Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

Re: [Freesurfer] freeview load overlay error...
by Gonzalo Rojas Costa 19 Nov '10

19 Nov '10

Dear Dr. Wang: I got the message: "mris_info zstat3_rh.w nquads=8321536, nvertices=2 ERROR: MRISread: file 'zstat3_rh.w' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory" Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 18-11-2010 15:57, Gonzalo Rojas escribió: > Message: 4 > Date: Mon, 15 Nov 2010 09:36:17 -0500 > From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] freeview load overlay error... > To: freesurfer(a)nmr.mgh.harvard.edu > > What does mris_info show on the overlay file? > > On 11/14/10 11:08 PM, Gonzalo Rojas Costa wrote: >> Hi: >> >> I generated a surface with: >> >> mri_vol2surf --src zstat3.nii.gz --src_type nifti --srcreg >> ../registro.dat >> --hemi lh --projfrac 0.5 --out ./zstat3_lh.w --out_type w >> >> then I tried to load zstat3_lh.w using freeview, but I got the error: >> >> "MRISreadBinaryCurvature: incompatible vertex number in file >> /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w >> >> could not read overlay data from >> /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w" >> >> >> Why ?... How can I solve the problem ?... >> >> Sincerely, >> >> >> Gonzalo ROjas Costa >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Graphics Segfaults
by Michael Waskom 19 Nov '10

19 Nov '10

Hey Nick/Krish, Is there a way to exit tksurfer/tkmedit from a tcl script that doesn't trigger a segfault? Thanks! Cheers, Mike

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Qdec errors: Mapping Label to Subjects
by Jessie Chen 18 Nov '10

18 Nov '10

Hi Everyone, I am trying to extract volume and thickness data from a list of subjects for several ROIs that Freesurfer does not automatically define (ie. Broca's area). My plan was to load a .dat table into Qdec with a column of subject IDs and a column with a dummy continuous variable. Then I would use Qdec to draw some labels, which I would later use with mris_anatomical_stats. So far, I used Qdec to draw a label and am now trying to map the label to all the subjects. However Qdec keeps giving me errors. (I'm using Freesurfer v4.0.2). (1) The first error continuously pops up, but I seem to be able to ignore it: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0xdf9640): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0" I saw that a previous user also had this problem and was told that it was due to Freesurfer v4.0.2 missing the fsgdfPlot.tcl file. However, I checked my $FREESURFER_HOME/lib/tcl directory, and it appears to already have this file, so I'm not sure if this is the problem. (2) The other error I get, which seems to be causing the mri_label2label command to fail is this: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 33: vno = 175287, max = 163842 command failed: mri_label2label --srclabel /ifs/edevel/UCLA_FREESURFER/OUTPUT/qdec/Jessie/ROI_labels/lh.insula_dummydat_11-18-10.label --srcsubject fsaverage --trgsubject 20171 --trglabel /ifs/edevel/UCLA_FREESURFER/OUTPUT/qdec/Jessie/ROI_labels/lh.insula_dummydat_11-18-10.label --regmethod surface --hemi lh This seems to be the more pressing problem, and I'm lost as to how to fix it. Any suggestions would be greatly appreciated. Thanks in advance! - Jessie Chen

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Errors for talairach transformation
by liang wang 18 Nov '10

18 Nov '10

Hi FSusers, The terminal displays errors when I run "recon-all -autorecon1 -subjid ..." to get a skull-stripped brain image. The processing exits with the following errors regarding talairach transformation. Here is the talairach.xfm: MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 39.07553864 15.93667889 -36.86604309 -1474.05761719 1861.34423828 844.27008057 -1897.87268066 -75416.71093750 -606.90667725 -274.30368042 622.14581299 24711.26757812 ; Any suggestions would be appreciated. Best, Liang #-------------------------------------------------------------------- #@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010 /mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010 -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540

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Basal Ganglia Components
by Dhinakaran Chinappen 17 Nov '10

17 Nov '10

Dear all, Hope your research is going smoothly. My question refers to the basal ganglai components. I previously shot an email which Prof. Fischl was kind enough to reply to: the basal ganglia is not computed as a structure of its own in FreeSurfer. These are the structures of the basal ganglia one can gather: (1) striatum (Caudate and putament) (2) Ventral Striatum - (a) nucleus accumbens (b) most ventral aspects of caudate and putament (3) Celobus pallidus (internal and external sectors) (4) Substancia Nigra (5) Subthalamic nucleus Here are my questions: => Structures (1), (2), (3) and (4) can be found... however, am having trouble locating the segmentation label number for the subthalamic nucleus. => The output for (4) is not reported in asegstats2table (while other structures are). Any other suggestions to extract the volume out? Thanks, Dhinakaran.

