Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Free surfer license error
by Muhammad Naveed Iqbal Qureshi 15 Jul '13

15 Jul '13

Hello,I have successfully installed freeon my mac pro server.but when i try to run the tkmedit it is giving the following error message, although I have copied the license information in freesurfer home directory.[Geodesics:~] EGI% tkmedit bert orig.mgz--------------------------------------------------------------------------ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.Kindly reply me as soon as possible.Thank you Best Regards, Muhammad Naveed Iqbal Qureshi BK21 Student Graduate Research Assistant Computer Vision and Multimedia Lab Department of Computer Engineering Chosun University 375, Seosuk-dong, Dong-gu, Gwangju, 501-759, South Korea Tel: (+82) 62-230-7756 Email: mniqureshi(a)hotmail.com URL: http://cvm.chosun.ac.kr/ P please don't print this e-mail unless you really need to

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Do I need to edit wm.mgz after deleting extra dura?
by ye tian 15 Jul '13

15 Jul '13

Dear Freesurfers, I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. Thank you very much! Sincerely, Ye

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Re: [Freesurfer] Working with MEMPRAGE
by Kayle Sawyer 15 Jul '13

15 Jul '13

Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt <whatsdac(a)umich.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.02.1305091043500.13418(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> >>>> Thanks Bruce, >>>> >>>> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >>>> >>>> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >>>> >>>> jon >>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>> >>>>> Hi Jon >>>>> >>>>> yes, the subject and hemi need to be defined (they are required parameters) >>>>> Bruce >>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>> >>>>>> Hi all, >>>>>> combed through the mail archives to figure out how to work with multi echo >>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>> commands is the appropriate >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>>>> jon >>>>>>

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Post-hoc anonymizing subject: binary files
by Andrew Ward 15 Jul '13

15 Jul '13

Hi folks, I am wondering if anyone has run into this problem before, and has a solution. We are trying to post-hoc anonymize FreeSurfer reconstructions. It's a simple matter to move the reconstruction directory, as well as to replace any instances of the old subject ID in text files (e.g. stats or log files). However, when I open any of the binary files (e.g. lh.pial) in a text editor, the last line includes the mris_make_surfaces command called to make the surface. This includes the old, pre-anonymized subject ID. I am worried about reading & writing these files using an ASCII editor, because I don't want to corrupt the binary encoding. Additionally, because the binary format is not public, there appear to be no tools to read & write to these ASCII tails in the binary data. Is there a way to either strip these lines, or to replace the reference to the old subject ID with the anonymized ID (this option is preferable)? Ideally, we don't want to have to reconstruct every binary file using the updated subject ID. Thanks for the help! Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Rm 10.008 Charlestown, MA 02129 Phone: 617-726-6213 Fax: 617-726-5760

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Re: [Freesurfer] application of mri_cvs_register question
by Anastasia Yendiki 15 Jul '13

