Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

Convert QDEC Talaraich coordinates to MNI152
by Vy Dinh 28 Sep '12

28 Sep '12

Dear Freesurfer Experts, I would like to create ROIs for the MNI152 template using coordinates obtained from our QDEC Monte Carlo Simulations results. However, the QDEC results only list the Talairach Coordinates. Is there a program that I can use to convert these tal coordinates to MNI152? Thanks, Vy

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Re: [Freesurfer] TRACULA Question
by Anastasia Yendiki 28 Sep '12

28 Sep '12

Hi Gabor - The info that tracula uses is which aparc+aseg labels each pathway neighbors at each point along its trajectory. It learns this information from the 33 subjects in the atlas, where the pathways were labeled manually, and then applies that knowledge to reconstruct the pathways in your subject. As long as the aparc+aseg of your subject is consistent with the ones in the atlas, you're fine. But if you think that the version you used to generate your aparc+aseg, and the latest version, that the aparc+aseg's in the atlas were generated with, have significant differences, this *may* be a problem. The extent of the problem will depend on how often the problematic label occurs next to one of the 18 pathways that tracula reconstructs and how different the label is b/w the versions. A small diference will probably not affect tracula at all. Your aparc+aseg's were generated with freesurfer 4.5, and there was no tracula atlas generated with that version of aparc+aseg's. Hope this helps, a.y On Fri, 28 Sep 2012, Gabor Perlaki wrote: > Dear Anastasia, > > Thanks a lot your answer. My fear is that the pars triangular > segmentation also seems bad, because it is right lateralized in most > of our analyzed data. Here is the post about this issue: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024541.html > > Is it also OK with Tracula? > > Thank you in advance, > Gabor > > 2012/9/27 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Gabor - Tracula doesn't use the BA labels, only the labels in the >> aparc+aseg. I hope this answers your question. >> >> a.y >> >> >> On Sun, 16 Sep 2012, Gabor Perlaki wrote: >> >>> Dear Anastasia, >>> >>> Earlier I was posted an issue about BA44/pars triangular: >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html >>> >>> Because TRACULA also uses the cortical parcellation it may be >>> important to handle this issue somehow. Is it handled in TRACULA >>> analysis? Does it affect the result of WM-volumes? >>> >>> Thank you for your answer, >>> Gabor >>> _______________________________________________ >>> 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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Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails
by Ed Gronenschild 28 Sep '12

28 Sep '12

Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resulting from using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 16 > Date: Thu, 27 Sep 2012 11:29:06 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <506470C2.5060906(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking > that no one would ever go above it, or maybe should never go above > it. I > can create tables at higher smoothing levels, but 34mm is a lot of > smoothing. How much did you apply to the data? > doug > > On 09/27/2012 05:48 AM, Ed Gronenschild wrote: >> Hi, >> >> I want to apply a cluster correction with mri_glmfit-sim with >> the --cache option: >> >> mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs >> >> It fails with the error message that it can't find the file: >> >> FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- >> z.csd >> >> (FSDir is the directory where FreeSurfer is located, >> version 5.0.0, Mac OSX10.5) >> >> Looking at the content of the ....fsaverage/lh/cortex directory >> than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 >> are present. >> >> In the log file from mri_glmfit I can read that the residualFWHM >> is 34.005014. Since this FWHM is automatically derived by >> mri_glmfit, does it mean that I can never use the --cache option >> in this case? >> >> Cheers, >> Ed

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CT Method Comparison
by Garikoitz Lerma-Usabiaga (Gari) 27 Sep '12

