Freesurfer

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30132 discussions

dmri_train error
by Michielse Stijn (SP) 17 Jun '11

17 Jun '11

Hello FreeSurfer users, Currently I'm trying to analyze DWI data using the new TRACULA package. The packages looks promising and I managed to process a few tracts (the ILF and UNC) But now I would like to process more tracts at once. So I ran the trac-all subroutines to check every step. All goes well until the Pathway priors have to be generated. The subroutine is "trac-all -prior -c dmrirc" with all 18 tracts specified in the configuration file. My dataset contains 4 participants for the first run. The error occurs in "dmri_train" and says: dmri_train(75687) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort So there is something wrong in the dynamic memory allocation. The process takes up to 3GB of memory. The system contains: Memory: 16 GB 1066 MHz DDR3; Model Identifier: MacPro4,1; Processor Name: 2 x Quad-Core Intel Xeon; Processor Speed: 2 x 2.93 GHz System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0 Can someone help me out on this error? Kind regards, Stijn Michielse Maastricht University

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Unsupported slice timing problem
by Louie Perkins 17 Jun '11

17 Jun '11

We recently ran into an issue with Freesurfer's mri_convert tool where it gives an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5). Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice_code possibilities are not included in the if-statement, NIFTI_SLICE_ALT_INC2 and NIFTI_SLICE_ALT_DEC2. These are defined in include/nifti1.h (comment says they were added in 2005), so I'm checking to see if there is a reason they are not allowed, or if this bit of code was just never updated to reflect the latest nifti1.h. Thanks for any help, -Louie Perkins

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ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
by Jeff Sadino 17 Jun '11

17 Jun '11

Hello, When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects Directory, and then reran them using the FS5 recon-all stream. This updated their subject folders with the FS5 changes, but not in as many places as I would have thought. For example, on 6 test subjects, I created their FS5 folders from FS4 folders that I copied over and then ran the FS5 recon-all stream. I also created another copy of their FS5 folders from scratch. The average difference in their ICV values was -12,000 mm^3. Is it to be expected that FS5 reconstructions running on FS4 folders will not include all possible improvements? If I want to get an accurate an ICV measurement as possible, is it advisable to rerun all of my subjects in FS5, starting from scratch? As always, thank you for your valuable assistance! Jeff Sadino

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Name of the atlas
by Dalwani, Manish 16 Jun '11

16 Jun '11

What atlas does aparc2009 represent? Regards, Manish Dalwani Sr. PRA Dept. of Psychiatry University of Colorado

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Overlay issues on freeview
by iacono＠nmr.mgh.harvard.edu 16 Jun '11

16 Jun '11

Hi all, I am trying to overlay a map on a specific subcortical structure (the caudate). -I obtained the surface of the structure using the command: mri_tessellate structure.nii.gz 1 lh.structure.surf -then I projected my map on the surface using: mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear Everything seems to work properly. I am able to see the result using tksurfer. However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus. Could you give me an advice about that? Thanks Maria

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Re: [Freesurfer] Whole brain parcellation.
by Sudhin A. Shah 16 Jun '11

16 Jun '11

Hi Sorry for bothering you again, but I am not sure I understand. I was running whole brain correlation analysis (voxel by voxel). BUT for comparison purposes, I want to compute region by region correlation matrix. So, I want to divide up the brain into freesurfer parcellated regions - i.e. with no overlap, but with full coverage of whole brain. I have looked at FreeSurferColorLUT.txt and am confused because there are several sets and overlap (eg. 19 and 55 vs 2035..) If I use the following, can I ensure no overlap and full coverage? 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86 2)Cortex: 1002- 1034, 2002- 2034 I am asking if there is an established list of whole brain parcellations before I rely on label names to choose the ROIS On 06/13/11, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Anything that is non-0 will cover the whole brain. > doug > > Sudhin A. Shah wrote: > > Hi, thank you. Is there a range in the labels that will ensure that I am including the whole brain? I.e. I see labels for Cx, but not subcortical.. > > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain? > > > > Thank you, > > S > > > > > > > > On Jun 13, 2011, at 10:59 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > > > > >> That is fine, or you can use mri_binarize with the --match option. The numbers that correspond to each label can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as I described in my previous email with tkmedit: > >> > >> tkmedit subject orig.mgz -aux aseg.mgz -aseg > >> > >> doug > >> > >> > >> Sudhin A. Shah wrote: > >> > >>> I mean that I am using FSL to create binary masks from freesurfer parcellated regions. Unless there is a better way :) > >>> > >>> S > >>> > >>> > >>> > >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >>> > >>> > >>> > >>>> What do you mean you are doing it with FEAT? > >>>> > >>>> Sudhin A. Shah wrote: > >>>> > >>>> > >>>>> Hello, > >>>>> > >>>>> I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. > >>>>> > >>>>> I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. > >>>>> > >>>>> Thank you, > >>>>> > >>>>> S > >>>>> > >>>>> > >>>>> ------------------------------------------------------------------------ > >>>>> > >>>>> _______________________________________________ > >>>>> 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) > >>>>> > >>>>> > >>>> -- > >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>>> > >>>> _______________________________________________ > >>>> 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-mail > >>>> contains patient information, please contact the Partners Compliance HelpLine at > >>>> http://www.partners.org/complianceline (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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > >> > > > > > > > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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) > -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514

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Custom color table overlay for ROI analysis
by Shashwath Meda 16 Jun '11

16 Jun '11

Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this? Thanks, Shashwath

5 7

pre-bedposted data in tracula
by Scott Sorg 16 Jun '11

16 Jun '11

Hello, If I already ran bedpostx on my diffusion data, how can I skip this step in tracula and still get it to run smoothly. Thank you, Scott

3 2

mri_cc error
by Vanessa Lim 16 Jun '11

16 Jun '11

Hi, does anyone know what to do here please? I can see it in file manager. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz CG will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz mghRead(/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz, -1): could not open file mri_cc: could not read aseg volume from /home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz also assuming I fix this error how do I resume from this point (or another point) the rest of recon-all autorecon2? Thanks, Vanessa

2 1

display amygdala only in tkmedit?
by Ariel Brown 15 Jun '11

15 Jun '11

Hi There, I'm trying to come up with an image of the amygdala to display on a single subject's brainmask.mgz. Can I display the aseg labels individually in tkmedit? Thanks so much, Ariel --------------- Ariel Brown, PhD Research Fellow Department of Psychiatry Mass General Hospital & Harvard Medical School Visiting Scientist Department of Brain & Cognitive Sciences Massachusetts Institute of Technology

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