Re: [Freesurfer] tksurfer problem

Ran, To solve this problem, upgrade your NVIDIA graphics driver. I'm not sure what the source of this problem is, but I have seen it before, and upgrading the driver seems to fix it. Nick On Tue, 2006-10-17 at 23:55 -0600, Ran Tao wrote: Hi, I have a problem about tksurfer command. After

[Freesurfer] regdat2xfm problem

Hi everybody, I have a problem with regdat2xfm. I have a reg.dat file that I made using tkregister2 to register a couple of volumes (targ .mgz and mov .img) from one of my subjects. Now, if I try to use the reg.dat file with tkregister2 and the two original files, everything is fine: I ask

Re: [Freesurfer] regdat2xfm problem

That program is obsolete. You can actually use the new version of tkregister2 to create an xfm file, tkregister2 --targ targ.mgz --mov mov.img --regheaders --reg reg.dat --xfmout reg.xfm I'm sure you don't have the new version, so I've put it here:

Re: [Freesurfer] regdat2xfm problem

Stephano, That version of tkregister2 requires the VXL libs. I've posted the binaries for that library for various OSs here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks For cenots4, the file is called vnl-libso-centos4.tar.gz. Copy it to the directory where you keep

[Freesurfer] tkmedit problem, crash on loading aseg

Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all

[Freesurfer] having problem in running recon-all...

Hello,I am having problem in running the following command:recon-all -i 2996926_02.img -s 2996926_02 I used to run the command before without any problem. Recently my linux has been updated to suse version, would that be a source of problem. The console display the following error:

[Freesurfer] tkmedit problem

Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI)

Re: [Freesurfer] tkmedit problem

Hi Nick- Yes, I am. If tksurfer would still work on an Intel, then this appears to be the problem. Will wait for a new release. Thanks. Anthony Nick Schmansky wrote: Anthony, Are you using a new Intel-processor based Mac? If so, we don't support that just yet. The 'X Error' message is

[Freesurfer] nu_correct problem

Hi Bruce: I installed the new version of freesurfer. I found that nu_correct does not work properly, the error message is spawn: exec of nu_estimate_np_and_em failed: No such file or directory nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) so I try to

[Freesurfer] mri_convert problem

I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I

Re: [Freesurfer] mri_convert problem

to convert Dicom files to mgz try to use following: mri_convert -it dicom -i dicom_file -o your_file.mgz to get more options type mri_convert -- help Silvester [EMAIL PROTECTED] wrote: I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some

Re: [Freesurfer] mri_convert problem

Dave, It looks like a version of recon-all from 2004 is being used, which predates the -i flag. Have you installed the newest version of freesurfer (v3.0)? Or use mri_convert to create the 001.mgz, 002.mgz input files in your subjid/mri/orig directory, and run recon-all from there. Nick I am

Re: [Freesurfer] mris_anatomical_stats problem

hmm, I'm not sure you can specify -a and -l. Not sure what it would mean. Try taking the -a out. Does that file exist? On Fri, 2 Jun 2006, adam walczak wrote: Hello, I am trying to run mris_anatomical_stats using a label that I have created in tksurfer, but I get a strange error when I

[Freesurfer] mri_vol2surf problem

Hello, I am trying to overlay my own ROIs onto the pial surface using mri_vol2surf. this is my command line: mri_vol2surf --src wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u --src_type analyze --srcreg wrawKH_MAE3_4/register.dat --fwhm 3 --hemi lh --surf pial --surfreg

Re: [Freesurfer] mri_vol2surf problem

It's trying to get the subject from the register.dat file, which must have subject-unknown as it's first line. doug adam walczak wrote: Hello, I am trying to overlay my own ROIs onto the pial surface using mri_vol2surf. this is my command line: mri_vol2surf --src

[Freesurfer] having problem in runing recon-all

Hello, I am having a problem in running recon-all command. I have run this command without any problem. Today I moved the image into another directory and getting the following error: mri_convert /ensc/IMAGE4/STUDENTS/SANSARI/freesurfer/subjects/4365

[Freesurfer] wmfill problem

Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start of step two (tessellate RH white matter) I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot

Re: [Freesurfer] wmfill problem

you need to use the volume scanner coords in tkmedit, not the indices. On Thu, 22 Dec 2005, Sven Panis wrote: Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start

Re: [Freesurfer] wmfill problem

actually, I think it needs to be talairach coords. The next version will use indicies (and so will be independent of the tal transform). doug you need to use the volume scanner coords in tkmedit, not the indices. On Thu, 22 Dec 2005, Sven Panis wrote: Hi surfers, I experience a problem

Re: [Freesurfer] Normalization problem

Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity

[Freesurfer] mri_convert problem?

