > Thanks for all the help! > > - MP > > > On Wed, Jul 24, 2013 at 11:11 AM, Mark Plantz < > markplantz2016(a)u.northwestern.edu> wrote: > >> Nevermind, it turned out to be a permissions issue. Thanks! >> >> >> On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz < >> markplantz2016(a)u.northwestern.edu> wrote: >> >>> Thanks for the reply Doug. I recently ran the bbregister command and >>> attempted to view the results using tkregister2. I received the following >>> error: >>> >>> dhcp-165-124-23-232:Desktop IngvalsonLab$ tkregister2 --mov >>> /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/mri/avgseg.mgz >>> --reg /Users/IngvalsonLab/Desktop/register.dat --surf >>> >>> tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume >>> /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/mri/avgseg.mgz >>> reg file /Users/IngvalsonLab/Desktop/register.dat >>> LoadVol 1 >>> ZeroCRAS 0 >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ >>> Diagnostic Level -1 >>> regio_read_register(): Undefined error: 0 >>> Error reading subject from /Users/IngvalsonLab/Desktop/register.dat >>> ERROR: reading /Users/IngvalsonLab/Desktop/register.dat >>> dhcp-165-124-23-232:Desktop IngvalsonLab$ >>> >>> I do not believe it is a permissions issue? >>> >>> Could it simply be that the register was bad? Is there an easy way to >>> open up the register.dat.mincost file to check the registration? >>> >>> Thanks again, >>> >>> MP >>> >>> >>> On Tue, Jul 23, 2013 at 9:32 PM, Douglas Greve < >>> greve(a)nmr.mgh.harvard.edu> wrote: >>> >>>> >>>> You can try using bbregister. Normally, you don't use bbregister on a >>>> segmentation, but the segmentation index numbers just happen to be >>>> "T1-weighted". >>>> doug >>>> ps. Please remember to copy the list when responding. thanks! >>>> >>>> >>>> >>>> On 7/23/13 9:51 AM, Mark Plantz wrote: >>>> >>>> Hi Doug, >>>> >>>> Sorry about that vague explanation. So I received a series of >>>> infant brain atlases from a UNC medical research group ( >>>> http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…) >>>> I have a series of infant MRI's that I would like to segment (using the >>>> infant atlases, instead of the default adult atlas in FreeSurfer). >>>> >>>> As a preliminary step, I was attempting to check the alignment of >>>> one of the atlas files ('avgseg.mgz') with one of the input brains >>>> ('brain.mgz'). [I attached these two files, just in case]. >>>> >>>> So my command line would be: >>>> >>>> tkmedit $Subject brain.mgz -segmentation avgseg.mgz >>>> $FREESURFER_HOME/FreeSurferColorLUT.txt >>>> >>>> The result was the previously attached image. I was just wondering if >>>> there is any way to shift the two images manually so the alignment is >>>> better? Or maybe the two files are simply not compatible with one another? >>>> >>>> Thanks for all the help! >>>> >>>> Best, >>>> >>>> Mark >>>> >>>> >>>> >>>> >>>> On Mon, Jul 22, 2013 at 3:53 PM, Douglas N Greve < >>>> greve(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> Hi Mark, I have no idea what you are doing. Can you send a command >>>>> line? >>>>> Are either of the images generated by FS? >>>>> doug >>>>> >>>>> >>>>> >>>>> >>>>> On 07/22/2013 03:56 PM, Mark Plantz wrote: >>>>> > Hello FreeSurfers, >>>>> > >>>>> > I recently obtained a set of infant templates. Out of curiousity, >>>>> > I decided to view one of the input brains with the provided segmented >>>>> > volume file. It appears that there is some misalignment. I wouldn't >>>>> > expect the alignment to be perfect, since I am basically overlaying >>>>> an >>>>> > average of multiple brains onto one. However, it looks like this >>>>> > misalignment may be caused by either: 1.) the segmentation volume >>>>> file >>>>> > being shifted down or 2.) the slices not lining up properly (i.e. one >>>>> > file starts before the other). >>>>> > >>>>> > Any ideas what could cause a problem like this? Could it be that >>>>> > the segmented files are simply not compatible with FreeSurfer? >>>>> > >>>>> > Thanks for the help, >>>>> > >>>>> > Mark >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > 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. >>>>> >>>>> >>>> >>>> >>> >> >

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recon-all error
by Smian 24 Jul '13

24 Jul '13

Hi everyone, To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700 I have already performed recon-all on MPRAGE data. I have also carried out the following steps: 1) Reconstruct cortical surface 2) Register T1 to the surface 3) Sample T1 at a given cortical depth 4) Register surface to fsaverage I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this? Any help would be appreciated! Thank you!

