Sorry, I did not see that one of the volumes was 256x256x255. I cannot replicate here on your data using 5.3 under linux. Can you say exactly what you do in freeview? Also, what version of FS are you using? And what platform?
On 08/03/2016 06:50 AM, Isabelle Deschamps wrote: > I had the problem before and was told the the output of mri_info > should be 256 x 256 x 256 for the dimensions of the brainmask and T1. > When I run mri_info on the brainmask.mgz that I modified I have 256 x > 256 x 255 but the T1 I have 256 x 256 x 256. The zstart and zend are > also different between the brainmask and T1. Could that be the source > of the problem? > > *Modified brainmask:* > mri_info > /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz > > Volume information for > /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz > type: MGH > dimensions: 256 x 256 x 255 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -127.5, zend: 127.5 > > *T1:* > mri_info > /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz > Volume information for > /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > > *Non-modified brain mask:* > mri_info /Users/Isabelle/Desktop/S14/brainmask_orig.mgz > Volume information for /Users/Isabelle/Desktop/S14/brainmask_orig.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > > I am not sure why I get this error and why the change in dimensions, > zstart and zend between the brainmask and T1. For all other > participants that do not have an error the information of mri_info for > dimensions, zstart and zend is the same for the brainmask and T1. So I > am very confuse as to why these 4 participants are exiting with the > same error. I am not sure what I am doing wrong in this case. > > Thanks, > > Isabelle > > On 3 Aug 2016, at 06:00, freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-ow...@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> > >> Today's Topics: >> >> 1. DTI of frontostriatal tracts (Ritobrato Datta) >> 2. Re: Multiple Comparison Question for surface-based analyses >> (Douglas N Greve) >> 3. Re: brain mask and T1 are not the same size (Douglas N Greve) >> 4. Save Overlay via Command Line (Jordan Chad) >> 5. Re: MNI coordinates of all the vertices of fsaverage >> (Douglas N Greve) >> 6. Retinotopy questions (Xiaomin Yue) >> 7. Re: DTI of frontostriatal tracts (Anthony Dick) >> 8. Re: DTI of frontostriatal tracts (Ritobrato Datta) >> 9. Re: Labels to MNI152, SPM compatible (Thomas Yeo) >> 10. Re: Multiple Comparison Question for surface-basedanalyses >> (Ajay Kurani) >> 11. mapping error (Caroline Beelen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 2 Aug 2016 12:26:43 -0400 (EDT) >> From: Ritobrato Datta <rida...@mail.med.upenn.edu >> <mailto:rida...@mail.med.upenn.edu>> >> Subject: [Freesurfer] DTI of frontostriatal tracts >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Message-ID: >> <1643573287.53129960.1470155203784.javamail.r...@zimbra.upenn.edu >> <mailto:javamail.r...@zimbra.upenn.edu>> >> Content-Type: text/plain; charset=utf-8 >> >> Hello All, >> >> We are studying adolescents with HIV and are interested in >> frontostriatal tracts (anything from frontal cortex to >> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. >> >> Is anyone aware of DTI based atlases where these tracts are defined >> in MNI or some other standard space ? >> >> Any suggestions will be very helpful. >> >> Best >> >> Ri >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 2 Aug 2016 12:54:01 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] Multiple Comparison Question for >> surface-based analyses >> To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <57a0d029.7020...@nmr.mgh.harvard.edu >> <http://nmr.mgh.harvard.edu>> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> I have been doing simulations similar to #1 (Eklund) using >> surface-based analysis on both thickness and fMRI. I'll prepare a report >> of the results, but the early indications are that the same effect is in >> play, though it does not look like the effects are as bad as in Eklund. >> >> For thickness analysis using applied smoothing of 5 or 10 mm FWHM, for a >> voxel-wise threshold of .001, the false positives are appropriate (ie, >> 5%). For a voxel-wise threshold of .01, the false positives is only a >> little off (about 7%); for a voxel-wise threshold of .05, the FPR is >> about 13%. If the data are not smoothed at all, then the false positive >> rates go way up. The reason appears to be the same as found in Eklund >> (ie, the autocorrelation function has a heavier-than-Gaussian tail). I >> did the analysis by randomly selecting 40 subjects from a homogeneous >> data set of 809 subjects aged 18-25. I then made two groups of 20 >> subjects each and ran a two-group test, then found clusters significant >> based on our Monte Carlo (Gaussian) simulations. I repeated this