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Fw: ERROR with cvs_avg35 template
by Antonella Kis 23 Nov '11

23 Nov '11

Dear Lilla, Thanks again for your valuable help. I tried to run the mri_cvs_register for one of my subjects P07 (the structural data). By looking on the mri_cvs_register --help I see that is I want to register Subj1 to average CVS space I need to run: mri_cvs_register --mov Subj1ID Is this Subj1ID the Freesurfer file that I have after preprocessing in my case P07 (the file that contains bem, mri, label, stats, etc) or is the structural data only such as P07.nii.gz? I was trying to run it as: setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /home/elysa/Documents/Antonella/DTI_FS mri_cvs_register --mov P07 but I got an ERROR: Using the CVS template as registration target... Log file is /home/elysa/Documents/Antonella/DTI_FS/P07_to_cvs_avg35.mri_cvs_register.1111212326.log Mon Nov 21 23:26:32 EST 2011 --mov P07 $Id: mri_cvs_register,v 1.15.2.8 2011/05/23 12:37:47 lzollei Exp $ EW-LNX3 Linux EW-LNX3 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The outdir: /home/elysa/Documents/Antonella/DTI_FS/P07/cvs cvs_avg35 : at least one mean and/or Gaussian curvature file is missing (.H, .K) /usr/local/freesurfer/subjects//cvs_avg35/surf: No such file or directory. Can you please help me to solve this error? Maybe I need the cvs_avg35 template? Can you please attach the template for me? If I want to do a subject-to-subject registration (for example I am choosing the best target as template to be C24) should I run: mri_cvs_register --mov P07 --template C24 again what should be my subjects ID the structural data such as P07.nii.gz or the preprocessing data P07 or my dti file? Many thanks for your time and help. Antonella ________________________________ From: "lzollei(a)nmr.mgh.harvard.edu" <lzollei(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> Sent: Friday, November 18, 2011 2:11 PM Subject: Re: cvs_avg35 Hi Antonella, > I know that mri_vol2vol just applies the transform. --no-save-reg just > tells the > command not to save a copy of the inverse transform that gets applied. My > question is do I need to run the mri_vol2vol with the fla --no-save-reg > or with the flag --save-reg if I want to resample the diffusion data of > one subject in the structural space and same later in the CVS space? Do I > need to save the invers transform or not? That flag is not important at all for your purposes. We suggest using --no-save-reg in order to avoid having multiple copies of files around. There is no --save-reg, by the way, as that is the default behavior. --Lilla > ________________________________ > 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: Thursday, November 17, 2011 4:40 PM > Subject: RE: cvs_avg35 > > > Hi Antonella, > >> 1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I >> saw online the same question was posted on June 2011 but there is no >> answer for the question online: >> >> http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/155066… > > Have you run the cvs_registration code? If you have, then you have to have > the template. If you have not, I can make the template subject available > for you for download. > >> 2) Since for my TBSS TBSS study was used by the TBSS the nonlinear >> registration FNIRT (is about 15 times faster than IRTK on FA data and >> possibly a little more 'accurate') I would like to use for a Tal space a >> non-linear talairach registration. Can you please give >> me some directions on how I can do this? What is the default Tal >> registration (linear or non-linear) for dt_recon? > > dt_recon produces a linear registration to the Tal space. If you have ran > recon-all on your structural data you should also have access to > talairach.m3z that aligns your subject in the fsaverage space. > >> 3) When dt_recon is aligning the diffusion data in the Tal space is in >> fact aligning the register.dat data (difussion data already aligned to >> the structural data) and the output is the fa-tal.nii.gz? If not why I >> need the register.dat file? > > I don't understand your question, but > * register.dat is the registrationfile that encodes the transform going > from the diffusion to the structural space. If you want to resample any of > your diffusion related files in the structural space you will need to use > mri_vol2vol and that file to do so. > * fa-tal.nii.gz is a completely different file. It is the fa volume that > got resampled in the Tal space using a linear transformation > (talairach.xfm via the structural data). > >> 4) So