Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30051 discussions

Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

Thanks for your prompt response. > Is this the most current version of FreeSurfer? We have the 07-24-2003 version, however I am sure that we saw this working with this version of Freesurfer last summer. If possible we would prefer to stick with our current version and avoid updating and re-installation. > What input are you giving to load the bfloat? In tksurfer File->Load Overlay, we specified the file y_doss-thickness-250lh_000.bfloat Robert ----- Original Message ----- From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> Date: Thursday, June 3, 2004 3:10 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > Hi Brian, > > > > Thanks for the e-mail. Unfortunately we are still having > problems getting the graph window to appear. Here is what we have: > > > > 1) > > > load the y values into tksurfer to see scatter plots. > > We tried to load the .bfloat file as an overlay, and got this > message in the log window: > > > > sclv_read_bfloat_values: error in FunD_New > > > > Not a directory > > > > > > 2) Here are the messages I get in the log window when loading > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > INFO: ignoring tag Creator > > INFO: ignoring tag SmoothSteps > > INFO: ignoring tag SUBECTS_DIR > > INFO: ignoring tag SynthSeed > > Read one slice only. Did you put all the slices in the same > directory?> WARNING: Could not get the graph title. > > WARNING: Could not get the measurement label. > > WARNING: Could not get the subject name. > > WARNING: Could not get the data file name. > > ERROR: Could not get number of classes. > > > > > > Thanks for your help, > > > > Robert > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kevin Teich > > > >

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Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

Hi Brian, Thanks for the e-mail. Unfortunately we are still having problems getting the graph window to appear. Here is what we have: 1) > load the y values into tksurfer to see scatter plots. We tried to load the .bfloat file as an overlay, and got this message in the log window: sclv_read_bfloat_values: error in FunD_New Not a directory 2) Here are the messages I get in the log window when loading y_doss-thickness-250lh.fsgd file (No graph window appears): INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBECTS_DIR INFO: ignoring tag SynthSeed Read one slice only. Did you put all the slices in the same directory? WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. Thanks for your help, Robert

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tkmedit cpu usage
by Jason Bacon 03 Jun '04

03 Jun '04

Hi all, Is it normal for tkmedit to saturate the cpu when freesurfer is idle? We have two researchers running the tutorial, and the tkmedit process never stops crunching the cpu, no matter how long it's been since they initiated something. We're running the latest snapshot for Linux and OS/X. Thanks, Jason

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scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 02 Jun '04

02 Jun '04

Hello, I would like to be able to click on a vertex in tksurfer and see a scatter plot of all individual subject's thickness at that vertex--to see what went into our between group comparison (implemented w/ mris_glm) and the resulting sigt value at that point. I saw a display that looked like this before, but I do not remember how to create it. Is this possible, and how do I create the plot? Thank you for your help, Robert Twomey Center for the Study of Learning Georgetown University

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func2roi
by Tamara Knutsen 01 Jun '04

01 Jun '04

i do not yet have any anatomically defined area labels, and i have a functional comparison that activates the area i want as my ROI, but some other areas as well. is it possible to manually edit the functionally thresholded mask to have only the ROI i want, by somehow deleting the undesired voxels (or changing their value to 0)? let me know. thanks, t

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relationship between white and pial surfaces
by Satrajit Ghosh 31 May '04

31 May '04

Is there an easily quantifiable relationship between the white and pial surfaces? Such as: pial_vertex = white_vertex + vertex_thickness*vertex_normal; I understand that vertex_normals could be computed in different ways (Eg, Desbrun et al 2000). If so, could we find out which computation scheme is used (a reference would be sufficient)? Thanks, Satra -- Satrajit S. Ghosh Department of Cognitive and Neural Systems, Boston University (I): http://www.cns.bu.edu/~satra

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Freesurfer & tkmedit
by X.Chitnis＠iop.kcl.ac.uk 28 May '04

