Freesurfer July 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
88 discussions

trouble using inorm-sess
by Sebastian Moeller 10 Jul '06

10 Jul '06

Hi List, we have some problems with inorm-sess and some data sets. No matter how we set -tresh (well, 0.1, 0.5, 0.75 or 1.0) some of our functional runs produce errors/warnings. (and the "INFO: no voxels found under thershold" messages, but they look benign). The warning are mostly divides by zero, but they still result in inorm-sess exiting SUCCESSFULLY, they coincide with the INFO... lines so they might be expected. But some of the runs are weirder, they give "??? Subscripted assignment dimension mismatch. \n Error in ==> fast_inorm at 88 \n twf_under(nthslice,:) = mean(y2(iunder,:));" Unfortunatelly looking inside fast_inorm.m does not give me any clue, what is going on. If there is anything I can do to help debug this problem, let me know. BTW the same data can be safely normalized after smoothing (using spatialsmooth-sess). freesurfer 3.0.3 Linux-centos4_x86_64-pub, Matlab 7.1 x86_64, running suse Linux 10.1 ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] printing out from tksurfer and tkmedit
by Don Hagler 09 Jul '06

09 Jul '06

Here you go. No guarantees of usability or support. >From: Chacko Cherian <chacko_cherian(a)yahoo.com> >To: Don Hagler <dhaglerjr(a)hotmail.com>, fischl(a)nmr.mgh.harvard.edu, >kteich(a)nmr.mgh.harvard.edu >CC: chacko_cherian(a)yahoo.com, freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] printing out from tksurfer and tkmedit >Date: Wed, 5 Jul 2006 16:15:05 -0700 (PDT) > >Thanks Don.That would be really useful. > >Chacko. > >--- Don Hagler <dhaglerjr(a)hotmail.com> wrote: > > > If there is interest, I could post my shell script > > for generating a tcl > > script and running tksurfer (with an option to write > > to rgb). I have > > another one that will render all w files in a > > particular directory (as > > rgb's) and another that will render all frames from > > an mgh (painted surface) > > file (as tif's). > > > > With the older version of tksurfer, you can render > > offscreen, which is > > convenient for batches of files (because otherwise > > your monitor is unusable > > for a long time). > > > > > > >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > >To: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> > > >CC: Chacko Cherian <chacko_cherian(a)yahoo.com>, > > >freesurfer(a)nmr.mgh.harvard.edu > > >Subject: Re: [Freesurfer] printing out from > > tksurfer and tkmedit > > >Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT) > > > > > >but you could write a tcl script to do it > > automatically > > >On Fri, 30 Jun 2006, Kevin Teich wrote: > > > > > >>>How can I can I print out the display images from > > tksurfer and > > >>>tkmedit other than manually saving them into tiff > > and then printing > > >>>them.IS there any way to print them directly? > > >> > > >>No, sorry, saving TIFFs is the only output that > > tkmedit and tksurfer > > >>do of that kind. > > >> > > >> > > >_______________________________________________ > > >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 > > > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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dependency issue for "tk" related binaries
by apseyed＠bu.edu 08 Jul '06

08 Jul '06

In testing: $ /usr/local/freesurfer/bin/tkmedit /usr/local/freesurfer/bin/tkmedit: error while loading shared libraries: libtix8.1.8.3.so: cannot open shared object file: No such file or directory $ sudo rpm -Uvh glut-3.7-12.i386.rpm itcl-3.2-88.i386.rpm tix-8.1.4-88.i386.rpm /usr/local/freesurfer/bin/tkmedit: error while loading shared libraries: libtk8.4.so: cannot open shared object file: No such file or directory I have tk-8.3.5-92 installed and thus /usr/lib/libtk8.3.so. When i tried to install tk-8.4.5-8.i386.rpm, I ran into a dependency conflict problem: error: Failed dependencies: libtcl8.4.so is needed by tk-8.4.5-8 tcl = 8.4.5 is needed by tk-8.4.5-8 libtk8.3.so is needed by (installed) tix-8.1.4-88 tk = 8.3.5-92 is needed by (installed) tk-devel-8.3.5-92 libitcl3.2.so is needed by (installed) tix-8.1.4-88 libitk3.2.so is needed by (installed) tix-8.1.4-88 itcl is needed by (installed) tix-8.1.4-88 I tried to install tcl-8.4.5-7.i386.rpm, and got another slew of deps: error: Failed dependencies: libtcl8.3.so is needed by (installed) expect-5.38.0-92 libtcl8.3.so is needed by (installed) tk-8.3.5-92 libtcl8.3.so is needed by (installed) tix-8.1.4-88 tcl = 8.3.5-92 is needed by (installed) tcl-devel-8.3.5-92 libitcl3.2.so is needed by (installed) tix-8.1.4-88 libitk3.2.so is needed by (installed) tix-8.1.4-88 itcl is needed by (installed) tix-8.1.4-88 so then i tried to force the install. --nodeps for both of the above. then i tried again: $ /usr/local/freesurfer/bin/tksurfer /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory which is included in xorg-x11. after installing xorg: /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory so I installed: gsl-1.1.1-5.i386.rpm then: /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libitk3.2.so: cannot open shared object file: No such file or directory which I already installed, and when i installed again, it is asking for libtk8.3.so again, which was overridden with nodeps. Now, I installed the version 3.0.3 that said is compatible with redhat 9, which is close to what I am running, can you offer any suggestions? Thanks, Patrice

