Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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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RE: [Freesurfer] WMFilll and talairach coordinates
by Fornito, Alexander 17 May '05

17 May '05

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] Segmentation error
by Fornito, Alexander 17 May '05

17 May '05

Great. Thanks!! -----Original Message----- From: florent segonne [mailto:fsegonne@csail.mit.edu] Sent: Wed 5/18/2005 1:22 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation error Hello Alex, This warning message appears during the watershed segmentation process. The final brain shape is compared to a statistical atlas and the correctness of the segmentation (of the shape) is evaluated. It turns out that the validation is often too restrictive and often generates a useless warning message. As a consequence, you should most often ignore this message. If the skull stripping appears to be incorrect, this message might then become of interest. In any case, we'll shortly fix this. Best, Florent

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WMFilll and talairach coordinates
by peggy christidis 17 May '05

17 May '05

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

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Segmentation error
by Fornito, Alexander 17 May '05

17 May '05

Hi, When running segment_subject, I get a meesage saying THE SEGMENTATION IS PROBABLY NOT CORRECT at the validation stage. Any hints as to what might be causing this and how to fix? Thanks, Alex

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FW: [Freesurfer] Appropriate post-editing processing
by Fornito, Alexander 16 May '05

16 May '05

-----Original Message----- From: Fornito, Alexander Sent: Tue 5/17/2005 12:51 PM To: Bruce Fischl Cc: Subject: RE: [Freesurfer] Appropriate post-editing processing For lh.white and lh.pial it is: euler # = v-e+f = 2g-2: 0 - 0 + 0 = 0 --> 1 holes F =2V-4: 0 != 0-4 (-4) 2E=3F: 0 = 0 (0) total defect index = 2 As far as I'm aware my version of Freesurfer is up to date (we downloaded within the past month). You've confused me abit - I thought the point of manual editing was to get a topologically correct surface? Thanks for your help, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 5/17/2005 11:58 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Appropriate post-editing processing what is the euler number? It should be 2 in all cases - you shouldn't have to edit to get a topologically correct surface. In some cases it was 1 or 0, but Florent fixed those problems a while ago, so if you have an up-to-date version of mris_fix_topology it should be 2. cheers, Bruce On Tue, 17 May 2005, Fornito, Alexander wrote: > Hi all, > I've created the final surface on one of my images and noticed that mris_euler_number has detected defects. I've gone back to edit what i think is the problem and was wandering if I need to go through the whol process again (create surface -> Fix topology correction -> Create final surface), or if I can just run create final surface again. > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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