Freesurfer

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30050 discussions

Mris_sample_parc
by Satrajit Ghosh 12 Mar '04

12 Mar '04

I can't find the mris_sample_parc command any longer in the distribution. Is this available somewhere or is there a substitute for it? Thanks, Satra

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mri_normalize update
by Kevin Teich 11 Mar '04

11 Mar '04

The processing of control points in volume/surface creation in mri_normalize, used by csurf and recon-all, is broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble: Darwin, 872KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Darwin.tar… Linux, 1263KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Linux.tar.… To unpack, move the file you download to your freesurfer/ directory, cd there, and run "tar zxvf <filename>". It will install bin/<OS>/mri_normalize. -- Kevin Teich

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Tkmedit update for display transforms
by Kevin Teich 11 Mar '04

11 Mar '04

Display transforms in tkmedit are broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble: Darwin, 1890KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit-20040311-Darwin.tar.gz Linux, 1712KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit-20040311-Linux.tar.gz To unpack, move the file you download to your freesurfer/ directory, cd there, and run "tar zxvf <filename>". It will install bin/<OS>/tkmedit and lib/tcl/tkmedit.tcl. -- Kevin Teich

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Re: question about average7...
by Doug Greve 11 Mar '04

11 Mar '04

Ray Fix wrote: > > Hello List, > > Question 1: > Where does the sample average7 come from? I searched through the > manuals, googled, searched around a little but was unable to find any > info. For example, is this the averaged brains of 7 male subjects in > there 40s? It's a 7th order icosahedron (163842 vertices). I think the orig coordinates are supposed to be talariach coordinates averaged over some subjects (but it does not overlay very well on the talairach brain). Bruce can give you more details. > Question 2: > My plan is to create my own ICBM labels using average7 and then apply > them via mri_label2label to two groups of subjects (which happen to be > pediatric data). Does this stand any chance of working? I would be > very interested if their are any other approaches you recommend. It all depends on how you're going to map the labels. What coordinate system are the ICBM labels in? doug > Thanks for your guidance, > > Ray Fix -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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parcellation - missing areas
by Rutvik Desai 10 Mar '04

10 Mar '04

When converting annotations to labels, mri_annotation2label shows some missing areas (it prints "Skipping"). Are these areas skipped because the parcellation algorithm as not able to find clear boundries to define them? Is there a way to get around this (i.e., have the algorithm take its best guess about that area)? thanks, Rutvik

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talairach transformation
by Sergey A Solovyev 10 Mar '04

10 Mar '04

Hi, I am getting consistent errors with one subject. After running: >mri_convert orig orig/orig.mnc >mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm (or, >talairach $subj_id >talairach2 $subj_id, does not matter) I check if it is correct: view the talairach transform in tkmedit by clicking on the VOLUME button to start tkmedit (or starting it directly on the command line), then doing file->transforms->load transform for main volume, and selecting the talairach.xfm. If it is correct, the transferred brain should be slightly tilted forward, and the inter-hemispheric fissure should be pretty much vertical (with x=0 on the midline). Unfortunately, I am getting a significant leftward shift (in coronal orientation). Surface reconstruction is problematic. For example, in the left hemisphere it seems that no voxels to the right of the (0 0 0) point were used. Therefore, lh surface is 50% of what it should be, topology is very wrong... Any attempt to fix it with manually defining the cutting planes, or editing the volume, failed.. Could you please suggest how to fix talairach transformation? thank you, Serge

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choosing parcellation schemes
by Frederic Dick 10 Mar '04

10 Mar '04

Hi all is there a flag in parcellate_subject for switching between the two parcellation schemes (Destrieux/Kennedy et al)? Or maybe the latter isn't included in the distribution yet? (I didn't see it in $CSURF_DIR/average...) cheers, Fred

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Tksurfer problem
by Pål G. Larsson 10 Mar '04

10 Mar '04

I have encountered a problem with the last update. The Tksurfer comes up with a greyish graphics window and a relative small control window without text, menus or anything. The .xdebug_tksurfer log is empty; as the csurf log contains: ###################################################### csurf0.9: log ending: Wed Mar 10 15:56:48 CET 2004 ###################################################### ############# Command Log ############# ########### Medit Log ########### ############ Surfer Log ############ env tksurferinterface=csurf patchname= /usr/local/freesurfer/bin/Linux/tksurfer -ELVHEIM_TROND rh pial -tcl /tmp/TmpTclSurf.7597 ltMNIread: could not open file /usr/local/freesurfer/subjects/ELVHEIM_TROND/mri/transforms/talairach.xfm No such file or directory Xlib: connection to ":0.0" refused by server Xlib: No protocol specified surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: in subjects "scripts" dir surfer: session root data dir ($session) set to: surfer: /sse/gyrus2/subjects/ELVHEIM_TROND surfer: /usr/local/freesurfer/subjects/ELVHEIM_TROND/mri/T1/COR-.info surfer: Talairach xform file not found (ignored) surfer: vertices=149374, faces=298744 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.new.tcl can't read "env(MRI_DIR)": no such variablesurfer: couldn't dis/enable menu set 0: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 1: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 2: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 4: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 5: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 6: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 7: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 8: invalid command name "tkm_SetMenuItemGroupStatus" surfer: couldn't dis/enable menu set 9: invalid command name "tkm_SetMenuItemGroupStatus" tksurfer: run tcl script: /tmp/TmpTclSurf.7597 Pål G. Larsson National Centre for Epilepsy Norway E-mail: pal.g.larsson(a)epilepsy.no Tel: (+47) 67554253

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FW: Tksurfer problem
by Pål G. Larsson 10 Mar '04

10 Mar '04

> I have encountered a problem with the last update. The Tksurfer comes up > with a relative small control window without text, menus or anything. The > log gives some lines approx: Could not dis/enable menu set #, Invalid > command:.......... > Also there seems to be no colouring of the surface - no texture. > > I did only do an upgrade, and former versions have worked nicely. What can > I do? > > In the log there is an other error Can't read env(MRI_DIR). Csurf/tksurfer > reads my mri without a problem, so what is it needed for, and what should > MRI_DIR contain? > > Pål G. Larsson > National Centre for Epilepsy > Norway > >

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FW: Tksurfer problem
by Pål G. Larsson 10 Mar '04

10 Mar '04

> I have encountered a problem with the last update. The Tksurfer comes up > with a relative small control window without text, menus or anything. The > log gives some lines approx: Could not dis/enable menu set #, Invalid > command:.......... > Also there seems to be no colouring of the surface - no texture. > I did only do an upgrade, and former versions have worked nicely. What can I do? > In the log there is an other error Can't read env(MRI_DIR). Csurf/tksurfer > reads my mri without a problem, so what is it needed for, and what should > MRI_DIR contain? > > Pål G. Larsson > National Centre for Epilepsy > Norway > >

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