Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

Re: [Freesurfer] Hippocampal Sub field segmentation (fwd)
by Bruce Fischl 17 Nov '11

17 Nov '11

FYI ---------- Forwarded message ---------- Date: Thu, 17 Nov 2011 13:26:46 -0600 From: "Heckers, Stephan H" <stephan.heckers(a)Vanderbilt.Edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Joshua Lee <jkilee(a)ucdavis.edu> Cc: Koen Van Leemput <koen(a)nmr.mgh.harvard.edu>, Shashwath <shashwath123(a)gmail.com>, Freesurfer <freesurfer(a)nmr.mgh.harvard.edu>, Alan Francis <alandarkenergy(a)gmail.com>, Jean Augustinack <jean(a)nmr.mgh.harvard.edu>, "Konradi, Christine" <christine.konradi(a)Vanderbilt.Edu> Subject: Re: [Freesurfer] Hippocampal Sub field segmentation Dear all - Bruce is correct (he usually is): I have some opinion on this. Please see the attached poster from last year that plots total number of hippocampal interneurons along the anterior-posterior axis of the human hippocampus. We have similar data for pyramidal cells and subsector volume. The bottom line: CA 1 is the largest sector in the uncus, but about 40% of the uncus is NOT CA1. It seems to me that the neuroimaging community is waking up and realizing that subfield anatomy of the hippocapmus varies quite a bit along the anterior-posterior axis. We have many whole human hippocampal specimens and have quite a bit of data on the subfields. We might have to publish this now ... Stephan --- Stephan Heckers, MD William P. and Henry B. Test Professor Chair, Department of Psychiatry Psychiatrist-in-Chief, Vanderbilt Psychiatric Hospital 1601 23rd Avenue South, Room 3060 Nashville, TN 37212 (615) 322 2665 -- On 11/17/11 12:46 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >Hi Joshua > >I'll cc Jean Augustinack and Stephan Heckers, who I know have opinions on >this issue :) > >cheers >Bruce > >On Thu, 17 Nov 2011, Joshua Lee wrote: > >> >> There is great variability between the different segmentation protocols >>used >> by different research groups, and I think people are eager for a >>standard to >> facilitate comparison and replication. By becoming part of Freesurfer, I >> suspect that your segmentation algorithm will become that standard. >> >> Luckily, I think it is one of truest I've seen to conforming to the >>Duvernoy >> atlas. Whether Duvernoy's work is the appropriate standard I am not >> qualified to say, but he does seem to be cited quite often as the basis >>for >> the various protocols in the wild. However, there might still be some >> differences between Duvernoy and the scheme used by the Freesurfer >>subfield >> segmentation. >> >> Particularly, Duvernoy seems to indicate that in the head and the tail >>CA1 >> seems to be the only subfield present in the anterior 1/3 of the head >>and >> posterior 1/3 of the tail. Looking coronally, subiculum seems to extend >> further laterally in the head and tail than in the body of the >>hippocampus. >> Lastly, CA1 seems to continue further medially on the superior side of >>the >> hippocampus in the head and tail than in body. CA3, by my reading of >> Duvernoy, seems to be tiny in the head and tail. >> >> All these are fairly minor points. Still, I wouldn't mind some comments >>on >> these observations, as they were changes I have been proposing to make >>in >> the segmentation protocol used in my lab. >> >> Best, >> >> >> Joshua >> >> Joshua Lee >> Graduate Student >> Center for Mind and Brain & >> Department of Psychology >> University of California, Davis >> 530.747.3805 >> >> >> On Thu, Nov 17, 2011 at 9:30 AM, Koen Van Leemput >><koen(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Joshua, >> >> I'm not a neuroanatomist so I can't really answer that question. >> My >> aim has just been to replicate what a human expert has given us >> as >> segmentation examples on a number of different subjects. >> >> I know that different labs follow very different conventions for >> labeling the subfields manually. Perhaps someone else can chime >> in? >> >> Koen >> >> >> On Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee <jkilee(a)ucdavis.edu> >> wrote: >>> At least by my reading of the Duvernoy Human Hippocampus atlas, the >> most >>> anterior and posterior extents of the