27 Sep '12

Dear Freesurfers, We've been comparing 2 different methods to obtain CT averages for 4 Volume ROI-s (volume ROI-s were in Colin27 space). We've used the 40 buckner subjects for the comparisons. METHOD L2L: bbregister >> mri_vol2surf (mgh) >> mri_binarize (mgh) >> mri_cor2label (label) >> mri_label2label >> mris_anatomical_stats METHOD S2S: bbregister >> mri_vol2surf >> mri_preproc (mri_surf2surf) >> mri_segstats After performing t-test-s over the results, we can observe that the results are in many cases different. -- Is there a way to choose the "best" method? Which one should we use for our work and why? Many thanks again for your help, Gari PD We've tabulated a third method as well: METHOD SurfRend: Surfrend (.w) >> mri_surf2surf(.mgh) >> mri_binarize(.mgh) >> mri_cor2label (.label) >> mris_anatomical_stats

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Re: [Freesurfer] output problem after recon-all
by pietro de rossi 27 Sep '12

27 Sep '12

sorry, I didn't realize I hadn't replied to the whole list :-) so this recon-all -i <name of one slice in the right dicom series> -s <subject id> -all is the command for the whole pipeline if I understand correctly.... does <subject id> represents the folder where the dcm files are? sorry for bothering again.. 2012/9/27 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > can you cc the list on these emails? Your command line should be: > > recon-all -i <name of one slice in the right dicom series> -s <subject id> > -all > > cheers > > Bruce > > > On Thu, 27 Sep 2012, pietro de rossi wrote: > > the command line was >> >> recon-all -autorecon1 -autorecon2 -subjid name_of_folder_with_dcm_files >> >> then >> >> recon-all -autorecon2 -autorecon3 -subjid name_of_folder_with_dcm_files >> >> >> >> 2012/9/27 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Pietro >> >> what was your recon-all command line? You need to specify >> different subject identifiers (-s <subject identifier>) for the >> different datasets >> >> Bruce >> On Thu, 27 Sep 2012, pietro de rossi wrote: >> >> Hi Freesurfers, >> I have another quintessentially beginner's problem.... >> >> I ran 5 scans through the entire pipeline (-autorecon1 >> -autorecon2 and >> -autorecon2 -autorecon-3) >> >> when I check the output going >> >> tksurfer [name_of_folder_with_dcm_**files] rh (or lh) >> inflated >> >> and then >> >> tkmedit [name_of_folder_with_**dcm_files] norm.mgz >> -segmentation aseg.mgz >> $FREESURFER_HOME/**FreeSurferColorLUT.txt >> >> the scans look all the same....it is like the last scan I >> processed was >> overwritten on the previous ones....does it make sense? >> >> thank you very much, >> >> Pietro >> >> -- >> Pietro De Rossi, MD >> ------------------------------**------- >> Sapienza Università di Roma, Facoltà di Medicina e >> Psicologia, Dipartimento >> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), >> Ospedale >> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma >> >> NESMOS Department (Neurosciences, Mental Health and >> Sensory Functions), >> School of Medicine and Psychology, Sapienza University, >> Sant?Andrea Hospital, >> Via di Grottarossa 1035-1039, 00189 Rome, Italy >> >> Neurobehavioral Clinical Research Section, Social and Behavioral >> Research >> Branch, National Human Genome Research Institute (NHGRI), >> National >> Institutes of Health (NIH), Bethesda, Maryland 20892, USA >> >> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> -- >> Pietro De Rossi, MD >> ------------------------------**------- >> Sapienza Università di Roma, Facoltà di Medicina e Psicologia, >> Dipartimento >> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale >> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma >> >> NESMOS Department (Neurosciences, Mental Health and Sensory Functions), >> School of Medicine and Psychology, Sapienza University, Sant?Andrea >> Hospital, >> Via di Grottarossa 1035-1039, 00189 Rome, Italy >> >> Neurobehavioral Clinical Research Section, Social and Behavioral Research >> Branch, National Human Genome Research Institute (NHGRI), National >> Institutes of Health (NIH), Bethesda, Maryland 20892, USA >> >> -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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output problem after recon-all
by pietro de rossi 27 Sep '12

