Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Re: [Freesurfer] combining masks in freesurfer ??
by Subhabrata Chaudhury 30 May '13

30 May '13

Hello Doug, Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface data, right ? Best wishes Subha ----- Original Message ----- From: Douglas N Greve Sent: 05/30/13 05:40 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] combining masks in freesurfer ?? you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: > Hi All, > Is there a way to combine multiple binary volumetric masks into a > single binary volumetric mask in freesurfer ? > Please let me know. > Thankyou > Subha > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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/ _______________________________________________ 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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tkmedit on ssh remote machine error
by Jon Wieser 30 May '13

30 May '13

hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) i have set X11forwarding to yes in the /etc/sshd_config file so xeyes works ok remotely Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
by Glen Lee 30 May '13

30 May '13

Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen

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Re: [Freesurfer] mris_divide_parcellation color table error (fwd)
by Bruce Fischl 30 May '13

30 May '13

Hi Tina is this (attached) more what you wanted? If so, then I think you want to use mris_make_face_parcellation instead of mris_divide_parcellation. I can't remember what they used in that paper, but in mris_divide_parcellation I try to have the different units within a parcel have similar colors (which evidentally fails when you split it so finely) Bruce On Thu, 30 May 2013, Tina Jeon wrote: > I am running version 5.3- the latest version. I also tried running the codes > on v5.0 and got the same result. Is there any way I can change the color > table so that the colors of the parcellation are unique? > > Thanks, > Tina > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wednesday, May 29, 2013 8:41 PM > To: Tina Jeon > Subject: Re: [Freesurfer] mris_divide_parcellation color table error > > Sure > > > > On May 29, 2013, at 9:36 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> wrote: > >> The colors are visually different by a shade then loop every 4 or so colors. >> I think the color table may be running on a loop? I can send the annot and >> surface file if you need that as well. >> >> Best, >> Tina >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, May 29, 2013 8:02 PM >> To: Tina Jeon >> Subject: Re: [Freesurfer] mris_divide_parcellation color table error >> >> p.s. can you send me the splittable text file ? I seem to have deleted >> it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon >> wrote: >> >>> Yes same result as with freeview. >>> >>> Sent from my iPhone >>> >>> On May 29, 2013, at 7:46 PM, "Bruce Fischl" >>> <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> Hi Tina >>> Did you try visualizing it in tksurfer? >>> Bruce >>> >>> >>> >>> On May 29, 2013, at 7:22 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> >>> wrote: >>> >>> Hello freesurfers, >>> >>> >>> >>> I am trying to create a figure similar to the Hagmann et >>> al 2008 paper with 998 rois overlaid onto the surface, >>> however, I am finding that there is no random, unique >>> color for each parcellation unit like described in the >>> help file for mris_divide_parcellation. >>> >>> >>> >>> I have attached a snapshot of my annotation file overlaid >>> onto the surface, as you can see, the color iterates the >>> same/similar color for a particular label. Can you tell me >>> what I am doing wrong? Is there a pre-existing atlas as >>> described in the Hagmann paper? >>> >>> >>> >>> My input: >>> >>> mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh >>> ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 >>> -03-25.gcs ./lh.aparc.998rois.annot >>> >>> >>> >>> mris_divide_parcellation subject_name lh >>> ./lh.aparc.998rois.annot ./splittable.txt >>> ./lh.annotation.998rois_26.annot >>> >>> >>> >>> >>> >>> Many thanks, >>> >>> >>> >>> Tina Jeon, MS >>> >>> UT Southwestern Medical Center ‘14 >>> >>> >>> >>> >>> _____________________________________________________________________ >>> _______ >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >>> >>> <neonate_buckner40_atlas.png> >>> >>> <splittable.txt> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >> <splittable.txt> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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WARNING: tcsh v6.17.06 has an exit code bug!
by Andrew Bock 30 May '13

