Freesurfer September 2010

freesurfer@nmr.mgh.harvard.edu

93 participants
127 discussions

Mri_label2label problem?
by Pye, Brandon (NIH/NIMH) [F] 21 Sep '10

21 Sep '10

Hey guys, We are using mri_label2label to convert a label created from a cluster (using mri_surfcluster) from an average subject to each individual subject. We have 6 individual labels that we are converting. All of the analysis is done using surface data. I use the command in the generalized form listed below: Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh 5 of the 6 labels transfer well, but a 6th label translated to the correct anatomical location, but the number of labeled vertices is greatly reduced after the translation. This problem persists across all subjects. There doesn't appear to be much interior to the label, just a lot of the outline of the label (i.e. If the outline of the label is yellow and the interior is blue, I see a lot of yellow and not much blue, as if there are a bunch of small "islands"). The region on them most inferior part of the lateral surface approximately where the temporal and occipital lobes meet. Any ideas what might be going on? Thanks, --------------------------------------------------------------------- Brandon Pye Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 402-3893 Fax: (301) 402-0921 brandon.pye(a)nih.gov

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segfault
by Righart, Ruthger Dr. 21 Sep '10

21 Sep '10

Dear Sir/Madam, I am a new user of freesurfer and had the following error when I tried in tkmedit tool to make a snapshot of the volume. Please find below the contents of the file .xdebug_tkmedit Best Regards, Ruthger Righart ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... tkmedit started: Tue Sep 21 14:22:11 2010 tkmedit.bin 1001 1001-M36-T1.mgz $Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5 $ Set user home dir to /Network/Servers/isd06363.isd.med.uni-muenchen.de/Shared Items/homefolder/rrighart Set subject home dir to /Volumes/ext_rrighart/CADASILData/1001 Using interface file /Applications/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Segfault Verifying volume xDebug stack (length: 4) 03: Volm_SaveToSnapshot( this=0x38c6600 ) 03: Verifying volume 02: SnapshotVolume () 02: Saving snapshot 01: main() 01: Entering main loop 00: 00:

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sample data discrepancies
by Katie Mahon 20 Sep '10

20 Sep '10

Hi Experts, I am extremely new to Freesurfer and I have a basic question that I didn't see answered in the archives (but it is very likely I missed it!). I downloaded the sample data (buckner_data) and ran the orig.mgz files through all of the steps so that I could compare my 'stats' values with those given in the sample data . The values I get for the segmentation volumes are different from those in the sample data files- why is this? They are not wildly different, just off a bit for each case. Thanks very much, Katie

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convert 4d volume time series to GIFTI surface time series
by Hansen, Kathleen (NIH/NIMH) [F] 20 Sep '10

20 Sep '10

Dear all, Any help that you could give on this pretty basic question would be much appreciated. I've been trying to use the excellent fmri-to-anatomical registration produced by Freesurfer's bbregister to convert a 4d volume time series to a GIFTI surface time series. So far, I have tried using mri_vol2surf and mris_convert as below, with no success. In this example, the dataset volume_time_series.nii is of size 64x64x37x96, where 96 is the number of time points. I would really appreciate it if anyone spots and would correct the usage error(s) that I must have made. ?? Thank you, Kathleen mri_vol2surf --mov volume_time_series.nii --reg good_registration.dat --hemi lh --o surface_time_series_lh.mgh --projfrac 0.5 --interp nearest srcvol = volume_time_series.nii srcreg = good_registration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.white Done reading source surface Reading thickness /nfs/data17/hansenka/ntopy/surf/D/D06/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 11133 Reshaping 19 (nvertices = 137275) Writing to surface_time_series_lh.mgh Dim: 7225 1 19 mris_convert surface_time_series_lh.mgh surface_time_series_lh.gii ERROR: MRISread: file 'surface_time_series_lh.mgh' has 0 vertices!