27 Sep '12

Hi Freesurfers, I have another quintessentially beginner's problem.... I ran 5 scans through the entire pipeline (-autorecon1 -autorecon2 and -autorecon2 -autorecon-3) when I check the output going tksurfer [name_of_folder_with_dcm_files] rh (or lh) inflated and then tkmedit [name_of_folder_with_dcm_files] norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt the scans look all the same....it is like the last scan I processed was overwritten on the previous ones....does it make sense? thank you very much, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Tracula Error: bvecs and bvals don't have the same number of entries
by Loi 27 Sep '12

27 Sep '12

Dear FreeSurfers, I am trying to run trac-all -prep on a single subject, and get the following error: dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message. Does anyone know how I can solve this problem? Thank you, Joy-Loi ********************* My configuration file: setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set subjlist = id101 set runlist = 1 set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt set nb0 = 10 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz #set trainfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) set ncpts = 5 set usetrunc = 1 ********************* My bvals: 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 ********************* My bvecs: 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219

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significant variation in Hippocampal volume in between scans of same subject
by Rashmi Singh 27 Sep '12

27 Sep '12

Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same. Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491 ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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Re: [Freesurfer] message bouncing
by Rashmi Singh 27 Sep '12

27 Sep '12

Well, Correct me if I am doing something wrong while posting my emails. Whenever I post my emails to freesurfer-request(a)nmr.mgh.harvard.edu my emails bounces. So today I emailed my post to Bruce's email, freesurfer(a)nmr.mgh.harvard.edu and freesurfer-request(a)nmr.mgh.harvard.edu. I got a bounce reply from the freesurfer-request(a)nmr.mgh.harvard.edu email. So let me know what am doing wrong? Rashmi On 9/27/12 11:52 AM, "Help Desk Elf --- Chris Johnson" <help(a)nmr.mgh.harvard.edu> wrote: > Rashmi, > > I'm seeing an archive of a post from today at 12:04:28 EDT 2012. >Are you still having trouble? You are definitely still on the list. > >> I see. Nick and/or help: can you investigate? >> >> thanks >> Bruce >> >> >> On Thu, 27 Sep 2012, Rashmi Singh wrote: >> >>> Reply, >>> Yes I started posting since last year, but suddenly after July this >>>year >>> my posts have started bouncing back. >>> That is why I finally emailed my issue to your personal id today. >>> Thank you ! >>> Rashmi. >>> >>> >>> On 9/27/12 11:31 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >>>wrote: >>> >>> > Hi Rashmi >>> > >>> > are you a member of the list? >>> > >>> > Bruce >>> > >>> > On Thu, 27 Sep 2012, Rashmi Singh wrote: >>> > >>> > > Hello Bruce, >>> > > I am somehow unable to send message to the Freesurfer request >>>board. >>> > > All my >>> > > e mails are bouncing. >>> > > Please advise. >>> > > Rashmi >>> > > >>> > > >>> > >>> > >>> > 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. >>> > >>> >>> >>> >>> >> >> >> >> > >-- Chris Johnson (http://help.nmr.mgh.harvard.edu) > >-------------------------------------------------------------------------- >----- >Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu >Systems Administrator |Web: >http://www.nmr.mgh.harvard.edu/~johnson >NMR Center |Voice: 617.726.0949 >Mass. General Hospital |FAX: 617.726.7422 >149 (2301) 13th Street |"Life. Don't talk to me about life." >Marvin the >Charlestown, MA., 02129 USA | Paranoid Android >-------------------------------------------------------------------------- >-----

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TRACULA Question
by Gabor Perlaki 27 Sep '12

27 Sep '12

Dear Anastasia, Earlier I was posted an issue about BA44/pars triangular: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html Because TRACULA also uses the cortical parcellation it may be important to handle this issue somehow. Is it handled in TRACULA analysis? Does it affect the result of WM-volumes? Thank you for your answer, Gabor

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Freesurfer September 2012