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Re: [Freesurfer] infant atlas segmentation
by Douglas Greve 24 Jul '13

24 Jul '13

You can try using bbregister. Normally, you don't use bbregister on a segmentation, but the segmentation index numbers just happen to be "T1-weighted". doug ps. Please remember to copy the list when responding. thanks! On 7/23/13 9:51 AM, Mark Plantz wrote: > Hi Doug, > > Sorry about that vague explanation. So I received a series of > infant brain atlases from a UNC medical research group > (http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…) > I have a series of infant MRI's that I would like to segment (using > the infant atlases, instead of the default adult atlas in FreeSurfer). > > As a preliminary step, I was attempting to check the alignment of > one of the atlas files ('avgseg.mgz') with one of the input brains > ('brain.mgz'). [I attached these two files, just in case]. > > So my command line would be: > > tkmedit $Subject brain.mgz -segmentation avgseg.mgz > $FREESURFER_HOME/FreeSurferColorLUT.txt > > The result was the previously attached image. I was just wondering if > there is any way to shift the two images manually so the alignment is > better? Or maybe the two files are simply not compatible with one another? > > Thanks for all the help! > > Best, > > Mark > > > > > On Mon, Jul 22, 2013 at 3:53 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Mark, I have no idea what you are doing. Can you send a command > line? > Are either of the images generated by FS? > doug > > > > > On 07/22/2013 03:56 PM, Mark Plantz wrote: > > Hello FreeSurfers, > > > > I recently obtained a set of infant templates. Out of > curiousity, > > I decided to view one of the input brains with the provided > segmented > > volume file. It appears that there is some misalignment. I wouldn't > > expect the alignment to be perfect, since I am basically > overlaying an > > average of multiple brains onto one. However, it looks like this > > misalignment may be caused by either: 1.) the segmentation > volume file > > being shifted down or 2.) the slices not lining up properly > (i.e. one > > file starts before the other). > > > > Any ideas what could cause a problem like this? Could it be that > > the segmented files are simply not compatible with FreeSurfer? > > > > Thanks for the help, > > > > Mark > > > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 <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. > >

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how to use mri_surf2surf to smooth sulc ?
by fatma zribi 24 Jul '13

24 Jul '13

Dear Bruce, Would you mind help me. I have to smooth a sulc data with the command mri_surf2surf but it don't work. I have triyed with curv data it work very well i have put this command : mri_surf2surf --hemi lh --s s000_open_brain_sanlm_+TIR_normlalized --sval sulc --src_type sulc --fwhm-trg 10 --trg_type sulc --tval sulc.10 the message of error tell me that the type not defined Thank you very much for your help. With best regards, Fatma

2 1

mri_ca_train bug
by Mark Plantz 24 Jul '13

24 Jul '13

Hello freesurfers, I recently ran into a problem with mri_ca_train, a function that creates a .gca atlas from a manually segmented volume and input volume(s). My command line is: mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca The results: processing subject CMH-11461, 1 of 1... reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/norm.mgz filling holes in the GCA... 404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled) computing covariances for subject CMH-11461, 1 of 1... average std = 6.1 using min determinant for regularization = 3.7 298584 singular and 4268 ill-conditioned covariance matrices regularized writing trained GCA to /Users/IngvalsonLab/Desktop/atlas1.gca... classifier array training took 0 minutes and 27 seconds. dhcp-165-124-23-230:LabMRIData IngvalsonLab$ dhcp-165-124-23-230:LabMRIData IngvalsonLab$ dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas1.gca reading T1 data from subject's mri/T1.mgz directory training on 2 subject and writing results to /Users/IngvalsonLab/Desktop/atlas1.gca *************************************************************************** processing subject CMH-11460, 1 of 2... reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz *************************************************************************** processing subject CMH-11461, 2 of 2... reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/T1.mgz filling holes in the GCA... 468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled) computing covariances for subject CMH-11460, 1 of 2... GCAupdateNodeCovariance(17, 35, 28, 4): could not find label dhcp-165-124-23-230:LabMRIData IngvalsonLab$ According to the fswiki, the same bug was eliminated in the 2009 version. For some odd reason, this command works with one subject, but not with multiple subjects. Any ideas? Thanks in advance, MP

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Freesurfer July 2013