[Freesurfer] Situation with OASIS
Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results of your great effort available? Thanks in advance for the great job (and reply of course). Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] reg -feat2anat error reg -feat2anat error
Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. What should I do? Best wishes Carolyn -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Mon 21/05/2007 17:16 To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Mon May 21 10:38:18 BST 2007 /disc2/Kate/Flatmap1 /home/progs/freesurfer/bin//reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz... 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 /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag --- Initializing exf2anat from crude std2anat tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat LoadVol0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz Ttarg: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/progs/fsl/etc/standard/avg152T1_brain.img Tmov: -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Input registration matrix (computed) 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 30.861; 0.000 -1.000 0.000 -52.627; 0.000 0.000 0.000 1.000; --- Input registration matrix 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 30.861; 0.000 -1.000 0.000 -52.627; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 30.861; 0.000 -1.000 0.000 -52.627;
[Freesurfer] ANCOVA model in Freesurfer
Dear Freesurfer users I am trying to create the GroupDescriptorFile 1 for an ANCOVA in order to analyze local cortical thickness. I intend to compare two groups while controlling for age and mean cortical thickness. Am I right that I can leave out the term class and model group as a variable? GroupDescriptorFile 1 Title CorticalThickness Variables Group Age MeanThickness Input Control01 ControlSubject 27 3.14 Input Control02 ControlSubject 31 3.28 Does the variables all have to be integers or can it be also a string? Thanks for helping Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Situation with OASIS
Hi Martin, it's all processed and checked, and we're now working (with BIRN) on tools to put it online. cheers, Bruce On Mon, 4 Jun 2007, Martin Kavec wrote: Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results of your great effort available? Thanks in advance for the great job (and reply of course). Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Masking at the individual level
Dear FreeSurfers,
Quick question about masking. I routinely make a brainmask for each subject
and include the mask flag in the mkanalysis (see below), but I note that
when I run contrasts and plot results-either for individual subjects or for
group-level stuff-I get statistical results for voxels outside the brain.
I'd like to mask the extra-brain voxels out at the individual level, so that
they don't get included at any point in my group level analyses. How do I do
this? More generally, does the brainmask serve only a visual/display
function or can I use it to constrain what I'm doing stats on (which is what
I want it to do)?
Thanks for your endless help!
Dan Dillon
PS. This is a a typical mkanalysis step . . .
mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5
-paradigm mg_3_7.par -designtype event-related -funcstem fmcs
tcsm6 -nconditions 13 -polyfit 2 -taumax 30 -inorm -mask brain -timeoffset
-1.25 -TER .1 -autostimdur -force
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RE: [Freesurfer] reg -feat2anat error reg -feat2anat error
Hi Doug This is what happened when I ran it with --debug Kate/Flatmap1 reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. After I replaced the binaries that you suggested in previous emails, the other processes would now no longer run... Healthy_Volunteers/Colton_Structural mri_convert -i Colton.nii.gz -subjid Colton -autorecon1 mri_convert: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Flatmap1/Healthy_Volunteers tkregister2 --mgz --s Colton -fstal tkregister2: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory I changed mri_convert and tkregister2 back to their original version and they worked fine again. When I run the old version of reg-feat2anat I still get the original error: ERROR: could not read /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24 Not sure what is going on? Best wishes Carolyn -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Mon 04/06/2007 15:07 To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error reg -feat2anat error wow, not sure what's going on there. Can you add --debug to the cmd line, caputre the terminal output, and send it to me? Furlong, Carolyn wrote: Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. What should I do? Best wishes Carolyn -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Mon 21/05/2007 17:16 To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Mon May 21 10:38:18 BST 2007 /disc2/Kate/Flatmap1 /home/progs/freesurfer/bin//reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz... 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 /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag --- Initializing exf2anat from crude std2anat tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov
Re: [Freesurfer] Masking at the individual level
I have never masked out out-of-brain voxels. For visualization purposes,
I usually mask out in tkmedit by loading the brain.mgz as aux and then
applying aux as a mask from the View menu. It is strange that you are
getting out-of-brain activation in the group analysis. How close is it
to the edge? Remember, that talairach is only accurate to an inch or so.
doug
Dan Dillon wrote:
Dear FreeSurfers,
Quick question about masking. I routinely make a brainmask for each
subject and include the mask flag in the mkanalysis (see below), but I
note that when I run contrasts and plot results--either for individual
subjects or for group-level stuff--I get statistical results for
voxels outside the brain. I'd like to mask the extra-brain voxels out
at the individual level, so that they don't get included at any point
in my group level analyses. How do I do this? More generally, does the
brainmask serve only a visual/display function or can I use it to
constrain what I'm doing stats on (which is what I want it to do)?
Thanks for your endless help!