15 Jul '13

Hi Matt - Try anatorig2diff.bbr.dat. a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > Hi Anastasia, > Here it is: > anat2anatorig.dat anatorig2diff.bbr.dat anatorig2diff.bbr.dat.sum diff2mni.bbr.mat > anat2anatorig.dat~ anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat mni2anat.mat > anat2anatorig.mat anatorig2diff.bbr.dat.log anatorig2mni.mat mni2anatorig.mat > anat2diff.bbr.mat anatorig2diff.bbr.dat.log.old cvs mni2diff.bbr.mat > anat2mni.mat anatorig2diff.bbr.dat.mincost diff2anat.bbr.mat > anatorig2anat.mat anatorig2diff.bbr.dat.param diff2anatorig.bbr.mat > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 15, 2013 2:56 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] application of mri_cvs_register question > > > Got it. Can you send me a listing of the contents of the xfms/ directory? > Conversions b/w formats can be done with tkregister2, but the .dat file > should normally be there since it's the default format for bbregister. > > On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > >> Right, that's been my problem :( Maybe something went wrong, but I didn't see any problem in the log files. Actually, the command I showed below had a typo (I used --mat rather than --reg to get that error). Is there a way to convert *.mat to *.dat? >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >> Sent: Monday, July 15, 2013 2:44 PM >> To: Hoptman, Matthew >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] application of mri_cvs_register question >> >> >> Hi Matt - The --reg option expects a .dat file. There should be one >> produced by bbregister in the xfms/ directory? >> >> a.y >> >> On Mon, 15 Jul 2013, Hoptman, Matthew wrote: >> >>> Hi Anastasia, >>> Yes, that was my problem. I think I need to use >>> mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z >>> ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z >>> --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o >>> diffvol2CVS.nii.gz --no-save-reg >>> >>> >>> I now get: >>> Using the m3z file as it is; no assumed location. >>> regio_read_register(): Success >>> Error reading R[3][0] from diff2anat.bbr.mat >>> >>> Matrix from regfile: >>> -0.001 0.972 -0.234 -3.311; >>> -0.001 0.234 0.972 69.949; >>> 0.000 0.000 0.000 1.000; >>> 0.000 0.000 0.000 0.000; >>> >>> I was stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? >>> Thanks >>> Matt >>> >>> -----Original Message----- >>> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >>> Sent: Monday, July 15, 2013 2:30 PM >>> To: Hoptman, Matthew >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] application of mri_cvs_register question >>> >>> >>> Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to >>> the CVS template. To map from individual diffusion to the CVS template, >>> you'd have to first use diffusion-to-anatomical affine transform file >>> under xfms/. >>> >>> Hope this helps, >>> a.y >>> >>> On Mon, 15 Jul 2013, Hoptman, Matthew wrote: >>> >>>> Hi Anastasia, >>>> Not really, what I now have is: >>>> <subject>/dmri/xfms/cvs >>>> Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. >>>> >>>> The files in <subject>/dmri/xfms/cvs are: >>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>>> final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz >>>> final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz >>>> final_CVSmorph_tocvs_avg35_inMNI152.m3z >>>> lh.dbg_surf.pial >>>> lh.dbg_surf.white >>>> lh.resample.aparc.annot >>>> lh.resample.pial >>>> lh.resample.white >>>> nlalign-afteraseg-norm.mgz >>>> nlalign-aseg.mgz >>>> rh.dbg_surf.pial >>>> rh.dbg_surf.white >>>> rh.resample.aparc.annot >>>> rh.resample.pial >>>> rh.resample.white >>>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>>> transform.txt >>>> >>>> >>>> -----Original Message----- >>>> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >>>> Sent: Monday, July 15, 2013 12:19 PM >>>> To: Hoptman, Matthew >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] application of mri_cvs_register question >>>> >>>> >>>> Hi Matt - For how to tell tracula to use CVS registration, see "Specify >>>> the inter-subject registration method" here: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>> >>>> Does this answer your question? >>>> >>>> a.y >>>> >>>> On Mon, 8 Jul 2013, Hoptman, Matthew wrote: >>>> >>>>> >>>>> Hi all, >>>>> >>>>> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal >>>>> integration and inter-subject registration” tutorial is: >>>>> >>>>> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >>>>> >>>>> >>>>> >>>>> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a >>>>> *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> >>>>> >>>>> Matthew J. Hoptman, PhD >>>>> Research Scientist V >>>>> Nathan S. Kline Institute for Psychiatric Research >>>>> >>>>> Research Associate Professor in Psychiatry >>>>> NYU School of Medicine >>>>> >>>>> >>>>> >>>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >>>>> otherwise protected by law. If you received this >>>>> e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or >>>>> copying the e-mail. >>>>> >>>>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >>>>> >>>>> >>>>> >>>>> _________________________________________________________________________________________________________________________________________________________________ >>>>> Conserve Resources. Print only when necessary. >>>>> >>>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor >>>>> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >>>>> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >>>>> SYSTEM. Thank you for your cooperation. >>>>> >>>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >>>>> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >>>>> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >>>>> SYSTEM. Thank you for your cooperation. >>>>> >>>> >>>> >>>> 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. >>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >>>> >>>> >>>> >>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >>> >>> >>> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > >

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Re: [Freesurfer] AC/PC positions and other questions
by François Tadel 15 Jul '13

15 Jul '13

Hi Doug, Thanks for the quick reply. A few more details: > What do you mean by "position" (AC/PC)? Do you mean the col, row, slice? We don't find the actual AC or PC. Yes: 3D coordinates in any identified coordinate systems. For now, we are asking our users to mark those points manually. It would be great to skip that step and have those points placed automatically. We could get the AC point from the linear Talairach transform. To transform the TalXYZ=(0,0,0) for AC to the coordinate system of the surfaces (for instance: lh.pial), should I take the translation found in the file "talairach.xfm" (4th column) ? > What file should I read to get the labels corresponding to the aseg.mgz file? > $FREESURFER_HOME/ASegStatsLUT.txt Is there a file in the segmentation folder I could read it from? We are typically using the results of freesurfer segmentation on computers where FS is not installed... > Is there an easy way to generate surfaces for all the regions defined in aseg.mgz? Ok, mri_tesselate + mris_smooth work well for what I'm doing. Thanks Francois -- François Tadel, MSc MEG / McConnell Brain Imaging Center / MNI / McGill University 3801 rue University, Montreal, QC H3A2B4, Canada

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using two vs one scan(s) for optimal surface reconstruction
by Marie Schaer 15 Jul '13