several >> thousand times. Any significant clusters were interpreted as false >> positives. These results are much better than Eklund, but Eklund was >> analyzing fMRI data. >> >> I'm still working on the fMRI data. It is much more complicated because >> the results depend on the assumed stimulus schedule (eg, 10 sec blocks >> vs 30 sec blocks) and whether a one-group or two-group anaysis is done; >> nuisance variables also play a role. At very low cluster-forming >> thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01, >> the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is >> all for an applied smoothing level of 5mm. >> >> All of these results are preliminary, so don't take them as true and >> established yet. As a reminder, you can always do a permutation test >> using mri_glmfit-sim. Eklund found that permutation did pretty well in >> most cases. >> >> doug >> >> >> On 8/2/16 12:43 AM, Ajay Kurani wrote: >>> Hello Freesurfer Experts, >>> Recently there were two article published regarding clusterwise >>> simulations for volumetric fmri analyses and potential errors for >>> underestimating clusterwise extent thresholds. >>> >>> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >>> 2) biorxiv.org/content/early/2016/07/26/065862 >>> <http://biorxiv.org/content/early/2016/07/26/065862> >>> <http://biorxiv.org/content/early/2016/07/26/065862> >>> >>> One issue pointed out from these articles seems software specific, >>> however the second issue is determining the proper clustersize. The >>> heavy-tail nature of spatial smoothness seems to be ignored and a >>> gaussian shape is generally assumed, leading to an underestimation of >>> the spatial smoothness which can affect cluster size calculations. >>> The issues are highlighted in the second article above. >>> >>> I created my own monte carlo simulation in Freesurfer for a specific >>> brain template and I wanted to find out if these concerns also apply >>> to my surface based simulations? I am not sure if it does since the >>> monte carlo tool is a GRF simulation as opposed to an analytic >>> equation, however given that these articles were highlighted very >>> recently, I wanted to ensure I am running things appropriately for >>> surface based cortical thickness/dti analyses. >>> >>> Thanks, >>> Ajay >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 2 Aug 2016 13:18:09 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] brain mask and T1 are not the same size >> To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <57a0d5d1.20...@nmr.mgh.harvard.edu >> <http://nmr.mgh.harvard.edu>> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> The voxel size and dimensions of all three volumes are the same: 256^3 >> and 1mm^3. Why do you think they are not? >> >> On 08/02/2016 09:17 AM, Isabelle Deschamps wrote: >>> Yes, of course. The upload is now active. >>> >>> Thank you again for your help, >>> >>> Isabelle >>> On 2 Aug 2016, at 08:55, freesurfer-requ...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> >>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >>> >>>> Re: [Freesurfer] brain mask and T1 are not the same size >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@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 >> gr...@nmr.mgh.harvard.edu <mailto: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/ >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 2 Aug 2016 14:17:28 -0400 >> From: Jordan Chad <jc...@research.baycrest.org> >> Subject: [Freesurfer] Save Overlay via Command Line >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> <CA+FdjQX9T0cr50M4awGdW0YJHM3n32FrFcQ9AvGM_+=vmb1...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hello, >> >> I am trying to perform between-subject statistics on cortical DTI data in >> certain ROIs. >> >> I can do this by overlaying the DTI data on the surfaces on tksurfer, >> load >> and mask the label with the ROI, and then go to File -> Save Overlay. >> After >> doing this for all subjects I can perform statistics on the output files. >> >> However, it is not practical to do this for all >200 subjects for >> each ROI. >> Is there a way to go about this process on the command line? >> >> Thank You, >> Jordan Chad >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160802/080b7431/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 2 Aug 2016 15:40:33 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] MNI coordinates of all the vertices of >> fsaverage >> To: Sabin Khadka <mr.sabinkha...@gmail.com>, >> "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <57a0f731.9050...@nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> By default they are in talairach. But you can get mni305 by adding >> --nofixmni to the surfcluster command line >> >> On 08/02/2016 03:36 PM, Sabin Khadka wrote: >>> Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From >>> previous post you mentioned these are in mni305 space but if I look at >>> the log file it say TalX, TalY, TalZ. I am a little confused. >>> >>> And how can I convert these coordinates to MNI152 space? >>> >>> thanks for your help. >>> >>> Cheers, >>> Sabin Khadka >>> >>> On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> ps. you can always just load the xyz in the label into matlab and >>> compute the centroid >>> >>> >>> On 8/1/16 10:23 AM, Sabin Khadka wrote: >>>> Anyone? >>>> >>>> Cheers, >>>> Sabin Khadka >>>> >>>> On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka >>>> <mr.sabinkha...@gmail.com <mailto:mr.sabinkha...@gmail.com>> wrote: >>>> >>>> Hi Doug, I tried to pick up from the thread below to get MNI >>>> coordinates of each destrieux parcellation region. >>>> >>>> >>>> >>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html >>>> >>>> I created label files from >>>> mri_annotation2label --subject fsaverage --hemi lh(/rh) >>>> --annotation aparc.a2009s --outdir label_destrieux # which >>>> works fine >>>> >>>> And I tried to get the coordinates of each labels using >>>> >>>> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness >>>> --clabel <label file> --sum <output file> --centroid --thmin >>>> 0 --hemi lh --subject fsaverage >>>> >>>> But, all left labels would produce the same coordinates and >>>> so does right labels. (I've attached few example files here >>>> with). Also, it says TalX, TalY, TalZ are these coordinates >>>> in MNI or Talairach? >>>> >>>> Thanks for help. >>>> >>>> >>> >>> 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. >>> >>> >> >> -- >> 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/ >> >> >> >> ------------------------------ >> >> Message: 6 >> Date: Tue, 2 Aug 2016 21:55:38 +0000 >> From: Xiaomin Yue <yu...@hotmail.com> >> Subject: [Freesurfer] Retinotopy questions >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <blu406-eas159bdb45b45ce0f30358a01b3...@phx.gbl> >> Content-Type: text/plain; charset="utf-8" >> >> Hi, >> I am running a retinotopy analysis using fsfast 5.3. ?The design has >> 15 TR blank before and after wedge presented for 30 TR with 7 >> repeats, and ring presented ?for 24 TR with 7 repeats. ?Here is my >> analysis:?mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip >> 15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par. >> The data doesn't look right. ?I assume that the analysis does require >> the stimuli presentation as a full circle, which means that the last >> 15 TR blank was accounted as the stimuli presentation time. If I am >> correct, ?is there simple way to take care of it in mkanalysis-sess? >> Second, the ring and wedge were presented in different frequency. It >> seems that the anslysis-sess does not take this into account in the >> current configration. Is there a way to specify this?? >> Thanks very much for the help.? >> Xiaomin? >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160802/d25a5166/attachment-0001.html >> -------------- next part -------------- >> _______________________________________________ >> 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. >> >> ------------------------------ >> >> Message: 7 >> Date: Tue, 2 Aug 2016 18:34:53 -0400 >> From: Anthony Dick <ad...@fiu.edu> >> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <ef9ff21a-e069-a7b7-74e8-04ab84e11...@fiu.edu> >> Content-Type: text/plain; charset="windows-1252"; format=flowed >> >> Hello, >> >> See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 >> >> Anthony >> >>> On 8/2/16 12:26 PM, Ritobrato Datta wrote: >>>> Hello All, >>>> >>>> We are studying adolescents with HIV and are interested in >>>> frontostriatal tracts (anything from frontal cortex to >>>> caudate/putamen/nucleus accumbens) and tracts connected to the >>>> amygdala. >>>> >>>> Is anyone aware of DTI based atlases where these tracts are defined >>>> in MNI or some other standard space ? >>>> >>>> Any suggestions will be very helpful. >>>> >>>> Best >>>> >>>> Ri >>>> _______________________________________________ >>>> 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. >>>> >>> >> >> -- >> Anthony Steven Dick, Ph.D. >> Associate Professor >> Director, Cognitive Neuroscience Program and Graduate Certificate in >> Cognitive Neuroscience >> Department of Psychology >> Florida International University Modesto A. Maidique Campus AHC4 454 >> 11200 S.W. 8th Street >> Miami, FL 33199 >> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 >> Email: ad...@fiu.edu >> Webpage: http://myweb.fiu.edu/adick >> Join the Society for the Study of Human Development: >> http://www.sshdonline.org >> >> >> >> ------------------------------ >> >> Message: 8 >> Date: Tue, 2 Aug 2016 19:41:51 -0400 (EDT) >> From: Ritobrato Datta <rida...@mail.med.upenn.edu> >> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <1403815860.53391808.1470181311536.javamail.r...