Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Re: [Freesurfer] [FreeSurfer] multiple sets of control points
by Bruce Fischl 26 Sep '13

26 Sep '13

Hi Francesco please cc the list so that others can answer! This isn't the way recon-all works, but I think you can achieve what you want by copying the control.dat to control.1.dat or some such before you add additional control points so you can always go back to a previous version cheers Bruce On Thu, 26 Sep 2013, Francesco Siciliano wrote: > Hi Bruce, > > When I edit a brain a second and third time, it is helpful to create new control point files while maintaining the old ones. Because edits are not an exact science, I've noticed that sometimes new problems arise after a first edit. In my experience, creating a new control.dat file and overwriting the old one will undo the edits of the original set of control points (hence why it is useful to have multiple sets such that the original set remains in place and the second set can adjust new errors that have arisen). I understand what you mean - I try to place all of the control points I need in one sweep - however I cannot anticipate with certainty the combined effect of my edits, thus some situations call for multiple sets of control points on subsequent edits. Is it not possible to have multiple sets of control points recognized during a recon-all? > > Thanks, > Francesco > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, September 26, 2013 12:06 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu; Louis Nicholas Vinke > Subject: Re: [Freesurfer] [FreeSurfer] multiple sets of control points > > Hi Francesco > > recon-all assumes that all the control points are in the single file > <subject>/tmp/control.dat. Why are you separating them? Can you combine > them? > > cheers > Bruce > On Thu, 26 Sep 2013, Francesco Siciliano wrote: > >> Hello, >> I am currently having an issue getting my recon's to recognize multiple sets >> of control points. When I create a control point set, I make sure I select >> "control points", place them on the brainmask, and save them in the "tmp" >> folder as control.dat, control2.dat, control3.dat, etc. >> >> I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> There does not seem to be a problem when I just have one set of control >> points. However, when I have multiple sets, I can see where control points >> have not been taken into account and have not altered the intensity of the >> voxels at all. I currently have them re-running with the command recon-all >> -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference. >> >> However, as I said before, one set of control points was previousy effective >> simply using the command recon-all -autorecon2 -autorecon3 -s Subject1 >> >> Any ideas? >> >> Thanks, >> Francesco >> >> >> >> Francesco Siciliano, B.A. Research Assistant >> Department of Child and Adolescent Psychiatry >> The New York State Psychiatric Institute >> Columbia University >> 1051 Riverside Drive, Unit 74 >> New York, NY 10032 >> (212) 543-6155 >> >> > > > 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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Editing multiple volumes simultaneously in Freeview
by Jonathan Holt 26 Sep '13

26 Sep '13

I'd like to know whether or not this is possible. I am unable, at this point to figure it out. In the volumes tab I've selected both of my volumes but it seems like voxel editing only takes effect on whichever volume is in the top position. I'd like to know if I could edit both at the same time similar to tkmedits brush option allowing one to edit both main and auxiliary volumes simultaneously. Jon

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Re: [Freesurfer] Watershed and Normalization Problem.
by Erica Tatham 26 Sep '13

26 Sep '13

Hello NMR users, Here is a link to my files containing the below Watershed Error. <http://gate.nmr.mgh.harvard.edu/filedrop2/?p=in9je36> Thank you for taking the time to look at the files. Erica Tatham Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep 2013, Erica Tatham wrote: Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede from here. I have not tried to add control points as I am fairly novice to freesurfer and not quite sure how to complete this task. Thank you for any advise you are able to give, Cheers, Erica Error: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.

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Mixed effects: is data ordering always required?
by Aldo Cordova 26 Sep '13

26 Sep '13

FreeSurfer's LME wiki site states: "For computational efficiency reasons, these tools require the data ordered according to time for each individual (that is, your design matrix needs to have all the repeated assessments for the first subject, then all for the second and so on)." The dataset I need to process includes pairs (and trios) of brothers, and although they're definitely clustered statistical units, there is no pre-defined sorting of individuals within a family (at least in this study). Please note that mine is not a longitudinal study, and the need for a cluster-correction arises from brotherhood... Is FreeSurfer's LME still the appropriate choice? How should this dataset be processed in FreeSurfer for cortical thickness analysis? Would you recommend another option? Regards, Ricardo