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make_average_subject
by tulu＠ms36.hinet.net 17 Nov '10

17 Nov '10

2 1

label statistics
by Sasa Kivisaari 17 Nov '10

17 Nov '10

Hi all, Is there a way of ouputting all the thickness values (vertex by vertex) within a specified label? I would like to get some more information out of my labels than is provided by mris_anatomical_stats. All the best, Sasa

2 1

3D view in freeview
by Marco Loggia 17 Nov '10

17 Nov '10

Dear all, I am trying to use the 3D view in freeview to prepare some figures, and would like to be able to rotate the volume along one axis only (e.g., yaw). Is there a way to constrain the rotation with the mouse, and/or to enter the numerical value of parameters such as azimuth and elevation? Thanks, 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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export in stl format
by Miguel Burgaleta 17 Nov '10

17 Nov '10

Hi FreeSurfers, I am converting the pial surface (?h.pial) into STL format and importing it into Blender as described in http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel. However, I would like to end up with a render of the whole brain (i.e. including both hemispheres, cerebellum, brainstem, etc). Is there any easy way to do this from the FreeSurfer's output? Thanks! Miguel

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Re: [Freesurfer] Mean lGI value extraction
by Marie Schaer 17 Nov '10

17 Nov '10

Sorry Prapti, I was confused, the exact commands are: mris_anatomical_stats -a aparc.annot -t pial_lgi -f #SUBJ/stats/ lh.aparc_lgi.stats #SUBJ lh and then aparcstats2table --subjects #SUBJ1 #SUBJ2 ... --hemi lh --meas thickness --parc aparc_lgi --t YOUR_OUTPUT_TABLE Hope it will work, Marie On 17 nov. 10, at 02:44, Prapti Gautam wrote: > > > Hi Marie, > > I've done what was suggested but I've encountered a problem. I will > recount my steps: > > I used mri_anatomical_stats to create a file called lh.lgi.stats in > the label directory of subjects. I've double checked to see that the > file indeed contains lgi values and not thickness values (they are > different values from a separately tabulated files for thickness) > > next I'm trying to pass this file as the input to the > aparcstats2table with the command you specified. The syntax I ran is: > > > aparcstats2table --hemi lh --subject test --measure thickness -- > tablefile test/label/lh.lgi.stats -t lh.lgi.table > > My output is now saved in the file lh.lgi.table, but it contains > thickness values instead of lgi values from the tablefile. Can you > please tell me what I am missing here? > > thank you, > > Prapti > > -----Original Message----- > From: Marie Schaer [mailto:Marie.Schaer@unige.ch] > Sent: Wed 11/17/2010 12:39 AM > To: Prapti Gautam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mean lGI value extraction > > Hi Prapti, > > Normally you can use aparcstats2table exactly as you would do with > thickness, given that the column corresponding to thickness values in > the tablefile that you produced with your mris_anatomical_stats are > indeed lgi values (i.e. you used mris_anatomical_stats -t pial_lgi -f > lh.lgi.stats, which allows you to use: aparcstats2table -- > subjects ...... --hemi ?h --measure thickness --tablefile ? > h.lgi.stats). > > Let me know if you encounter any problem, > > Marie > > > On 16 nov. 10, at 04:28, Prapti Gautam wrote: > >> dear all, >> >> I am trying to extract the mean values of lgi from the cortex from a >> group of subjects. I found the following command useful in >> extracting for one subject: >> >> mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c >> lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh >> >> However, I have a lot of subjects I wish to extract this for and I >> was wondering if there is a command that will extract these values >> similar to the aparcstats2table command (where all the subjects and >> the mean values for each parcellation is in one output file) >> >> thanks, >> >> Prapti >> >> _______________________________________________ >> 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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Freesurfer November 2010