30 May '13

Hello everyone, I just updated to Freesurfer 5.3.0, my OS is Ubuntu 12.04. When I run 'recon-all -i <T1 image> -subjid <subject name>' I receive the following error: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! The directory structure appears to be set up correctly, and the command finishes without error. I do not receive this error when using Freesurfer 5.1.0. I have yet to run 'recon-all -all -subjid <subject name>' in 5.3.0. Any ideas on what produces this error? is it safe to ignore? Thanks in advance, Andrew

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Re: [Freesurfer] mris_divide_parcellation color table error
by Tina Jeon 30 May '13

30 May '13

I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> wrote: > The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. > > Best, > Tina > > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Wednesday, May 29, 2013 8:02 PM > To: Tina Jeon > Subject: Re: [Freesurfer] mris_divide_parcellation color table error > > p.s. can you send me the splittable text file ? I seem to have deleted > it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon > wrote: > >> Yes same result as with freeview. >> >> Sent from my iPhone >> >> On May 29, 2013, at 7:46 PM, "Bruce Fischl" >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> >> Hi Tina >> Did you try visualizing it in tksurfer? >> Bruce >> >> >> >> On May 29, 2013, at 7:22 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> >> wrote: >> >> Hello freesurfers, >> >> >> >> I am trying to create a figure similar to the Hagmann et >> al 2008 paper with 998 rois overlaid onto the surface, >> however, I am finding that there is no random, unique >> color for each parcellation unit like described in the >> help file for mris_divide_parcellation. >> >> >> >> I have attached a snapshot of my annotation file overlaid >> onto the surface, as you can see, the color iterates the >> same/similar color for a particular label. Can you tell me >> what I am doing wrong? Is there a pre-existing atlas as >> described in the Hagmann paper? >> >> >> >> My input: >> >> mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh >> ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 >> -03-25.gcs ./lh.aparc.998rois.annot >> >> >> >> mris_divide_parcellation subject_name lh >> ./lh.aparc.998rois.annot ./splittable.txt >> ./lh.annotation.998rois_26.annot >> >> >> >> >> >> Many thanks, >> >> >> >> Tina Jeon, MS >> >> UT Southwestern Medical Center ‘14 >> >> >> >> >> _____________________________________________________________________ >> _______ >> >> UT Southwestern Medical Center >> The future of medicine, today. >> >> <neonate_buckner40_atlas.png> >> >> <splittable.txt> >> >> _______________________________________________ >> 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. >> >> >> > <splittable.txt>

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Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
by Yizhou Ma 30 May '13

30 May '13

Hi Michael, This method seems cool. I'll try to implement it. Thank you so much. Best, Cherry On Wed, May 22, 2013 at 4:17 PM, Harms, Michael <mharms(a)wustl.edu> wrote: > > I've also posted in the past on a set of "expert options" that helped > our surfaces in the temporal lobe considerably. You should be able to > locate that post in the archives. > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mharms(a)wustl.edu > > From: Yizhou Ma <ym850(a)nyu.edu> > Date: Wednesday, May 22, 2013 2:30 PM > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu>, Chris Watson < > Christopher.Watson(a)childrens.harvard.edu> > > Subject: Re: [Freesurfer] temporal lobe left out in pial surface - edits > on brainmask.mgz or brain.finalsurfs.mgz? > > Ok. I'll give it a try. Thanks, Chris & Bruce! > > > On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Cherry >> >> Chris is right. Putting control points in the WM will help the pial >> surface as well. >> >> cheers >> Bruce >> >> On Wed, 22 May 2013, Yizhou Ma wrote: >> >> Hi Chris, >>> Thanks a lot. I agree that control points should actually only be put in >>> white matter. I'm just not sure if I can expand the pial surface to a >>> satisfactory extend if I only do edits in the white matter. It seems to >>> me >>> that the problem here is that the signal weakened in the lower part of >>> the >>> brain so that the gray matter doesn't have adequate intensity to be >>> included >>> in the pial surface (the values are around 30). >>> >>> Thanks, >>> Cherry >>> >>> >>> On Wed, May 22, 2013 at 3:14 PM, Chris Watson >>> <Christopher.Watson(a)childrens.**harvard.edu<Christopher.Watson(a)childrens.harvard.edu>> >>> wrote: >>> You need to place the control points in the white matter, not >>> around it. >>> >>> On 05/22/2013 03:04 PM, Yizhou Ma wrote: >>> Dear FS experts, >>> I have a subject where large portions of temporal lobe is not >>> included in the pial surface. A member in my lab has suggested >>> edits on brain.finalsurfs.mgz. However, in the following page it >>> is indicated that edits on brain.finalsurfs.mgz is only intended >>> for cases regarding inclusion of cerebellum. Can anyone please >>> let me know which volume I should be working on in this case? >>> >>> http://ftp.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**PialEdits<http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits> >>> >>> Thanks, >>> Cherry >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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-mai >>> l >>> contains patient information, please contact the Partners Compliance >>> HelpLin >>> e at >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in er >>> ror >>> but does not contain patient information, please contact the sender and >>> prop >>> erly >>> dispose of the e-mail. >>> >>> >>> >>> >>> >>> > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. >