15 Jul '13

Hi all, Small question related to the number of structural runs required for optimal results: I was wondering whether someone tested the assumption that using two scans rather than one improves the segmentation process and the cortical surface reconstruction / thickness estimation? I've not been able to find any publication on it, but maybe my search was not extensive enough. Thanks a lot for your answer, Marie

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Re: [Freesurfer] application of mri_cvs_register question
by Anastasia Yendiki 15 Jul '13

15 Jul '13

Got it. Can you send me a listing of the contents of the xfms/ directory? Conversions b/w formats can be done with tkregister2, but the .dat file should normally be there since it's the default format for bbregister. On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > Right, that's been my problem :( Maybe something went wrong, but I didn't see any problem in the log files. Actually, the command I showed below had a typo (I used --mat rather than --reg to get that error). Is there a way to convert *.mat to *.dat? > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 15, 2013 2:44 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] application of mri_cvs_register question > > > Hi Matt - The --reg option expects a .dat file. There should be one > produced by bbregister in the xfms/ directory? > > a.y > > On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > >> Hi Anastasia, >> Yes, that was my problem. I think I need to use >> mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z >> ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o >> diffvol2CVS.nii.gz --no-save-reg >> >> >> I now get: >> Using the m3z file as it is; no assumed location. >> regio_read_register(): Success >> Error reading R[3][0] from diff2anat.bbr.mat >> >> Matrix from regfile: >> -0.001 0.972 -0.234 -3.311; >> -0.001 0.234 0.972 69.949; >> 0.000 0.000 0.000 1.000; >> 0.000 0.000 0.000 0.000; >> >> I was stuck at that point. Lilla Zollei told me she'd look into it, but maybe you've communicated with her? >> Thanks >> Matt >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >> Sent: Monday, July 15, 2013 2:30 PM >> To: Hoptman, Matthew >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] application of mri_cvs_register question >> >> >> Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to >> the CVS template. To map from individual diffusion to the CVS template, >> you'd have to first use diffusion-to-anatomical affine transform file >> under xfms/. >> >> Hope this helps, >> a.y >> >> On Mon, 15 Jul 2013, Hoptman, Matthew wrote: >> >>> Hi Anastasia, >>> Not really, what I now have is: >>> <subject>/dmri/xfms/cvs >>> Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. >>> >>> The files in <subject>/dmri/xfms/cvs are: >>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>> final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz >>> final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz >>> final_CVSmorph_tocvs_avg35_inMNI152.m3z >>> lh.dbg_surf.pial >>> lh.dbg_surf.white >>> lh.resample.aparc.annot >>> lh.resample.pial >>> lh.resample.white >>> nlalign-afteraseg-norm.mgz >>> nlalign-aseg.mgz >>> rh.dbg_surf.pial >>> rh.dbg_surf.white >>> rh.resample.aparc.annot >>> rh.resample.pial >>> rh.resample.white >>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>> transform.txt >>> >>> >>> -----Original Message----- >>> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >>> Sent: Monday, July 15, 2013 12:19 PM >>> To: Hoptman, Matthew >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] application of mri_cvs_register question >>> >>> >>> Hi Matt - For how to tell tracula to use CVS registration, see "Specify >>> the inter-subject registration method" here: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>> >>> Does this answer your question? >>> >>> a.y >>> >>> On Mon, 8 Jul 2013, Hoptman, Matthew wrote: >>> >>>> >>>> Hi all, >>>> >>>> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal >>>> integration and inter-subject registration” tutorial is: >>>> >>>> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >>>> >>>> >>>> >>>> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a >>>> *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>> >>>> Matthew J. Hoptman, PhD >>>> Research Scientist V >>>> Nathan S. Kline Institute for Psychiatric Research >>>> >>>> Research Associate Professor in Psychiatry >>>> NYU School of Medicine >>>> >>>> >>>> >>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >>>> otherwise protected by law. If you received this >>>> e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or >>>> copying the e-mail. >>>> >>>> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >>>> >>>> >>>> >>>> _________________________________________________________________________________________________________________________________________________________________ >>>> Conserve Resources. Print only when necessary. >>>> >>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor >>>> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >>>> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >>>> SYSTEM. Thank you for your cooperation. >>>> >>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >>>> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >>>> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >>>> SYSTEM. Thank you for your cooperation. >>>> >>> >>> >>> 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. >>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >>> >>> >>> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > >

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FSFAST funcroi-sess problem
by Joseph Dien 15 Jul '13