hippocmapus (perhaps just a >> slice at >>> the tips in most scans) are almost entirely composed of the CA1 >> subfield. >>> Thoughts? >>> >>> Joshua >>> - >>> Joshua Lee >>> Graduate Student >>> Center for Mind and Brain & >>> Department of Psychology >>> University of California, Davis >>> >>> >>> >>> On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis >> <alandarkenergy(a)gmail.com> >>> wrote: >>>> >>>> Thanks Koen. >>>> >>>> On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput >>>> <koen(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> The answer is close to what Shashwath suggested, except that the >>>>> "Hippocampus" segmentation is really computed at the same time as >> all >>>>> the other subfields. For unfortunate reasons, the tail of the >>>>> hippocampus that is not further subdivided in our manual training >>>>> segmentations was called "Hippocampus" for lack of other good >> names - >>>>> it really should have been "Part of the Hippocampus Tail that We >>>>> Didn't Subdivide Manually". >>>>> >>>>> If you want to compute the total volume of the hippocampus, you'll >>>>> need to add the volume of this part, though.. >>>>> >>>>> Hope this helps, >>>>> >>>>> Koen >>>>> >>>>> >>>>> On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis >> <alandarkenergy(a)gmail.com> >>>>> wrote: >>>>>> Thanks Shashwath. >>>>>> >>>>>> On Wed, Nov 16, 2011 at 2:04 PM, Shashwath >> <shashwath123(a)gmail.com> >>>>>> wrote: >>>>>>> >>>>>>> Alan- I believe the label "hippocampus" here refers to the >> remaining >>>>>>> hippo >>>>>>> segment after the algorithm has completed labelling of all >> subfields. >>>>>>> In >>>>>>> essence this would not be a measure that conveys very >> meaningful info. >>>>>>> >>>>>>> Sent from my iPhone >>>>>>> >>>>>>> On Nov 16, 2011, at 1:01 PM, Alan Francis >> <alandarkenergy(a)gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Koen and FreeSurfers: >>>>>>>> >>>>>>>> I have a 3T dataset that has undergone processing using 5.1. >> I have >>>>>>>> also >>>>>>>> run the Hippo sub fields command. Here are my results: >>>>>>>> >>>>>>>> [root@NeuroImage-Gamma mri]# >> kvlQuantifyPosteriorProbabilityImages >>>>>>>> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt >>>>>>>> posterior_right_* >>>>>>>> posterior_Right-Hippocampus.mgz >>>>>>>> >>>>>>>> volumeInVoxels: >>>>>>>> right_CA1: 2473.34 >>>>>>>> right_CA2-3: 7530.08 >>>>>>>> right_CA4-DG: 4160.99 >>>>>>>> right_fimbria: 520.14 >>>>>>>> right_hippocampal_fissure: 376.772 >>>>>>>> right_presubiculum: 2780.65 >>>>>>>> right_subiculum: 4230.04 >>>>>>>> Right-Hippocampus: 2277.69 >>>>>>>> >>>>>>>> My question is : Since these are "subfields" of the >> Hippocampus, >>>>>>>> should >>>>>>>> not the sum of all subregions be equal the volume of the >> Right >>>>>>>> Hippocampus? >>>>>>>> >>>>>>>> Thanks so much! >>>>>>>> >>>>>>>> Alan Francis >>>>>>>> >>>>>>>> Beth Israel Deaconess Medical Center, BOSTON >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the >> person to >>>>>>>> whom >>>>>>>> it is >>>>>>>> addressed. If you believe this e-mail was sent to you in >> error and >>>>>>>> the >>>>>>>> e-mail >>>>>>>> contains patient information, please contact the Partners >> Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was >> sent to >>>>>>>> you >>>>>>>> in error >>>>>>>> but does not contain patient information, please contact the >> sender >>>>>>>> and >>>>>>>> properly >>>>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person >> to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error >> and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners >> Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent >> to you >>>>>> in >>>>>> error >>>>>> but does not contain patient information, please contact the >> sender and >>>>>> properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >> whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and >> the >>>> e-mail >>>> contains patient information, please contact the Partners >> Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to >> you in >>>> error >>>> but does not contain patient information, please contact the sender >> and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >> >> >>