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Exporting surface coordinates to Nifti header space
by schreibm＠informatik.hu-berlin.de 30 May '13

30 May '13

Hi Freesurfers! I'd like to load my original Nifti T1 image data (subject.nii) and the wm/gm-surface coordinate data (for instance lh.pial) in matlab as vectors in the same coordinate system. If I do it in the naive way, i.e. [x,y,z,1]=[i,j,k,1]*sform' for the Nifti coordinates resp. freesurfer_read_surf(...) for the surface nodes, then surface and Nifti appear not to be coregisterred. It looks as though there would be a spacial shift missing. Although having tried several matrices I cant figure out which is the one to choose. Inspecting the Data by Freeviewer I observe the same spacial shift, inspecting it by 'tkmedit subject_id brainmask.mgz lh.pial' everything is fine. Could you tell me, which transform I have to apply to the surface coordinates? That would be really nice. Thanks and best Regards, Max

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volume and mean value of a custom made white matter ROI
by Subhabrata Chaudhury 30 May '13

30 May '13

Hello Everyone, Greetings. I am learning freesurfer tricks. I am stuck and have a question. I have run 10 subjects through freesurfer. I have made custom volume regions for arcuate fasciculus for 10 subjects. Now I want to get some measurements inside this region. How do I get the volume of the region ? How do I get the mean T1 intensity in this region ? Can somebody share some script or point me to some script ? Will be very thankful. Subha

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Re: [Freesurfer] error loading volume brainmask.gcut.mgz
by Bruce Fischl 30 May '13

30 May '13

is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote: > Yes I did run mri_info, these are the results: > Volume information for brainmask.gcuts.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: INT (1) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = > 8.4909 > : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = > -0.4031 > : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = > -34.1638 > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1.0000 0.0000 -0.0000 136.4909 > -0.0000 0.0000 1.0000 -128.4031 > 0.0000 -1.0000 -0.0000 93.8362 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 -0.0000 -0.0000 136.4909 > -0.0000 -0.0000 -1.0000 93.8362 > -0.0000 1.0000 -0.0000 128.4031 > 0.0000 0.0000 0.0000 1.0000 > > Cheers > > > 2013/5/30 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > did you run out of disk space? Can you run mri_info on it? > On Thu, 30 May 2013, Claudia Dacquino wrote: > > Hi Freesurfers,I'm trying to remove some dura which > affect my surfaces with > the command > > recon-all -skullstrip -clean-bm -gcut -subjid > > but then I can't use tkmedit to check that. > The message I get is: > > Error: Loading volume brainmask.gcut.mgz Couldn't > read the anatomical > volume. Tkmedit couldn't read the volume you > specified. This could be > because the image format wasn't recognized, or it > couldn't find the proper > header, or the file(s) were unreadable, or it was > the wrong size. > > Actually I did check in brainmask.gcut.mgz directory > properties, and I saw > the size of image is something like 150 KB, instead > of 1 MB like is > brainmask.mgz. > > What is the problem? > > Thanks, > Claudia > > > > > 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 May 2013