by my understanding each subject will have a file called >> fa-tal.nii which in fact represents the subject's registration on the >> Tal-space? How about the mean diffusivity? I don't have only one file >> for this adc.nii. What if I want to do a non_FA values study on >> the tal space? > > You need to run the follwoing command, replacing fa with the scalar volume > of your interest. > > set reg = register.dat > set fa = fa.nii > set fatal = fa-tal.nii.gz > set cmd = (mri_vol2vol --reg $reg --tal --mov $fa --o $fatal) > >> 5) I understood that the 'registration.dat' file describes a rigid-body >> transformation from the diffusion to the structural space and in order >> to resample the structural volume in the diffusion space, I will need to >> apply the inverse of this transformation to my >> input volumes and to use for this the 'mri_vol2vol': >> >> mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \ >> --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ >> --inv --interp nearest --o >> $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ >> --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg >> Is the register.dat file created by this function mri_vol2vol? I >> believe the registration between the diffusion and structural space (so >> the register.dat file) has already >> been computed as part of the previous pre-processing step so while using >> the mri_vol2vol as above do I need to use the '--no-save-reg' flag as in >> the above example or the '--save-reg' flag? > > register.dat gets created using dt_recon and mri_vol2vol just applies that > transform. --no-save-reg just tells the command not to save a copy of the > inverse transform that gets applied. > >> 6) To resample the diffusion data of one subject in the CVS space do I >> need to run after dt_recon the mri_vol2vol as below? >> 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 $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ >> --o >> $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ >> --interp trilin --no-save-reg >> Do I need to run the mri_cvs_registration on the structural data in >> order to get the above .m3z file >> 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before I run the >> mri_vol2vol? >> If I want to have my second registration step done in the Tal space not >> CVS space since after running dt_recon I am getting the fa-tal.nii.gz >> and the fa-masked.mgz >> is this the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I >> use the CVS space)? In this case I don't need to run the last >> mri_vol2vol command? >> Sorry for asking so many questions but it is very confusing the online >> material. >> > Yes, you will run mri_cvs_register on the structural data and that will > compute your m3z file. > > fa-masked is in the native diffusion space and fa-tal is in the Talairach > space so they are not equivalent with each other, they don't live in the > same space. > > --Lilla > >> 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: Tuesday, November 15, 2011 5:11 PM >> Subject: RE:[Freesurfer] dt_recon registration >> >> >> Hi Antonella, >> >> > 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? >> >> $FREESURFER_HOME is different from your $SUBJECTS_DIR. Could you double >> check? >> >> > 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. >> >> Are you referring to a linear or a non-linear talairach registration? It >> will be you who needs to decide which space to use for analysis. You >> would want all your data to be well aligned in that space in order to >> achieve a meaningful group comparison. The decision >> might also depend on in which space you want to report your final >> results in. >> >> > 3) Do you have any suggestion regarding which registration is better >> to be used for this study? >> >> I am not familiar with your study, so it would be hard to say. >> >> > 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? >> >> dt_recon has two registration steps. One aligns the diffusion data >> (lowb) to the structural (registration.dat is the default name of the >> registration file) and the other aligns the diffusion data in the Tal >> space (the resampled fa file in that space is fa-tal). You >> can use both freeview and thregister to check the alignment of your >> volumes. >> >> Lilla >> >> >> >> >> >__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ >> _ >> > 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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reproducibleity between freesurfer 4.30 and freesurfer 5.1 for groupanalysis
by Knut J Bjuland 23 Nov '11