28 May '04

Hi, I'm a new user of Freesurfer and am having a problem viewing files. I installed the software on a PC running Mandrake Linux 10.0. Everything seemed fine. Mandrake comes with Tcl/Tk 8.4 rather than 8.3 which freesurfer looks for, so I made links back to (for example) libtcl8.3.so When I try to view the files through the "volume" button, the button changes to puple and says "quit volume" but no window appears, and after ~20 seconds it just goes back to "volume". No error message is generated in the log - it just says "Command Finished". Having searched the mailing list, I tried it from the command line with: /home/spbcxac/freesurfer/bin/Linux/tkmedit.static test T1 It pauses for a few seconds, as if it is trying to display something, but then goes back to the prompt without a window appearing. Again no error message is generated. I would be very grateful for any suggestions as to what I'm doing wrong! Best wishes Xavier Chitnis Institute of Psychiatry, London

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RAS to mm
by Rutvik Desai 27 May '04

27 May '04

Hello, I have FreeSurfer surface models created from Talairached AFNI (+tlrc) briks. I am interested in computing distances between nodes on these (orig or smoothwm) surfaces in mm units. The +tlrc briks are 161mm (R-L) X 191mm (A-P) X 151mm (I-S). with 1X1X1 mm^3 voxels. talairach.xfm or any such files or transformations were not used. As I understand, FreeSurfer would resample this brik into a 256 X 256 X 256 RAS coordinate space. There are the coordinates you see when you look at say a ?h.smoothwm.asc file. To interpret these coordinates in terms of mm, one could multiply the X coordinate by 161/256, Y by 191/25, and Z by 151/256. The distance between two nodes computed with these modified coordinates should be in mm. Is this correct or am I missing something? thanks, Rutvik

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cache_volume_range
by orphoebe＠polyu.edu.hk 27 May '04

27 May '04

Hi Bruce and Yasunari, Thanks for your suggestions. The setenv LANG C works for 'Out of memory' error. However, after I get through the mritotal, it comes with another error of 'Not implemented yet in cache_volume range...' as follows. I see that somebody asks this question before but I can't find the solution. Any suggestions? Thanks, Phoebe. ******************************* mri_add_xform_to_header /mnt/usb1/uch_language/inflated/040415_ckh/mri/transforms/talairach.xfm /mnt/usb1/uch_language/inflated/040415_ckh/mri/orig /mnt/usb1/uch_language/inflated/040415_ckh/mri/orig Thu May 27 15:56:30 GMT+8 2004 --------------------------------------------- Nu Intensity Correction Thu May 27 15:56:30 GMT+8 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, te=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [phoebe@marvin:/mnt/usb1/uch_language/inflated/040415_ckh/mri/] [2004-05-27 15:56:40] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_6196/ nu/nu0.mnc nu/nu1.imp Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................DoneNot Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() ---- Original message ---- >Date: Wed, 26 May 2004 14:45:07 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Out of memory error >To: orphoebe(a)polyu.edu.hk >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi Phoebe, > >I think this is a problem with the MNI tools that they know about. Someone >posted a solution here, which I think involved setting the LANG env >variable. Check out the MNI website. > >Bruce > >On Thu, >27 May 2004 orphoebe(a)polyu.edu.hk wrote: > >> Hi, >> >> I recently collected a 1-mm anatomical scan and tried to >> inflate it using the recon-all script. However, I got an >> error message 'Out of memory!' everytime at mritotal. I tried >> to increase the output size when I converted the dcm images to >> COR format, but it didn't work either. Do you have any >> suggestions? >> >> Thanks, >> Phoebe. >> >> --- >> Phoebe Suk-tak Chan, Ph.D. >> Assistant Professor >> Hong Kong Polytechnic University >> Department of Optometry and Radiography >> Hunghom, Kowloon >> Hong Kong SAR >> Tel: (852) 2766 6095 >> Fax: (852) 2764 6051 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Out of memory error
by orphoebe＠polyu.edu.hk 26 May '04

26 May '04

Hi, I recently collected a 1-mm anatomical scan and tried to inflate it using the recon-all script. However, I got an error message 'Out of memory!' everytime at mritotal. I tried to increase the output size when I converted the dcm images to COR format, but it didn't work either. Do you have any suggestions? Thanks, Phoebe. --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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