Freesurfer May 2005

freesurfer@nmr.mgh.harvard.edu

26 participants
53 discussions

BRIK and tkregister
by Joongnam Yang 24 May '05

24 May '05

Hi, I am using an old version of Freesurfer where retinotopy-analysis is enabled. If anyone having such experience, please help me. I am having trouble with csurf, and here is what I did. (1) changed Analyze file (*.hdr, *.img) into *.BRIK and *.HEAD using to3d (2) in csurf, under "session tools", I did "setup align/func scan" and it opens a window where I do "align scan dir" and it only accepts AFNI's *.BRIK and *.HEAD file. (that's why I did the conversion above). When I choose "align=>subj" to do the tkregister registration, it gives me the following error window. AFNI BRIK byte order (determined "only" from BYTEORDER_STRING parameter in this HEAD file): /............/bob+orig.HEAD is INTEL (LSB first) not SUN/SGI/MAC (MSB first) Change to MSB first? This error message was followed by either "cancel" or "force BRIK to MSB, Fix HEAD", but neither option worked, meaning the image shown on "tkregister" was all gobbled. The "subj" image is OK, but the "align" image is screwed. Could anyone give me a hint on where I should go from here? Thanks. Nam.

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Talairach help!!
by Fornito, Alexander 23 May '05

23 May '05

Hi all, Sorry to labour this point, but I'm stuck with the MNI tools and am having trouble progressing through my freesurfer analyses. I can't create the talairach.xfm and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc ----------------------------------------------------------------- INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 211 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/... Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages: segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' As far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex

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wm fill won't work with partial brain
by Bakkour, Akram 23 May '05

23 May '05

Hello, I have a high resolution image covering the back third of the brain obtained from surface coils and wm fill fails, it tells me that it doesn't find the corpus callosum. This makes sense because it is not a full brain. But I was wondering if there was a way around this and have the program continue to make progress rather than fail and stop. Thanks for the help! Akram.

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Re: remote VNC solution
by Daniel Goldenholz 19 May '05

19 May '05

I was just asked this same question twice in a short time, so I guess that is a sign that others might want to know the answer too. The short version of the question is: "How can I get freesurfer to work from a remote VNC setup?" The answer is, thanks to a hint from Paul Raines, very simple. When you set up your vncserver, use this command: vncserver.glx instead of the usual "vncserver". If you do, then the needed software will be included to draw tksurfer images, and then you can freesurf remotely. Happy surfing! Daniel Tommi Raij wrote: >Hi Daniel, > >I saw from the Freesurfer list that you asked Bruce about a year ago how >to use tksurfer scripts from remote VNC. Bruce suggested you use > >setenv renderoffscreen 1 > >before running tksurfer, but also said that the function might be broken. > >I am trying the get some semi-massive visualization scripts to work from >the other end of a VNC connection (on a Windows ME system) and cannot make >this work, and keep receiving the kind of errors that you apparently >encountered: > >surfer: single buffered window >no glx extension! >surfer: failed, trying double buffered window >Xlib: extension "GLX" missing on display "1.0". >Window type not found! >surfer: failed, no suitable display found > >Were you succesful in making this work, and if so, how? > >Thanks, > >Tommi > >

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RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 19 May '05

19 May '05

Hi Bruce I tried -it siemens too (based on some list question) and that did't work either, but I see now that hey are named .IMA not .ima Sorry, the FW-disk I got them from likely caused the problem. Thanks, Kristine -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 12:00 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files Hi Kristine, mri_convert should handle ima files. Have you tried -it siemens? Are they named .ima? cheers, Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: > Hi > > I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command > > mri_convert -ot cor <one filename in the sequence> <output file> > > but it doesn't work. Gives an error message "cannot parse..." (see attached error message). > > I'd be grateful for any suggestions. > > Thanks, > > Kristine > >

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MNI problems
by Fornito, Alexander 19 May '05

19 May '05

Hi, I've been having some problems with the MNI tools (I can't create the talairach.xfm) and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc ----------------------------------------------------------------- INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 211 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/... Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages: segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' I'm guessing "the mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory" is the culprit, but can't figure out what it is since, as far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex

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RE: [Freesurfer] WMFilll and talairach coordinates
by Fornito, Alexander 18 May '05