23 Nov '11

Hi I have used Freesurfer 5.1 for group statics. The same subjects have processed using Freesurfer 4.30 and Freesurfer 5.1. I get similar results for the group difference, but when I compare with IQ for one subpopulation, I get different results without fdr. However, when I apply FDR I get none significant results. If there had been significant results using Fdr, would it have been results that are more similar? I can send the result as tiff file. Knut J

1 0

Virtual Box crashes
by Popescu, V. 23 Nov '11

23 Nov '11

Dear all, Please help with the following problem: I am trying to run the FreeSurfer disk image on Virtual Box 4.1.6. I start it, I get: "GRUB loading please wait..." and then the Virtual Box crashes. It has 2048 MB base memory, 12 MB video memory. Thank you! Veronica

2 5

Cerebellum segmentation issues
by Warren Winter 22 Nov '11

22 Nov '11

Hi, We have a dataset of 80 subjects whose T1 MPR images (1x1x1 resolution, acquired on a Siemens 1.5T scanner) I processed with recon-all, and the segmentation of cerebellum looks questionable in nearly all of them. In some cases it is clear that non-cerebellar tissue is being labeled as cerebellum, and in other cases it is clear that the cerebellum is not being fully labeled (in both types of scenarios I confirmed by checking the voxels in all orientations). Attached are some example snapshots. In one, you can see that part of the brainstem is being labeled as cerebellum; in another, the cerebellum has not been fully labeled; and in the other two, there are disconnected "islands" labeled as cerebellum that should not be. (The suboptimal quality of the images in general is due to difficulties with scanning our young and abnormal subjects.) Can anybody suggest any fixes other than manual editing? I can upload a subject if requested. Thank you, Warren

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mri_convert not creating bvecs/bvals
by Matthew Carter 22 Nov '11

22 Nov '11

Hi, I was previously using dcm2nii to convert DWI dicom series to the nifti format. I want to change my process to use mri_convert instead, as I am having a lot of orientation problems using dcm2nii. My problem is that while dcm2nii extracted the bvecs/bvals into files separate from the nifti, mri_convert does not seem to be doing this. I looked on the mailing this for this problem, but it doesn't appear that anyone else is seeing this. Are there any command line switches or options I need to set to accomplish this? Thanks, Matt

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Re: [Freesurfer] Postdoctoral Fellowship
by Emily Rogalski 22 Nov '11

22 Nov '11

*POSTDOCTORAL TRAINEE POSITION AVAILABLE –* *APPLICATION DEADLINE 28 NOVEMBER 2011* Postdoctoral Fellowship Opportunity in the Cognitive Neurology and Alzheimer’s Disease Center at Northwestern University Feinberg School of Medicine. The trainee will work with Drs. Emily Rogalski and Marsel Mesulam on studies of language processing in primary progressive aphasia and investigations of healthy brain aging. Studies are focused on delineating language deficits associated with the progression of neurodegenerative disease as marked by structural and functional neuroimaging as well as event-related potentials. There is also an opportunity to investigate concomitants of healthy brain aging in advanced old age. The training position is competitive and supported by the Mechanisms of Aging and Dementia Training Grant. Applicants should have a PhD degree from an accredited university in cognitive aging, neuropsychology, cognitive neuroscience, or related field with experience in structural neuroimaging. *Applicant must be US citizen or permanent resident*. Experience with PET imaging is also desirable. Start date is negotiable but opportunity is available as early as December 1, 2011. Applicants should submit letters of interest, a CV, and three letters of recommendation to Kristine Zachrich, Northwestern Cognitive Neurology and Alzheimer’s Disease Center, 320 E. Superior St., Searle 11-467, Chicago, Illinois 60611; k-zachrich(a)northwestern.edu; 312-908-9023.

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mask from sig.mgh
by YUMI MAEDA 22 Nov '11

22 Nov '11

Hi, I want to make a mask file from the output file of mri_glmfit, sig.mgh. will you show me how to get it? thank you. YUMI

2 1

question about thickness file
by ZhiLiangLong 21 Nov '11

21 Nov '11

Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they are absolute values and values in lh.thickness.fwhm10.fsaverage.mgh file computed based on fsaverage template, that is, they represent relative values ? Any suggestions appreciated.

2 1

fs-fast tutorial data
by Verena Gramse 21 Nov '11

21 Nov '11

Hi, I am trying to follow the FS-FAST tutorial but I cant find the required data for it under the links specified on the tutorial site: ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz, ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz Could you tell me where I find the data? Thanks so much, Verena

2 1

Running 2 versions of Freesurfer on same computer
by Jennifer Addicks 21 Nov '11

21 Nov '11

Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset but I am now having various issues using FreeSurfer version 4.5. For Version 4.5, I path the freesurfer directories as follows (identical to before installing version 5.1): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh --------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands no longer function in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. Any help would be appreciated. thanks, Jennifer

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