Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

2 1

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

2 3

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.

2 1

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

2 3

Viewing auxiliary and main volumes simultaneously
by Jonathan Holt 25 Sep '13

25 Sep '13

Is there any way to accomplish this? Jon

5 5

Surface doesn't match error
by pfotiad＠nmr.mgh.harvard.edu 25 Sep '13

25 Sep '13

Hi FS Community, I have been using control points and adding wm voxels in the wm.mgz volume of a subject, in order to fix the reconstruction, and after doing so for a number of times, when I tried to run the command: tkmedit <subj_ID> brainmask.mgz -aux wm.mgz -surfs the following message popped up: Reading 574 control points... Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.pial): surface doesn't match /cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Reading 574 control points... Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl % and after tkmedit loads, the lh.pial is not shown. I ran mris_euler_number on lh.pial and lh.white and they are both equal to 2 as they should. I was wondering whether you happen to know why is this happening and how to fix it. (I am using FS 5.3) Thank you for your time! Best, Panos

2 2

Calculating surface values
by Jonathan Holt 25 Sep '13

25 Sep '13

I'm curious whether or not freesurfer, when calculating surface values, takes the original surface into account? If not, which surfaces are included in this calculation? jon

2 1

Brodmann Area Atlas
by Michael Kranz 25 Sep '13

25 Sep '13

Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas? Thanks, Mike

4 7

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

25 Sep '13

Thanks Anastasia. I have some problem when I use mri_binarize.FSL list and guide advise me to use label2surf. There are a way to obtain specific labels in .label instead of .nii.gz? 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 > > > > _______________________________________________ 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.

1 0

Post-surgery volumes and hippocampal subfield segmentation
by Germeyan, Sierra (NIH/NINDS) [F] 25 Sep '13

25 Sep '13

Hi all, A few questions. 1. Is there a way to run scans of post-surgical brains that takes resections into account and gives more accurate results than "recon-all -all"? 2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do this indirectly by finding the difference between total intracranial volume that FreeSurfer gave for scans pre- and post- surgery. However, I rarely obtained reasonable numbers with this method. 3. After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would give me the total hippocampal volume), and compared the sum to the hippocampal volume that FreeSurfer gave after running recon-all -all. They weren't the same! Why would these differ? Thanks very much for any advice you can give!

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