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[FreeSurfer] multiple sets of control points
by Francesco Siciliano 26 Sep '13

26 Sep '13

Hello, I am currently having an issue getting my recon's to recognize multiple sets of control points. When I create a control point set, I make sure I select "control points", place them on the brainmask, and save them in the "tmp" folder as control.dat, control2.dat, control3.dat, etc. I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1 There does not seem to be a problem when I just have one set of control points. However, when I have multiple sets, I can see where control points have not been taken into account and have not altered the intensity of the voxels at all. I currently have them re-running with the command recon-all -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference. However, as I said before, one set of control points was previousy effective simply using the command recon-all -autorecon2 -autorecon3 -s Subject1 Any ideas? Thanks, Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Douglas N Greve 26 Sep '13

26 Sep '13

Hi Daniel, please remember to post to the list instead of me directly ... to answer your question, this is probably just a matter of scaling. Try removing the mean and dividing by the standard deviation of the linear, quad, and cubic. More recent versions of FS should do this automatically. doug On 09/25/2013 06:01 AM, Daniel Klein wrote: > Hi Doug, > > thanks a lot. > I want to use qdec for this pupose. > > When i add Age (cubic) as continous factor and age as nuisance factor > in the model it works fine. > > In the model age (square) as continous factor and age as nuisance i > get the following error: > > Creating output directory > /Users/dolphinede/Desktop/Probanden/qdec/Untitled > Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh > INFO: gd2mtx_method is dods > Saving design matrix to > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat > Normalized matrix condition is 22042.4 > Design matrix ------------------ > 1.000 169.000 13.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 256.000 16.000; > 1.000 225.000 15.000; > 1.000 400.000 20.000; > 1.000 196.000 14.000; > 1.000 256.000 16.000; > 1.000 144.000 12.000; > 1.000 169.000 13.000; > 1.000 361.000 19.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 196.000 14.000; > 1.000 361.000 19.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 324.000 18.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 324.000 18.000; > 1.000 529.000 23.000; > 1.000 400.000 20.000; > 1.000 484.000 22.000; > 1.000 529.000 23.000; > 1.000 324.000 18.000; > 1.000 484.000 22.000; > 1.000 324.000 18.000; > 1.000 256.000 16.000; > 1.000 361.000 19.000; > 1.000 256.000 16.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 256.000 16.000; > 1.000 256.000 16.000; > 1.000 441.000 21.000; > 1.000 289.000 17.000; > 1.000 289.000 17.000; > 1.000 225.000 15.000; > 1.000 256.000 16.000; > 1.000 225.000 15.000; > 1.000 225.000 15.000; > 1.000 400.000 20.000; > 1.000 289.000 17.000; > 1.000 324.000 18.000; > 1.000 256.000 16.000; > 1.000 484.000 22.000; > 1.000 361.000 19.000; > 1.000 256.000 16.000; > 1.000 529.000 23.000; > 1.000 400.000 20.000; > 1.000 484.000 22.000; > 1.000 441.000 21.000; > 1.000 324.000 18.000; > 1.000 361.000 19.000; > 1.000 484.000 22.000; > 1.000 361.000 19.000; > 1.000 441.000 21.000; > 1.000 324.000 18.000; > 1.000 144.000 12.000; > 1.000 361.000 19.000; > 1.000 441.000 21.000; > 1.000 441.000 21.000; > 1.000 441.000 21.000; > 1.000 529.000 23.000; > 1.000 324.000 18.000; > 1.000 361.000 19.000; > 1.000 289.000 17.000; > 1.000 529.000 23.000; > 1.000 484.000 22.000; > 1.000 441.000 21.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 196.000 14.000; > 1.000 361.000 19.000; > 1.000 196.000 14.000; > 1.000 169.000 13.000; > 1.000 400.000 20.000; > 1.000 361.000 19.000; > -------------------------------- > ERROR: matrix is ill-conditioned or badly scaled, condno = 22042.4 > -------------------------------- > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > If you seek help with this problem, make sure to send: > 1. Your command line: > mri_glmfit --y > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods > --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf > fsaverage lh --label > /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat > --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat > > 2. The FSGD file (if using one) > 3. And the design matrix above > Error in Analyze: command failed: mri_glmfit --y > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh --fsgd > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/qdec.fsgd dods > --glmdir /Users/dolphinede/Desktop/Probanden/qdec/Untitled --surf > fsaverage lh --label > /Users/dolphinede/Desktop/Probanden/fsaverage/label/lh.aparc.label --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat > --C > /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts/lh-Avg-pial_lgi-Alter2-Cor.mat > > Best wishes > > Daniel > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Di, 24 Sept 2013 9:35 pm > Betreff: Re: [Freesurfer] Effects of age on different parameters > (thickness, lGI...) > > Hi Daniel, you can do this the way that you have specified, but, as you > point out, one of the covariates will have to be a nuisance variable, > meaning that it will not get tested. If you need to test all 3, then > you'll have to use mri_glmfit with and FSGD file > doug > > > On 09/24/2013 05:39 AM, Daniel Klein wrote: > > Dear FreeSurfer experts, > > > > I want to test linear, square and cubic effects of age on different > > parameters (thickness, lGI....) with qdec. > > > > I add age (square) and age (cubic) as column in my qdec table. > > > > Am i right to see only the square effects: > > Add Age square as continous factor and age (maybe age cubic too?) as > > nuisance factor in the model. > > > > Best wishes and thanks a lot. > > > > Daniel > > > > > > _______________________________________________ > > Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Surface to nifti prime vertices
by Connor Lane 26 Sep '13