@zimbra.upenn.edu> >> Content-Type: text/plain; charset=utf-8 >> >> Many thanks. >> >> Best >> >> Ri >> >> ----- Original Message ----- >> From: Anthony Dick <ad...@fiu.edu> >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Tue, 02 Aug 2016 18:34:53 -0400 (EDT) >> Subject: Re: [Freesurfer] DTI of frontostriatal tracts >> >> Hello, >> >> See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 >> >> Anthony >> >>> On 8/2/16 12:26 PM, Ritobrato Datta wrote: >>>> Hello All, >>>> >>>> We are studying adolescents with HIV and are interested in >>>> frontostriatal tracts (anything from frontal cortex to >>>> caudate/putamen/nucleus accumbens) and tracts connected to the >>>> amygdala. >>>> >>>> Is anyone aware of DTI based atlases where these tracts are defined >>>> in MNI or some other standard space ? >>>> >>>> Any suggestions will be very helpful. >>>> >>>> Best >>>> >>>> Ri >>>> _______________________________________________ >>>> 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. >>>> >>> >> >> -- >> Anthony Steven Dick, Ph.D. >> Associate Professor >> Director, Cognitive Neuroscience Program and Graduate Certificate in >> Cognitive Neuroscience >> Department of Psychology >> Florida International University Modesto A. Maidique Campus AHC4 454 >> 11200 S.W. 8th Street >> Miami, FL 33199 >> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 >> Email: ad...@fiu.edu >> Webpage: http://myweb.fiu.edu/adick >> Join the Society for the Study of Human Development: >> http://www.sshdonline.org >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ------------------------------ >> >> Message: 9 >> Date: Wed, 3 Aug 2016 10:43:40 +0800 >> From: Thomas Yeo <ytho...@csail.mit.edu> >> Subject: Re: [Freesurfer] Labels to MNI152, SPM compatible >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <canzvntaw8ja0f7npk9erqsqpcbhcgxrrvnm7t3wftqtnyn4...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Matyas, >> >> In freeview, looks fine to me. See attached. >> >> Can you send us your screenshot? >> >> Regards, >> Thomas >> >> On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.k...@gmail.com> >> wrote: >>> The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>> comes from >>> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, >>> and the description says it is the FSL MNI152 1mm template interpolated >>> and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume >>> (obtained by putting the FSL MNI152 1mm template through recon-all ). So >>> I supposed it is in MNI305 after it was processed with freesurfer. When >>> I overlap the >>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and >>> Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not >>> in MNI152. >>> >>> When I add the --invertmtx then the result is still the same, empty >>> image. >>> >>> I uploaded those images here: >>> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip , >>> if you want to try yourself. >>> >>> >>> Thank you, >>> >>> Matyas >>> >>> >>> >>> Dne 2.8.2016 v 14:55 Douglas Greve napsal(a): >>>> From the names, it looks like both the seg vol and the template >>>> vol are both in mni152. Where did >>>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>>> come from? One thing you can try is to invert the registration by >>>> adding --invertmtx to the command line. >>>> >>>> >>>> On 8/2/16 8:18 AM, Maty?? Kuhn wrote: >>>>> Hi Freesurfer experts, >>>>> >>>>> I just started to use Freesurfer and I was wondering how can I convert >>>>> images from MNI305 which uses Freesurfer to MNI152 which is used >>>>> by SPM. >>>>> We would like to get MNI152 template of Yeo parcelation >>>>> ( ) >>>>> so we can overlay with our results from SPM fMRI analysis. >>>>> >>>>> I tried this: >>>>> mri_label2vol --seg >>>>> /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz >>>>> \ >>>>> --temp >>>>> /path_to_analysis/Template_T1_IXI555_MNI152.nii \ >>>>> --reg >>>>> $FREESURFER_HOME/average/mni152.register.dat \ >>>>> --o /path_to_analysis/output_mni152.nii >>>>> >>>>> which resulted in image full of zeros (so maybe problem with >>>>> registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152 >>>>> template which is used by Computational anatomical toolbox 12 for SPM >>>>> from Christian Gaser and his group. >>>>> >>>>> Thanks in advance for any suggestions, >>>>> >>>>> Matyas >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://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. >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Screen Shot 2016-08-03 at 10.41.31 AM.png >> Type: image/png >> Size: 222427 bytes >> Desc: not available >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/b575e32f/attachment-0001.png >> >> ------------------------------ >> >> Message: 10 >> Date: Wed, 3 Aug 2016 02:45:47 -0500 >> From: Ajay Kurani <dr.ajay.kur...