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Hippocampal Sub field segmentation
by Alan Francis 17 Nov '11

17 Nov '11

Hi Koen and FreeSurfers: I have a 3T dataset that has undergone processing using 5.1. I have also run the Hippo sub fields command. Here are my results: [root@NeuroImage-Gamma mri]# kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz volumeInVoxels: right_CA1: 2473.34 right_CA2-3: 7530.08 right_CA4-DG: 4160.99 right_fimbria: 520.14 right_hippocampal_fissure: 376.772 right_presubiculum: 2780.65 right_subiculum: 4230.04 Right-Hippocampus: 2277.69 My question is : Since these are "subfields" of the Hippocampus, should not the sum of all subregions be equal the volume of the Right Hippocampus? Thanks so much! Alan Francis Beth Israel Deaconess Medical Center, BOSTON

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Hippocampal Sub-Field Segmentation
by Alan Francis 17 Nov '11

17 Nov '11

Hello Bruce et al, I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field Segmentation tools of 5.1 to process these? thanks so much, Alan BIDMC/ Psychiatry

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trouble with kvlQuantifyPosteriorProbabilityImages
by Marie Schaer 16 Nov '11

16 Nov '11

Hi all, I just ran the hippo-subfield segmentation on a batch of subjects. Everything went perfect for most of my subjects, however I got an outlier in the left CA1 for one subject who had a very large volume. After checking the results in freeview for this subject, I saw that the problem was that CA1 was including a big portion of white matter in its volume (see attached png). To try to solve the problem, I just reran the recon-all -hippo-subfield for the left hemisphere of this subject (which by the way did not solve the white matter inclusion). The problem I have now is that kvlQuantifyPosteriorProbabilityImages does not seem to "see" anymore the resulting volume on the left side and does not output any volume for the left side (see error below), although the output was properly created in the mri folder (i.e. all the posterior_left_* images are there and I can load them in freeview without any problem). Any guess? Many thanks for the help, Marie [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie% kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_left_* volumeInVoxels: [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie% kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* volumeInVoxels: right_CA1: 3050.22 right_CA2-3: 8579.62 right_CA4-DG: 4997.83 right_fimbria: 354.868 right_hippocampal_fissure: 302.39 right_presubiculum: 3784.79 right_subiculum: 5384.07 [maries-iMac:LONGITUDINAL_Stats/5272/mri] marie%

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Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
by Krish Singh 16 Nov '11