26 Sep '13

Hi all, I am trying to convert a surface file to nifti using mri_surf2surf. The problem is that my surface has a prime number of vertices, so I can't use —reshape. Is there a way around this issue? Thank you in advance, Connor Lane

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Tracula bval and bvec
by Garikoitz Lerma-Usabiaga 26 Sep '13

26 Sep '13

Hi Anastasia, I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Ok, so I understand that our problem is that we don't have MGH Siemens Dicom. So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one. I can edit "set dcm_list = " to include all the newly created .nii files, but My question is: - How can I specify every .bvec value for every subject? In the dmrirc file everything I see is a "set bvecfile = " option. Thank you very much, Gari

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R: Re: Import FS data to FSL
by stdp82＠virgilio.it 25 Sep '13

25 Sep '13

For FSL guide: Normal 0 false false false IT JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Cambria; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin;} I should transforms a group of labels into a surface Usage: label2surf -s <surface> -o <outputsurface> -l <labels> Compulsory arguments (You MUST set one or more of): -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files Optional arguments (You may optionally specify one or more of): -v,--verbose switch on diagnostic messages -h,--help display this message but I should create a lh/rh.frontal.label and use it for label2surf.With mdi_binarize I can create .nii.gz but no .label. Is that correct?How I can do it? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Import FS data to FSL 1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL. On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > Hi list, > > I have 2 questions, please. > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > (FSL)? > > 2-I'd like to export cortical masks from FS to FSL. > > An option is mri_binarize but this way failed in probtrackx (fsl). > FSL list have advised me that I should use label2surf command to convert > label to surface files. > > Where could find the .label (according to FreeSurferColorLUT.txt) to build > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > Do you have other ways that you advise me? > > > Thanks, > > > Stefano > > > > 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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Control points displaying differently in freeview as opposed to tkmedit
by Jonathan Holt 25 Sep '13

25 Sep '13

I've read in the mailing list archives people have had issues with tkmedit and free view displaying control points differently. For me the first brain I've loaded up has a single control point in free view that does not show in tkmedit. Others have complained of free view showing points seemingly at random? Is this a user related issue perhaps? Here are the contents of the control.dat file in question 55.000000 -60.000000 -41.000000 54.000000 -61.000000 -41.000000 53.000000 -62.000000 -41.000000 52.000000 -59.000000 -37.000000 52.000000 -63.000000 -40.000000 2.000000 48.000000 14.000000 2.000000 47.000000 13.000000 1.000000 46.000000 11.000000 1.000000 41.000000 8.000000 1.000000 40.000000 6.000000 0.000000 45.000000 10.000000 0.000000 44.000000 10.000000 0.000000 43.000000 10.000000 0.000000 39.000000 6.000000 0.000000 38.000000 6.000000 0.000000 37.000000 7.000000 -1.000000 42.000000 10.000000 info numpoints 17 useRealRAS 0 the errant control point is on slice 128 best viewed coronally. jon

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