18 May '05

-----Original Message----- From: Fornito, Alexander Sent: Thu 5/19/2005 10:27 AM To: Bruce Fischl Cc: Subject: RE: [Freesurfer] WMFilll and talairach coordinates Now I understand. And this information has to be in .xfm format? It can't be in .mat (FLIRT) or .tfn (AIR) format? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/19/2005 10:25 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates no, because we just keep the transform around, but only apply it for either reporting purposes, or apply the inverse to find anatomical features (e.g. the callosum) On Thu, 19 May 2005, Fornito, Alexander wrote: > Wouldn't that occur by using the MNI tools anyway? > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 5/18/2005 9:39 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] WMFilll and talairach coordinates > > > > just that you have sacrificed resolution. > > On Wed, 18 May 2005, Fornito, > Alexander wrote: > > > Other than that though, should there be any problem if I align my images prior to starting with freesurfer? > > Provided I align to the MNI 152 brain, it should still be in talaraich space... > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Wed 5/18/2005 10:55 AM > > To: Fornito, Alexander > > Cc: peggy christidis; freesurfer(a)nmr.mgh.harvard.edu > > Subject: RE: [Freesurfer] WMFilll and talairach coordinates > > > > > > > > 1. to report talairach coords. > > 2. To get cutting planes to separate the hemispheres when the head is at an > > angle. > > 3. To find the callosum if other heuristics fail. > > 4. To pick some control points in the white matter for intensity > > normalization. > > > > cheers, > > Bruce > > > > > > On Wed, 18 May 2005, Fornito, Alexander > > wrote: > > > > > Hi, > > > Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? > > > I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? > > > Thanks, > > > Alex > > > > > > -----Original Message----- > > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > > Sent: Wed 5/18/2005 6:00 AM > > > To: peggy christidis > > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] WMFilll and talairach coordinates > > > > > > > > > > > > Hi Peggy, > > > > > > we don't apply the transform, just keep it around, so blurring isn't a > > > problem. I don't know if AFNI knows how to write out .xfm files (the mni > > > transform format), but that would be the best solution. > > > > > > > > > Bruce > > > > > > On Tue, 17 May 2005, > > > peggy christidis wrote: > > > > > > > Hello, > > > > > > > > I'm having a bit of trouble with the "Create Surface" step in FreeSurfer. I > > > > have a single mprage scan that creates a decent first pass surface, but > > > > there's still some brainstem and cerebellum attached to it. I followed the > > > > troubleshooting guidelines in the FreeSurfer manual regarding Failure of > > > > Automatic Cutting Planes. I went to Expert Preferences --> WMFill, and > > > > inputed the appropriate coordinates to separate the brainstem and cerebellum. > > > > The coordinates I used were not in Talairach space, but I assumed this was > > > > okay because the manual says to use original coordinates if you don't have > > > > Talairach coordinates. However, when I re-ran "Create Surface", nothing > > > > happened (i.e., filled volume and surface both still show the > > > > pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing > > > > list archives and read that Talairach coordinates are indeed needed. > > > > > > > > Here's my question: The volume I'm using shows a head that's slightly tilted > > > > about 10 degrees to the left, so I should probably do the Taliarach > > > > transformation anyway. However, I don't have the mni_tools installed on my > > > > computer (I had major installation problems with them). Anyway, could I do a > > > > taliarach transformation outside of Freesurfer (like in AFNI) and then > > > > tranfer that talairached volume to FreeSurfer? My concern is that the > > > > transformation will blur the volume, making segmentation difficult. What > > > > should I do? > > > > > > > > Thanks, > > > > Peggy > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > > > >

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RE: [Freesurfer] WMFilll and talairach coordinates
by Fornito, Alexander 18 May '05