16 Nov '11

Oops. Sorry Andrew, that is a script that I think just takes some lines from the recon-all script. I can't remember whether I wrote it, or someone else (sorry), but here it is: -------------------------------------------------- #!/bin/bash # thresholds probabilities in one file to another at the optimal # threshold of p=0.8. this threshold is based on comparisons of actual # and predicted V1 boundary with and independent dataset (zilles # brains) infile=$1 outfile=$2 echo -n "thresholding the label..." cat $infile | sed "/^#/d;/^[0-9]*$/d;/.* 0\\.[0-7].*$/d" \ > /tmp/tmpthreshout numlab=`wc -l /tmp/tmpthreshout | sed "s/ .*$//"` echo "# v1 atlaspredict label file auto-generated" > $outfile echo $numlab >> $outfile cat /tmp/tmpthreshout >> $outfile echo "done" -------------------------------------------------- Just put these in a file called threshold_labelfile_at0p8, somewhere in your executable path (and make sure the x permission flag is set). Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk On 15 Nov 2011, at 19:47, Andrew Bock wrote: > Hi Krish, > > I'm still having some issues, right now I receive the error: > > threshold_labelfile_at0p8: command not found > > Any suggestions? > > Andrew > > On Tue, Nov 15, 2011 at 9:37 AM, Andrew Bock <abock(a)u.washington.edu> wrote: > Thanks Krish! > > Andrew > > > On Tue, Nov 15, 2011 at 9:29 AM, Krish Singh <singhkd(a)cardiff.ac.uk> wrote: > Hi Andrew, > > Glad it's not just me! I'm still not sure whether this is a generic problem with version 5.1.0 (which I use) or a local problem. > > I can only find a rather inelegant hack. What I do is complete the recon-all (5.1.0) and then run a bunch of steps using mris_spherical_average from version 4.4.0: > > Here's what I do <stuff in angle brackets is for you to fill in> > > cd $SUBJECTS_DIR > <PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label rh.v1.invivo.label rh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/rh.v1.prob.label > <PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label lh.v1.invivo.label lh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/lh.v1.prob.label > threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/lh.v1.prob.label ./<SUBJECTNAME>/label/lh.v1.predict.labe > threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/rh.v1.prob.label ./<SUBJECTNAME>/label/rh.v1.predict.label > mris_anatomical_stats -l ./<SUBJECTNAME>/label/lh.v1.predict.label <SUBJECTNAME> lh >> ./<SUBJECTNAME>/stats/hinds_v1_lh > mris_anatomical_stats -l ./<SUBJECTNAME>/label/rh.v1.predict.label <SUBJECTNAME> rh >> ./<SUBJECTNAME>/stats/hinds_v1_rh > > This seems to work, but I'm not sure if there is any fall-out from mixing versions. (Note you need to link or copy a version of V1_average into your SUBJECTS_DIR first) > > Good luck! > > Krish > > -- > Prof. Krish Singh > CUBRIC > School of Psychology / Ysgol Seicoleg > Cardiff University / Prifysgol Caerdydd > Park Place / Plas y Parc > Cardiff / Caerdydd > CF10 3AT, UK > Tel / Ffôn: 02920 874690 / 870365 > Fax / Ffacs: 02920 870339 > Email / Ebost : singhkd(a)cardiff.ac.uk > > > > > On 11 Nov 2011, at 22:04, Andrew Bock wrote: > >> Hello, >> >> I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): >> >> processing subject V1_average... >> MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ >> subjects/V1_average/surf/rh.white >> No such file or directory >> MRISreadOriginalProperties: could not read surface file white >> No such file or directory >> could not read surface positions from white >> No such file or directory >> >> >> As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. >> >> I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." >> >> Any help you can provide would be greatly appreciated! >> >> Thanks in advance, >> >> Andrew >> >> -- >> Andrew Bock, Ph.D. >> Department of Psychology >> University of Washington >> Seattle, WA 98195 >> Tel: 206.543.3817 >> Fax: 206.685.3157 >> abock(a)u.washington.edu >> _______________________________________________ >> 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] dt_recon registration
by Antonella Kis 15 Nov '11