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lh.thickness.fsaverage
by Siti Hajar 20 Sep '10

20 Sep '10

When I run recon all for my subject, I couldn't open lh.thickness.fsaverage.mgh (/usr/local/freesurfer/subjects/.../surf/lh.thickness.fsaverage.mgh.) I need to use that information to obtain the cortical thickness.Is it because the new updated freesurfer or it might come from other source of problem? Thank you...

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Re: [Freesurfer] recon-all quality control checks on large numbers of subjects
by Nick Schmansky 17 Sep '10

17 Sep '10

consult this page: http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems typically the problem is resolved by upgrading the nvidia driver (assuming you have such a graphics card). n. On Fri, 2010-09-17 at 15:17 -0700, Pradeep wrote: > Hello Nick, > > The data_check program works after some minor fixes. > > I now a have problem with tksurfer on our server > > The recon-all step ran with out any errors > > But > tksurfer AD_C165 lh smoothwm > displays only a part of the image and dose not give any error > messages. > > Machine Details: x86_64 GNU/Linux > FreeSurefer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > > So i downloaded the images to another computer and the display is good > here. > > Machine Details: i686 GNU/Linux > FreeSurfer Version: freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > Any suggestions on this would be greately appreciated. > > Thanks, > Pradeep > > > > > On Thu, Sep 16, 2010 at 5:32 PM, Pradeep <tpradeep(a)gmail.com> wrote: > Thanks for letting us know. > > Is there any other way to do the QA in batch ? > > Thanks, > Pradeep > > On Thu, Sep 16, 2010 at 3:52 PM, Nick Schmansky > > <nicks(a)nmr.mgh.harvard.edu> wrote: > > sorry, this is no longer supported. it was created by an ra > who left > > the center a few years ago. i suppose i should have > mentioned that in > > my original email. > > > > n. > > > > On Thu, 2010-09-16 at 15:51 -0700, Pradeep wrote: > >> Hell Nick, > >> > >> Looks like the recon_checker has some problems to fix > >> > >> Below is my log file. > >> > >> ############ > >> surf/rh.sphere surf/rh.sphere.reg surf/rh.lh.sphere.reg > >> surf/rh.avg_curv label/rh.aparc.annot stats/rh.aparc.stats > >> label/rh.aparc.a2005s.annot mri/aparc+aseg > >> .mgz > >> check to see if all files exist... > >> AD_C165 missing output files > >> AD_C165 has no surf/lh.rh.sphere.reg > >> > >> In recon_all_status_log_checker > >> > >> > WARNING: /working/pthiyyagura/freesurfer/data_checker/data_checker/sample-recon-all-status.log > >> does not exist. Skipping this > >> complete status log file... > >> > >> ############# > >> > >> > >> Its looking for lh.rh.sphere.reg. which would not exist. > >> Could you please look into this. > >> > >> Thanks, > >> Pradeep > >> > >> P.S also please chage > >> set scriptsDir = > >> > >> > >> > >> > >> > >> > >> > >> On Thu, Sep 16, 2010 at 11:41 AM, Nick Schmansky > >> <nicks(a)nmr.mgh.harvard.edu> wrote: > >> > see also this page: > >> > > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/QATools > >> > > >> > On Thu, 2010-09-16 at 14:13 -0400, Bruce Fischl wrote: > >> >> Hi Avram, > >> >> > >> >> that all souds reasonable to me. > >> >> > >> >> cheers > >> >> Bruce > >> >> On Thu, 16 Sep 2010, Avram Holmes wrote: > >> >> > >> >> > All, > >> >> > > >> >> > I'm setting up a processing stream for a sizable > dataset and I'd like > >> >> > to use .tcl scripts to save out images for some > preliminary quality > >> >> > control checks. It was my intention to output images > of the the > >> >> > curvature and structural parcelation overlaid on the > inflated surface > >> >> > (6 views for each hemi) and the lh/rh.white and > aseg.mgz segmentation > >> >> > overlaid on the volume (a midline coronal, sagital, > and axial slice). > >> >> > The idea would be that then we could go through and > quickly check > >> >> > which subjects may need manual intervention. > >> >> > > >> >> > I wanted to double check that the images I am saving > out are > >> >> > consistent with the checks that other folks are doing > and I'd love to > >> >> > get some feedback on what else I should look save. > >> >> > > >> >> > Thanks, > >> >> > Avram > >> >> > > >> >> > > >> >> _______________________________________________ > >> >> Freesurfer mailing list > >> >> Freesurfer(a)nmr.mgh.harvard.edu > >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> >> > >> >> > >> > > >> > _______________________________________________ > >> > 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. > >> > > >> > > >> > >> > >> > > > > > > > > > > -- > Pradeep Thiyyagura > Research Assistant > School of Mathematical and Statistical Sciences > Graduate Student > Computational Biosciences > Arizona State University > Tempe, AZ 85287-1804 > Pradeep.Thiyyagura(a)asu.edu > > > > > -- > Pradeep Thiyyagura > Research Assistant > School of Mathematical and Statistical Sciences > Graduate Student > Computational Biosciences > Arizona State University > Tempe, AZ 85287-1804 > Pradeep.Thiyyagura(a)asu.edu