18 May '05

Wouldn't that occur by using the MNI tools anyway? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates just that you have sacrificed resolution. On Wed, 18 May 2005, Fornito, Alexander wrote: > Other than that though, should there be any problem if I align my images prior to starting with freesurfer? > Provided I align to the MNI 152 brain, it should still be in talaraich space... > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 5/18/2005 10:55 AM > To: Fornito, Alexander > Cc: peggy christidis; freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] WMFilll and talairach coordinates > > > > 1. to report talairach coords. > 2. To get cutting planes to separate the hemispheres when the head is at an > angle. > 3. To find the callosum if other heuristics fail. > 4. To pick some control points in the white matter for intensity > normalization. > > cheers, > Bruce > > > On Wed, 18 May 2005, Fornito, Alexander > wrote: > > > Hi, > > Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? > > I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? > > Thanks, > > Alex > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Wed 5/18/2005 6:00 AM > > To: peggy christidis > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] WMFilll and talairach coordinates > > > > > > > > Hi Peggy, > > > > we don't apply the transform, just keep it around, so blurring isn't a > > problem. I don't know if AFNI knows how to write out .xfm files (the mni > > transform format), but that would be the best solution. > > > > > > Bruce > > > > On Tue, 17 May 2005, > > peggy christidis wrote: > > > > > Hello, > > > > > > I'm having a bit of trouble with the "Create Surface" step in FreeSurfer. I > > > have a single mprage scan that creates a decent first pass surface, but > > > there's still some brainstem and cerebellum attached to it. I followed the > > > troubleshooting guidelines in the FreeSurfer manual regarding Failure of > > > Automatic Cutting Planes. I went to Expert Preferences --> WMFill, and > > > inputed the appropriate coordinates to separate the brainstem and cerebellum. > > > The coordinates I used were not in Talairach space, but I assumed this was > > > okay because the manual says to use original coordinates if you don't have > > > Talairach coordinates. However, when I re-ran "Create Surface", nothing > > > happened (i.e., filled volume and surface both still show the > > > pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing > > > list archives and read that Talairach coordinates are indeed needed. > > > > > > Here's my question: The volume I'm using shows a head that's slightly tilted > > > about 10 degrees to the left, so I should probably do the Taliarach > > > transformation anyway. However, I don't have the mni_tools installed on my > > > computer (I had major installation problems with them). Anyway, could I do a > > > taliarach transformation outside of Freesurfer (like in AFNI) and then > > > tranfer that talairached volume to FreeSurfer? My concern is that the > > > transformation will blur the volume, making segmentation difficult. What > > > should I do? > > > > > > Thanks, > > > Peggy > > > _______________________________________________ > > > 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 > > > > > > > > >

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average curvature on individual subjects
by Frida Polli 18 May '05

18 May '05

Hi I just learned that it is possible to make an average curvature file from a bunch of subjects, but specify the output subject as an individual brain. given that, is it possible to put average7's curvature files onto an individual subject? thanks, frida

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RE: [Freesurfer] WMFilll and talairach coordinates
by Fornito, Alexander 18 May '05

18 May '05

Other than that though, should there be any problem if I align my images prior to starting with freesurfer? Provided I align to the MNI 152 brain, it should still be in talaraich space... -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres when the head is at an angle. 3. To find the callosum if other heuristics fail. 4. To pick some control points in the white matter for intensity normalization. cheers, Bruce On Wed, 18 May 2005, Fornito, Alexander wrote: > Hi, > Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? > I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? > Thanks, > Alex > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 5/18/2005 6:00 AM > To: peggy christidis > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] WMFilll and talairach coordinates > > > > Hi Peggy, > > we don't apply the transform, just keep it around, so blurring isn't a > problem. I don't know if AFNI knows how to write out .xfm files (the mni > transform format), but that would be the best solution. > > > Bruce > > On Tue, 17 May 2005, > peggy christidis wrote: > > > Hello, > > > > I'm having a bit of trouble with the "Create Surface" step in FreeSurfer. I > > have a single mprage scan that creates a decent first pass surface, but > > there's still some brainstem and cerebellum attached to it. I followed the > > troubleshooting guidelines in the FreeSurfer manual regarding Failure of > > Automatic Cutting Planes. I went to Expert Preferences --> WMFill, and > > inputed the appropriate coordinates to separate the brainstem and cerebellum. > > The coordinates I used were not in Talairach space, but I assumed this was > > okay because the manual says to use original coordinates if you don't have > > Talairach coordinates. However, when I re-ran "Create Surface", nothing > > happened (i.e., filled volume and surface both still show the > > pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing > > list archives and read that Talairach coordinates are indeed needed. > > > > Here's my question: The volume I'm using shows a head that's slightly tilted > > about 10 degrees to the left, so I should probably do the Taliarach > > transformation anyway. However, I don't have the mni_tools installed on my > > computer (I had major installation problems with them). Anyway, could I do a > > taliarach transformation outside of Freesurfer (like in AFNI) and then > > tranfer that talairached volume to FreeSurfer? My concern is that the > > transformation will blur the volume, making segmentation difficult. What > > should I do? > > > > Thanks, > > Peggy > > _______________________________________________ > > 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 > > >

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Freesurfer May 2005