Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

recon-all error
by Morgan Hough 02 Oct '05

02 Oct '05

I downloaded the latest freesurfer-dev and I was testing out my install with "recon-all -autorecon-all -subjid bert" and I am getting this error. mri_convert nu4.mnc nu.mgz mincRead(): can't find file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc reading from nu4.mnc... ERROR: converting nu to COR/mgz The file certainly isn't there and I don't see anything in mri/norm if that is where it should be. Here's what there is: [mhough@dhania bert]$ find . -name "*.mnc" ./mri/tmp-mri_motion_correct2-32472/cor-1.mnc ./mri/tmp-mri_motion_correct2-32472/cor-2.mnc ./mri/tmp-mri_motion_correct2-32472/cor-3.mnc [mhough@dhania bert]$ which nu_correct /usr/local/freesurfer/lib/mni/bin/nu_correct Just to double check it wasn't something special about bert I created a new directory for my one subject that I want to process and I got the same error. Thanks in advance. Cheers, -Morgan -- Morgan G. Hough, DPhil Candidate University of Oxford, Centre for Functional MRI of the Brain (FMRIB) John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom Tel: +44 (0) 1865 222545 / Fax: +44 (0) 1865 222717 e-mail: mhough(a)fmrib.ox.ac.uk / URL: http://www.fmrib.ox.ac.uk/~mhough

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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.

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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

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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

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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.

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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

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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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-autorecon1/-autorecon2
by Michele Perry 27 Sep '05

27 Sep '05

Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a decent portion of the meninges remain. I tried using recon-all -skullstrip -wsthresh <h> -subjid <ID> I ran that with h=20, h=10 and h=2. It didn't seem to help so I ran recon-all ... -autorecon2 In the aseg, the meninges are labelled as cerebral cortex. There are also places where non-cerebellar areas were labelled as cerebellum cortex. Is there an automated way to fix either of these or should I fix it with manual edits? Michele

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(no subject)
by jspielb2＠cyrus.psych.uiuc.edu 27 Sep '05

27 Sep '05

Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I downloaded and installed the Redhat version, I'm not sure if this was the correct version to use, but when I try to fix the perl path with the command given on the wiki, it says that the command is not found, nor is nu_correct, or mksubjdirs, tkmedit, mri_convert, or any others that I've tried. I convert the shell to tcsh and source SetUpFreeSurfer.csh, and that seems to work, except for an error about MINC. Dou you know what the issue might be with my setup? Thanks, Jeff

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higher resolution reconstructions and mri_watershed
by Thomas, Adam (NIH/NIMH) 27 Sep '05

27 Sep '05

I've been playing around with reconstruction at higher resolutions and have been getting some unusual behavior so I decided to do some testing on bert. I convert bert to 0.7mm isotropic and 366 slices with: mri_convert -cs 0.7 ~/subjects/bert/mri/orig ~/subjects/bert0.7/mri/orig Then I fired up recon-all. Bert's surface came out beautifully without doing any manual editing. There are 276,245 nodes in the surface instead of 137,497 when reconstructed at 1.0mm. The inflated surface also looks a bit more convoluted at 0.7mm than at 1.0mm. However when I tried to recon bert at 0.5, mri_watershed gave some interesting errors: Skull Stripping Thu Sep 1 19:07:40 EDT 2005 /misc/radium0/adamt/subjects/bert0.5/mri mri_watershed T1 brain ************************************************************ The input file is T1 The output file is 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=252 y=303 z=228 r=259 first estimation of the main basin volume: 73641890 voxels Error w=White Matter =Intensity too high (>240)...valid input ? warning: non-standard value for imnr1 (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for x (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for y (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for thick (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for psiz (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.inf o ERROR: mri_watershed exited with non-zero status Why would resampling to 0.5mm affect white matter intensity? Thanks, -Adam --- 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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