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Generating a 'non-zero' group mask
by Marco Loggia, PhD 17 Sep '10

17 Sep '10

Dear all, I am performing surface analyses on ASL CBF maps. As these maps do not cover the whole brain, and some masks have larger brain coverage than others, I would need to create a binary surface mask (in the fsaverage space) which would zero out the vertices where at least one of my subjects have a zero value. This map would then be used to spatially limit my statistical analyses in mri_glmfit. Any suggestions? Thanks a lot, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] mri_label2volume issues
by Michael Waskom 17 Sep '10

17 Sep '10

Hi Prapti, Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly. The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run: mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz Which will have 1s where your ROI is and 0s everywhere else. Best, Mike -------Original Message------- Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this. As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize? Thanks, Prapti -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere. doug Prapti Gautam wrote: > Hi Doug, > > Thanks for the reply. I have tried using the method you've suggested, > however, I'm stuck because mri_label2annot which I use to turn my label > into a annot file only works in one hemisphere while mri_aparc2aseg > works for the whole brain. Do you know a work around for this? > > Can I merge the annot files created from each hemisphere so that I can > pass it to mri_aparc2aseg? > > > Thanks, > > Prapti > > >

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Fwd: Problems with mri_label2vol
by Jose Angel Pineda Pardo 17 Sep '10

17 Sep '10

Hi everyone, Im using the instruction mri_label2vol, to resample the resulting aseg.mgz into the original Dicom Volume (same dimension as rawavg.mgz), as follows: *mri_label2vol --seg /Users/jangel85/Desktop/ejemplo/Results_FreeSurfer/mri/aseg.mgz --regheader /Users/jangel85/Desktop/ejemplo/Results_FreeSurfer/mri/aseg.mgz --o aseg-in-rawavg.mgz --temp /Users/jangel85/Desktop/ejemplo/Results_FreeSurfer/mri/rawavg.mgz * The problem that Im having, is that the resulting aseg-in-rawavg.mgz, has no names associated to the labels when I plot it in the Software that Im using (3D Slicer). Does anyone know, why is that happening and how can I correct it? Thanks in advance Jose

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mri_label2volume issues
by Prapti Gautam 17 Sep '10

17 Sep '10

Dear freesurfers, I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm l) but I can't seem to find the solution to it myself. The steps I've used are: Draw label in tksurfer, and save it and then use the following command. mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I've tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs option, but this hasn't made things better.. Has anyone encountered this problem before and knows how to solve it ? Am I missing something in the syntax? Thanks very much in advance, Prapti

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Freesurfer September 2010