@gmail.com> >> Subject: Re: [Freesurfer] Multiple Comparison Question for >> surface-basedanalyses >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CA+uskrDgnhv2SaRJHGHUQQVJseuEKQC6ov-=f7n0dyrtsge...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Doug, >> Thank you very much for your update regarding this issue. >> >> 1)Just curious, will LGI be included in this report as this is another >> analysis of interest? >> >> 2)As for the cortical thickness I originally used 15mm in the analysis so >> based on your email I think using 5-10mm may be more prudent in order to >> minimize FPR. From your email, I understand that mris_surf2surf >> (command I >> use to convert individual subject to fsaverage or template and smooth to >> 10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into >> account the long tail distribution. Does this mean that when using >> mri_mcsim on my own template, the cluster extents for a given smoothness >> will be undersampled due to the fact that the "true" smoothness is more >> than what is estimated in the simulation, correct? For instance, when I >> select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm >> estimate), and I would select a given cluster extent for p=0.05. >> However, >> in this case, 15mm may translate to a larger FWHM than the estimated >> 21mm, >> correct? >> >> 3)You mentioned that I can use mri_glmfit-sim which is permutation >> testing >> based. I am struggling a bit in understanding how this differs from the >> simulation ran with mri_mcsim/qdec? Does qdec monte carlo simulation >> option run mri_glmfit-sim in the background to estimate the smoothness >> which looks up the cluster extent within the mri_mcsim based on the >> estimated FWHM? If so, is this estimate incorrect due to the fact >> that the >> long tails are not taken into account? >> >> >> Thanks, >> Ajay >> >> On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hello Freesurfer Experts, >>> Recently there were two article published regarding clusterwise >>> simulations for volumetric fmri analyses and potential errors for >>> underestimating clusterwise extent thresholds. >>> >>> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >>> 2) biorxiv.org/content/early/2016/07/26/065862 >>> >>> One issue pointed out from these articles seems software specific, >>> however >>> the second issue is determining the proper clustersize. The heavy-tail >>> nature of spatial smoothness seems to be ignored and a gaussian shape is >>> generally assumed, leading to an underestimation of the spatial >>> smoothness >>> which can affect cluster size calculations. The issues are >>> highlighted in >>> the second article above. >>> >>> I created my own monte carlo simulation in Freesurfer for a specific >>> brain >>> template and I wanted to find out if these concerns also apply to my >>> surface based simulations? I am not sure if it does since the monte >>> carlo >>> tool is a GRF simulation as opposed to an analytic equation, however >>> given >>> that these articles were highlighted very recently, I wanted to >>> ensure I am >>> running things appropriately for surface based cortical thickness/dti >>> analyses. >>> >>> Thanks, >>> Ajay >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/f75c8a4a/attachment-0001.html >> >> ------------------------------ >> >> Message: 11 >> Date: Wed, 3 Aug 2016 10:00:18 +0000 >> From: Caroline Beelen <caroline.bee...@kuleuven.be> >> Subject: [Freesurfer] mapping error >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <40b86b2ee4c24b96b8d585eb822a0...@icts-s-exmbx26.luna.kuleuven.be> >> Content-Type: text/plain; charset="us-ascii" >> >> >> Dear FS, >> >> An aparc.annot ctab file was created but I got the following error: >> Colortable:aparc.annot.ctab >> Annotname: myaparc >> Nhitsfile nhits.mgh >> Nlabels 6 >> Labeltresh 0 0.00000 >> Loading freesurfer/fsaverage/surf/lh.orig >> 1 -1 not found >> 2 -1 not found >> 3 -1 not found >> Etc... >> Mapping unhit to unknown >> Found 132101 unhit vertices >> Writing annot to freesurfer/fsaverage/lh.myaparc.annot >> >> I guess my ctab file is incorrect? I included an example of a label >> with it. >> >> Thanks again for your help. >> >> Caroline >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: aparc.annot.ctab >> Type: application/octet-stream >> Size: 782 bytes >> Desc: aparc.annot.ctab >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment.obj >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: lh.fusiform.label >> Type: application/octet-stream >> Size: 223962 bytes >> Desc: lh.fusiform.label >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/762d4854/attachment-0001.obj >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> End of Freesurfer Digest, Vol 150, Issue 5 >> ****************************************** > > > > _______________________________________________ > 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