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recon-all exited with errors
by Nandita Shetty 07 Jul '06

07 Jul '06

Hi, I came across an error in the third stage of reconstruction using freesurfer. The images,scripts etc are at space/megraid/42/ACE/PILOTDATA/DATA_PROCESS The recon log says that recon-all exited with errors and stopped at Surf Reg rh. I am a new user and was hoping that you could help me out with the same. Also, I do know that the inflated brain is not ideal but nevertheless wanted to complete the reconstruction to get a feel of it. This is what the error log says MRISreadVertexPosition(smoothwm): could not open file ../surf/rh.smoothwm MRISreadOriginalProperties: could not read surface file smoo Thanks in advance for any help in this regard.

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mri_convert: dicom to nifti 4D
by Thomas, Adam (NIH/NIMH) [E] 07 Jul '06

07 Jul '06

I seem to be having some trouble converting a 4D time series from dicom to nifti format using mri_convert. Rather than outputting 144 frames of 38 slices each, it creates a volume with a single frame of 5472 slices (see below). Is there an argument I should be using to specify number of frames? I think there was a post on this back in April (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02656.htm l), but I can't seem to find an answer in the archives. Thanks, -Adam [adamt@master 004]$ mri_convert axialepi-00001.dcm test.nii mri_convert axialepi-00001.dcm test.nii reading from axialepi-00001.dcm... 5472 DICOM 3.0 files in list Found 5472 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 5472. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /misc/radium0/adamt/mirrorTracking/XX/2006-02-11-S2/XXXXXXXX/2006_02_11- 15667/004/axialepi-00001.dcm Date and time study date 20060211 study time 170403 series time 172558 acquisition time 172558 Identification patient name XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX manufacturer GE MEDICAL SYSTEMS Dimensions number of rows 64 number of columns 64 number of frames 5472 pixel width 3.28125 pixel height 3.28125 slice thickness 3.2 field of view 210 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 30 repetition time 2500 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -103.359 -132.14 75.59 last image position -103.359 -132.14 -42.81 image orientation 1 -0 0 -0 1 0 ------------------------------------------------- TR=2500.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, -1) writing to test.nii... [adamt@master 004]$ --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370

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howto cut "canonical" occipital patches?
by Sebastian Moeller 07 Jul '06

07 Jul '06

Hi All, I recently finished the surface transform of my first human brain with freesurfer. (All I had to do was run recon-all autorecon1, autorecon2 and autorecon3 in sequence, no manual edits necessary, joy, and that after doing monkey surfaces that required manual intervention at all polssible steps ;). Thanks for this great tool). Now I really would like to produce flat maps of my subjects occipital pole, and there is my question. What are the "canonical" cuts needed to produce "standard" occipital pole flat maps? I guess one cut will have to be along the calcarine sulcus, but how about the temporal lobe (I really would like to keep FFA and the STS if possible...). Thanks in advance & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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some questions about thickness map
by R. Chen 07 Jul '06

07 Jul '06

Hi, I want to know the what the thickness map represents. As Bruce said in 'measuring the thickness of human cerebral cortex from magnetic resonance images', page 1, paragraph 6, 'The distance between these two surfaces then gives the thickness of the cortical gray matter at any point.' What physical variable are measured in thickness map? Is it the distance between a vertex in gray/white surface and the corresponding vertex in pial surface. Whether each vertex in gray/white surface has a match point in pial surface, and vice verse? If true, this means there is a 1-1 mapping between those two surfaces. If thickness map represents gray matter. How can we get the average thickness of a ROI. Can we draw a ROI in pial surface, then overlay the thickness map to pial surface, and compute the average. Thanks, Ron --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

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macosx 10.3.9 and scuba 3.0.3
by Sebastian Moeller 06 Jul '06

06 Jul '06

Hi All, just tried 3.0.3 panther, scuba still crashes and takes X11 with it. ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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scuba and macosx 10.3.9
by Sebastian Moeller 06 Jul '06

06 Jul '06

Hi All, on my trusty iBook (10.3.9) trying to run scuba (from the 3.0.1 panther version) crashes the X-server (well Xquartz the windowmanager dies, taking the whole X11 with it). Will try 3.0.3. ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Autoseg and surface extraction
by Satrajit Ghosh 05 Jul '06

05 Jul '06

Dear Bruce, Does the autoseg information get used for surface extraction? For example, when autoseg classfies the ventricles and basalganglia, are the surface extraction routines supposed to treat these voxels as part of white matter and continue? Ideally at the end of the day any place where the surface runs through a non-cortical patch, the thickness would be zero? Thanks, Satra

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Freesurfer July 2006