15 Nov '11

Dear Lilla, Thank you very much for your valuable help. I still have few more questions and I will appreciate if you can further help me. 1) Why I don't have in my $FREESURFER_HOME/subjects the cvs_avg35/mri/norm.mgz? In my subjects directory I only have my subjects and nothing else. How can I get the cvs_avg35/mri/norm.mgz? 2) Do you believe that for my subjects-all children ages 6-13 the results are gone be OK if I use the talairach registration and re-sampling? As I mentioned in my previous email I would like to do a two-group study similar with TBSS so to do a statistical analysis on the FA and non_FA data such as mean diffusivity, to see if there are any clusters that may survive by multiple comparisons without any covariant. 3) Do you have any suggestion regarding which registration is better to be used for this study? 4) How I can check for each individual subject if the registration worked out well if for example I choose the talairach space? Do I run: tkregister2 --mov lowb.nii --reg register.dat --surf or which file is in fact the registered data file? Is the fa-tal.nii.gz or the lowb.nii.gz? You mentioned that the default registration is on talairch space and the I see on dt_recon tutorial that is also doing a registration of lowb to same-subject anatomical so I have two registration done when I run the dt_recon? Sorry I am very confused and I will very grateful if you can make this a little clear for me. Many thanks for your time and help. Best regards, Antonella ________________________________ From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, November 14, 2011 4:13 PM Subject: Re: [Freesurfer] dt_recon registration Hi Antonella, > 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this question > because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg. The talairach registration and re-sampling does take place by default, but that should not affect your further processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use --no-tal. > 2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL? Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files. > 3) Can I use the talairch registration or should I use the CVS? Depends on where you want to do your analysis. > 4) Should I add the flag --no-tal? You can. If you don't you just end up with two additional files. > This is what I was running: > > setenv FREESURFER_HOME /usr/local/freesurfer > setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon > > dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where > > P07_dti.nii.gz is my DTI volume > P07.bvals P07.bvects are the bvals and bvects for my subject > P07 is my structural recons data for my P07 subject > > > > 5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using > FSLs flirt (creates mask.nii and register.dat). > > mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ > --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ > --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ > --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space. > 6) Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space: > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ > --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ > --interp trilin --no-save-reg With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space. > 7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain > the cvs_avg35? It should be in $FREESURFER_HOME/subjects (as indicated above in your command --targ). --Lilla _______________________________________________ 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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Freesurfer on Windows!
by m.muthuraman＠neurologie.uni-kiel.de 14 Nov '11

14 Nov '11

Hello Friends, I am a newcomer to freesurfer and wanted to use it in windows. I downloaded as instructed the freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi-for windows the virtual box version is 4.1.6 and installed with the required settings as mentioned in your website. I tried it in two systems one with a windows xp, 4 GB RAM, Intel Core Quad CPU, 2,40 GhZ, 64 bit system and the other system Windows 7, Intel Xeon 2.53 Ghz(2 processors), 24 Gb RAM, 64 bit system In both the sytems i was able to configure the virtual box for the xubuntu linux but it starts and progress bar in the middle and then the application closes without any errors. Is this a known problem? Am i missing something? Thanking you With regards Dr.-Ing M.Muthuraman Klinik für Neurology Schittenhelmstrasse 10 Kiel-24105 Germany.

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dt_recon registration
by Antonella Kis 14 Nov '11

14 Nov '11

Dear Bruce, I was reading the dt_recon tutorial and also the tutorial for the DTI Basics and I am very confused regarding how I should use my dt_recon in order to register my subjects on the CVS space and do a group study for FA and mean diffusivity. 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this question because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg. 2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL? 3) Can I use the talairch registration or should I use the CVS? 4) Should I add the flag --no-tal? This is what I was running: setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where P07_dti.nii.gz is my DTI volume P07.bvals P07.bvects are the bvals and bvects for my subject P07 is my structural recons data for my P07 subject 5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using FSLs flirt (creates mask.nii and register.dat). mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg 6) Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg 7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain the cvs_avg35? Thank you very much for your time, your valuable explanations and help. Antonella

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CVS template for registration
by Antonella Kis 14 Nov '11

14 Nov '11

Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled & registered in CVS space (by running mri_cvs_register), but alternatively can be normalized in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Should I run mri_mni152_register? Is CVS a good template for younger subjects (children age 6-13)? Many thanks, Antonella

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DTI Group Analysis Study
by Antonella Kis 14 Nov '11

14 Nov '11

Hi, I am trying to do a DTI Group Analysis study using a MNI152 standard space for registration. 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I have to follow all the steps starting Setting Up a Configuration File to run Tracula and then to continue with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template? 3) How can I see if there are clusters that survives to multiple comparison in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters? Thank you. Antonella

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Freesurfer November 2011