Freesurfer September 2005

freesurfer@nmr.mgh.harvard.edu

44 participants
91 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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Re: Freesurfer Digest, Vol 19, Issue 49
by Blaise Frederick 24 Oct '05

24 Oct '05

On Sep 27, 2005, at 3:06 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 2 > Date: Tue, 27 Sep 2005 13:42:02 -0400 > From: Keith Schneider <ks(a)rcbi.rochester.edu> > Subject: [Freesurfer] mri_convert doesn't recognize DICOM files > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1F6EBE81-3EC6-41F9-840C-1C2E8B4C05A6(a)rcbi.rochester.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > I installed Freesurfer on a G5 Tiger Mac, but mri_convert and > mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a > Siemens Trio 3T) as DICOM files. Has anyone else encountered this? > > Other programs can read the DICOM files just fine. > > keith > > > ------------------------------ I have found exactly the same thing. The thing is, it _used_ to work... Using a G5 with 10.4.2, in a directory with DICOM files pulled off a Siemens Trio using Osirix, I execute the following: /usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot I get the following error (many, many times) mri_convert(1841) malloc: *** Deallocation of a pointer not malloced: 0xd10ea0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug However, when all is said and done, I get a correct analyze file. The binary in question is: -rwxr-xr-x 1 frederic frederic 2034036 Feb 18 2004 /usr/local/ freesurfer/bin/Darwin/mri_convert However, if I execute: /Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot2 it returns with: no DICOM files found. Exit This binary is from the newest distribution that I have: -rwxr-xr-x 1 frederic wheel 6236540 Jul 7 21:23 /Users/Shared/ freesurfer/bin/mri_convert So it looks like something broke. Unfortunately, I don't want to just use the old binary, because it is missing many output formats (particularly nii) Blaise Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and/or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, PHI by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

4 3

matlab functions for reading sphere.reg files
by Darren Weber 03 Oct '05

03 Oct '05

Hi, are there any matlab functions for reading sphere.reg files? What is their format and content? Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (1664), The Anatomy of the Brain and Nerves.

3 4

make_average_subject error?
by Brian Schweinsburg, Ph.D. 02 Oct '05

02 Oct '05

Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 SC012 ... I am running the latested dev release with Fedora Core 4. Any ideas as to the problem? Brian

2 6

installation, Tcl_CreateInterp
by Darren Weber 29 Sep '05

29 Sep '05

I tried to install the latest dev version, but given all the bugs, I'm trying to revert to a prior version that was working. So, I removed the latest dev installation and reinstalled a prior version of freesurfer onto an FC3 linux system. I checked some setup issues and then ran csurf, which was fine, but tkmedit/tksurfer required tcltk 8.3, so I installed tcl8.3 and tk8.3 from rpm and then created symbolic links in /usr/lib: ln -s libtkx8.3.so libtk8.3.so ln -s libtclx8.3.so libtcl8.3.so Now tkmedit/tksurfer will startup, but they both complain about: tksurfer: symbol lookup error: tksurfer: undefined symbol: Tcl_CreateInterp I don't know how to handle this one. Any suggestions? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (1664), The Anatomy of the Brain and Nerves.

1 0

MNI-derived perl scripts referencing /usr/pubsw/bin/perl
by Greg Harris 29 Sep '05

29 Sep '05

Dear FreeSurfer maintainers, When we download FreeSurfer and install it, we end up with files in ${FREESURFER_HOME}/lib/mni/bin that insist that perl be installed in /usr/pubsw/bin with script first lines as follows: autocrop:#! /usr/pubsw/bin/perl -w field2imp:#!/usr/pubsw/bin/perl -w imp2field:#!/usr/pubsw/bin/perl -w make_template:#!/usr/pubsw/bin/perl -w mritoself:#! /usr/pubsw/bin/perl -w mritotal:#! /usr/pubsw/bin/perl -w nu_correct:#!/usr/pubsw/bin/perl -w nu_estimate:#!/usr/pubsw/bin/perl -w nu_estimate_np_and_em:#!/usr/pubsw/bin/perl -w nu_evaluate:#!/usr/pubsw/bin/perl -w resample_labels:#!/usr/pubsw/bin/perl sharpen_volume:#!/usr/pubsw/bin/perl -w xfmtool:#! /usr/pubsw/bin/perl -w As it happens, our System Administration authority here is equally adamant that I should shout this complaint at you: "A LOT OF PEOPLE don't have /usr/pubsw at all." Of course, I know that these scripts come to you from Montreal Neurological Institute, and they TOLD you to tell all of us that /usr/pubsw is a REQUIREMENT so their scripts will not be sensitive to what version of perl is in use by any others here. Well, even so, it is our practice to change each of these files to replace '/usr/pubsw/bin' with something acceptable on our installation, '/usr/bin', every time we download an update. Perhaps, if these scripts are indeed version-specific, the specific version of perl that is required for Intel/Linux should be in the same ${FREESURFER_HOME}/lib/mni/bin directory and referenced as '#!./perl -w' in the MNI scripts. Or, what would you suggest instead? Greg Harris Iowa Psychiatry Brain Imaging Lab

2 1

frozen versions not working for recon-all after upgrade
by Elizabeth Fenstermacher 28 Sep '05

28 Sep '05

I've created a few frozen versions of the FreeSurferDev versions at various points and though they have been working without difficulty in the past I am now getting errors (seems to be difficulty finding tools) when I attempt to run the recon stream using them (though they are working to run other scripts I use without error). The command that I'm using also seems to be executing fine from the current dev version. I have saved the output I get from both frozen versions to ~efenster/scratch/fsfreeze-reconoutput (frozen version created on 5/25/05) and ~efenster/scratch/fsfrozen-reconoutput (frozen version created on 9/6/05) I am really not sure what could be causing these new difficulties and would greatly appreciate help. Thanks Eliz

1 0

Dear FS Help:
by Anthony Cacace 28 Sep '05

28 Sep '05

Dear FS Help: We were running the autorecon1 command: recon-all -subjid 18014B -autorecon1 -mgz There was some processing (of 1 run)...which reached "Intensity Normalization"...and stopped with: Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors Can you explain what this error is, how to fix it and proceed with processing Thank you.

2 1

Pial surface errors
by Fornito, Alexander 27 Sep '05

27 Sep '05

Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if there are any rules that might be useful to this end, or whether there is an alternative to fixing this problem? Thanks, Alex

2 1

Mris_sample_parc
by Satrajit Ghosh 27 Sep '05

27 Sep '05

Hi, I'm trying to create an annotation file from a volume is mris_sample_parc. Is there any way to have it resample at 0.5 the distance between the white and pial surfaces? Thanks Satra

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Freesurfer September 2005