15 Jul '13

I'm using Freesurfer 5.3.0 (well, actually I ran the original analyses with 5.2.0 and then am running this ROI follow-up with 5.2.0, could that be a problem? From the release notes, it didn't look like it would be an issue) Anyway, I've run the following set of commands: funcroi-config -roi /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg -annot /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot cluster-001 -analysis CPA.sm05.lh funcroi-sess -roi /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg -s CPA003 -d . I get the following output. When I checked the results with: tksurfer fsaverage lh inflated -overlay roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5 sure enough, it didn't look right. Instead of the cluster, I got speckles all over the surface. I used the Matlab command: [vertex_coords, faces] = read_surf('lh.white'); and found sure enough that the size of the vertex array was only 143827 whereas mri_info indicates that the ocn file has 163842 Any suggestions what I might be doing wrong? Thanks! Joe ------------------------------------------- /Volumes/Data/CP1/fsfast/CPA003 Fri Jul 12 18:23:28 EDT 2013 mri_annotation2label --subject CPA003 --hemi lh --annotation /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot --outdir /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label subject = CPA003 annotation = /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot hemi = lh outdir = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label surface = white Reading surface /Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white Loading annotations from /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143827 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143828 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143829 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143830 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143831 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143832 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 143833 i=00000000, in_array_size=143827 … MRISreadAnnotationIntoArray: vertex index out of range: 163838 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 163839 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 163840 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=00000000, in_array_size=143827 annot file: /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot reading colortable from annotation file... colortable with 3 entries read (originally none) Seg base 0 max index = 2 1 952 /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label 2 532 /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster2.label mri_label2label --hemi lh --srclabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label --srcsubject CPA003 --trglabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --trgsubject fsaverage --regmethod surface srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label srcsubject = CPA003 trgsubject = fsaverage trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Volumes/Data/CP1/freesurfer FREESURFER_HOME /Applications/freesurfer Loading source label. Found 952 points in source label. Starting surface-based mapping Reading source registration /Volumes/Data/CP1/freesurfer/CPA003/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white Reading target registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 952 nlabel points Performing mapping from target back to the source label 163842 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label 1367 mri_label2label: Done mri_label2label --hemi lh --srclabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --outmask /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz --regmethod surface --trglabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label --s fsaverage srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label srcsubject = fsaverage trgsubject = fsaverage trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Volumes/Data/CP1/freesurfer FREESURFER_HOME /Applications/freesurfer Loading source label. Found 1311 points in source label. Starting surface-based mapping Reading source registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white Reading target registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1311 nlabel points Performing mapping from target back to the source label 163842 Number of reverse mapping hits = 0 Checking for and removing duplicates Creating output /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label 1311 mri_label2label: Done Ended at Fri Jul 12 18:23:48 EDT 2013 funcroi-sess completed -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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Re: [Freesurfer] application of mri_cvs_register question
by Anastasia Yendiki 15 Jul '13

15 Jul '13

Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to the CVS template. To map from individual diffusion to the CVS template, you'd have to first use diffusion-to-anatomical affine transform file under xfms/. Hope this helps, a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > Hi Anastasia, > Not really, what I now have is: > <subject>/dmri/xfms/cvs > Within cvs, there are anatomical files that are registered to the CVS template, as below, but what I DON'T have is the application of these transforms to the DTI data. That's what I'm trying to puzzle out. > > The files in <subject>/dmri/xfms/cvs are: > c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log > c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log > final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz > final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz > final_CVSmorph_tocvs_avg35_inMNI152.m3z > lh.dbg_surf.pial > lh.dbg_surf.white > lh.resample.aparc.annot > lh.resample.pial > lh.resample.white > nlalign-afteraseg-norm.mgz > nlalign-aseg.mgz > rh.dbg_surf.pial > rh.dbg_surf.white > rh.resample.aparc.annot > rh.resample.pial > rh.resample.white > summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log > summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log > transform.txt > > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 15, 2013 12:19 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] application of mri_cvs_register question > > > Hi Matt - For how to tell tracula to use CVS registration, see "Specify > the inter-subject registration method" here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Does this answer your question? > > a.y > > On Mon, 8 Jul 2013, Hoptman, Matthew wrote: > >> >> Hi all, >> >> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal >> integration and inter-subject registration” tutorial is: >> >> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >> >> >> >> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a >> *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? >> >> >> >> Thanks, >> >> Matt >> >> >> >> Matthew J. Hoptman, PhD >> Research Scientist V >> Nathan S. Kline Institute for Psychiatric Research >> >> Research Associate Professor in Psychiatry >> NYU School of Medicine >> >> >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >> otherwise protected by law. If you received this >> e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or >> copying the e-mail. >> >> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> >> _________________________________________________________________________________________________________________________________________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor >> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >> SYSTEM. Thank you for your cooperation. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or >> otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from >> reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR >> SYSTEM. Thank you for your cooperation. >> > > > 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 . 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