I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img

RE: [Freesurfer] Normalization problem

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Normalization problem Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization

Re: [Freesurfer] mri_convert problem?

does the output dir exists? Do you have write permission? On Mon, 21 Nov 2005, Daniel Goldman wrote: I've been getting this error message whenever I try to convert to .mgz format: mri_convert

[Freesurfer] Normalization problem

I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control

[Freesurfer] A problem occurred while running recon-all in the new dev version

Hi! I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out? Many thanks! Shen-Mou Hsu

Re: [Freesurfer] A problem occurred while running recon-all in the new dev version

try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero padded number such as 001.mgz thanks, brian On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote: Hi! I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately,

RE: [Freesurfer] A problem occurred while running recon-all in the new dev version

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new dev version try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero padded number such as 001.mgz thanks, brian On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote: Hi! I

[Freesurfer] reconstruction problem

I am trying to recon a sagittal T1 series from a functional scan, originally in AFNI format. I converted it to COR using mri_convert -it brik /path/to/file.BRIK $SUBJECTS_DIR/subjid/mri/orig The first run of recon-all -stage1 (-nomotioncor) exited with errors (mri_fill exited with non-zero

[Freesurfer] Freeglut problem

Hi all I've installed Freesurfer and when I open csurf to edit segmentation on images, I get the following error: /usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Now, I've installed Freeglut

Re: [Freesurfer] Freeglut problem

Hi all I've installed Freesurfer and when I open csurf to edit segmentation on images, I get the following error: /usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Now, I've installed Freeglut and

Re: [Freesurfer] Talaraich problem

Hi Max, check the MNI web site (or our log). I think there is an easy fix to this. Something like: setenv LANG en_US or some such. cheers, Bruce On Tue, 22 Mar 2005, Calabrese Massimiliano wrote: Hi all I have a problem ( computer crash) during talairach program in recon-all -stage1 , does this

[Freesurfer] tkmedit problem

Hello, I am using freesurfer on suse 9.0. I have run into problem while using tkmedit tool. When I click on the volume button in csurf , it initially turns purple and then again becomes white without doing anything. It does not spit out error messege either. Using the log messege

[Freesurfer] csurf problem on RedHat Linux EL2.15

Hi, I am trying to run csurf (Feb 2004 version) on RedHat Linux Enterprise 2.15 system. We choose this version of Linux because it supports AMD64 (64-bit). I can start csurf interface, but cannot run either tkmedit or tksurfer, the error megs are: /usr/local/FreeSurfer/bin/Linux/tkmedit: error

Re: [Freesurfer] csurf problem on RedHat Linux EL2.15

You can try downloading the source and compiling it yourself: http://opengl.org/resources/libraries/glut.html On Thu, 12 Aug 2004, Xiaojian Kang wrote: Hi, I am trying to run csurf (Feb 2004 version) on RedHat Linux Enterprise 2.15 system. We choose this version of Linux because it supports AMD64

Re: [Freesurfer] SaveSegmentation problem fixed in tkmedit

I downloaded this file and when I try to run tkmedit I get the following error: tkmedit -f TFL_3006_6/mri/T1/ Couldn't find tkm_common.tcl: Not in % freesurfer/subjects I checked to make sure that the tkm_common.tcl file was in the $FREESURFER_HOME/lib/tcl/ and it was in the correct location.

[Freesurfer] having problem with motion correction.

error is: ??? Undefined function or variable 'afni2bvol'. -- ERROR: creating 011/fmc i'm just running: mc-sess -sf sf -df df at the command line (the files are correct, and the motion correction seems to start fine, but then it can't create these

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