Dan Dillon
PS. This is a a typical mkanalysis step . . .
mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5
-paradigm mg_3_7.par -designtype event-related -funcstem fmcs
tcsm6 -nconditions 13 -polyfit 2 -taumax 30 -inorm -mask brain
-timeoffset -1.25 -TER .1 -autostimdur -force
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] reg -feat2anat error reg -feat2anat error
what platform are you running on? Furlong, Carolyn wrote: Hi Doug This is what happened when I ran it with --debug Kate/Flatmap1 reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. After I replaced the binaries that you suggested in previous emails, the other processes would now no longer run... Healthy_Volunteers/Colton_Structural mri_convert -i Colton.nii.gz -subjid Colton -autorecon1 mri_convert: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Flatmap1/Healthy_Volunteers tkregister2 --mgz --s Colton -fstal tkregister2: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory I changed mri_convert and tkregister2 back to their original version and they worked fine again. When I run the old version of reg-feat2anat I still get the original error: ERROR: could not read /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24 Not sure what is going on? Best wishes Carolyn -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Mon 04/06/2007 15:07 To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error reg -feat2anat error wow, not sure what's going on there. Can you add --debug to the cmd line, caputre the terminal output, and send it to me? Furlong, Carolyn wrote: Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. What should I do? Best wishes Carolyn -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Mon 21/05/2007 17:16 To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Mon May 21 10:38:18 BST 2007 /disc2/Kate/Flatmap1 /home/progs/freesurfer/bin//reg-feat2anat --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz... 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 /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag --- Initializing exf2anat from crude std2anat tkregister2 --targ
Re: [Freesurfer] problem with tksurfer (fwd)
Dear Nick, Thanks for the suggestion! I have to admit that I had found it unlikely that the graphics driver could solve the problem but we made the download anyway and it has helped!! Thanks again Claus --- Claus Tempelmann email: [EMAIL PROTECTED] Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany On Thu, 31 May 2007, Nick Schmansky wrote: Claus, It looks like the image is being clipped. I would suggest updating the graphics driver directly from the NVidia website. On a number of occasions, I have encountered oddball problems like this with NVidia cards, that have been fixed with a driver update. It might be worthwhile to update both machines. Nick On Thu, 2007-05-31 at 16:51 +0200, Claus Tempelmann wrote: Hello everybody, Having worked with quite old versions of freesurfer for a long time we decided recently to install a newer version on two new computers. Both are running under the 64 bit version of SUSE Linux 10.2, both have a Dual Opteron processor, they have 6 GB (system 1) or 8 GB (system 2) and most hardware and software is quite comparable in my opinion. There is one major difference with the graphic cards, system 1 has an MSI GEForce 6600, whereas system 2 has an GEForce FX 7600GS. I'd expect that both cards are more than sufficient for freesurfer and I doubt that this difference can be the reason for the difference I have observed but may be some of you have experienced a similar problem and can help me out. What's the problem? All analysis steps of the standard procedure seem to work fine on both systems. However, I see a reproducible strange problem on system 2 when I try to use tksurfer on the standard data set (bert) coming with the package (freesurfer-Linux-rh9-stable- pub-v3.0.5.-full.tar). When I run the command tkregister bert lh inflated on system 1, everything looks like expected. But on system 2 something is wrong, the program tells the number of vertices and faces as usual and the numbers are the same as on system 2 (as they should, I'm using the same data set). Nevertheless, the output looks quite different, I'll try to attach a screenshot. The window shows up as usual and a small part of the inflated brain is shown at the right edge of the window but the rest of the brain is never shown. When I rotate this surface the visible part of the inflated brain is rotated correctly but the rest is always missing. Can anybody help? Thanks in advance Claus --- Claus Tempelmann email: [EMAIL PROTECTED] Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to import private color scales
dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? thanks, bye, pisti - [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to import private color scales
Sorry, there's no way to do that for overlay data. On Mon, 2007-06-04 at 13:23 -0400, Istvan Akos Morocz wrote: dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: mri_surfcluster problem
hi, sorry to bother the mailinglist again, but i haven't received a response to this question. i just wanted to make sure that it hadn't slipped through the cracks. any help would be very much appreciated, emily On 6/1/07, Emily Cooper [EMAIL PROTECTED] wrote: hi, i am having a strange problem with mri_surfcluster. i give it the following command line: mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt and i get this result in the summary: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.26.2.4 2006/07/13 17:50:28 greve Exp $ # $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ # CreationTime 2007/06/01-19:04:15-GMT # cmdline mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt # cwd /disks/gpfs/fmri/emily.permutations/correlation.permutations # sysname Linux # hostname andrew.bsd.uchicago.edu # machine i686 # FixVertexAreaFlag = 1 # # Input /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/ecooper/subjects # Minimum Threshold 0.5 # Maximum Threshold 1 # Threshold Signpos # AdjustThreshWhenOneTail 1 # Area Threshold6 mm^2 # Overall max 0.632052 at vertex 5494 # Overall min 0.12689 at vertex 750 # NClusters 2 # Total Cortical Surface Area 70394.7 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 10.6325494 85426.29-50.2 -16.0 -7.2 161181 20.2239300 23.61-31.7 -26.79.968 the problem is that this is just entirely incorrect. when i view the input dataset in tksurfer, it's clear just from scanning over the vertices that 161181 out of 163842 total of them do not have intensity values between .5 and 1 (thmin and thmx), let alone in a giant cluster together. furthermore, when i make a historgram of a text file containing these intensity values, it shows that the majority of them are less than .5, and thus shouldn't be recognized as part of a cluster based on my specifications in the mri_surfcluster command: $breaks [1] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 [13] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 $counts [1]10 205 1320 3881 7834 12333 16777 20168 21369 20405 17219 13789 [13] 10453 7479 4897 2988 1599 737 2838114 1 $intensities [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $density [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $mids [1] -0.075 -0.025 0.025 0.075 0.125 0.175 0.225 0.275 0.325 0.375 [11] 0.425 0.475 0.525 0.575 0.625 0.675 0.725 0.775 0.825 0.875 [21] 0.925 0.975 any ideas as to what is going wrong here? am i using the thmin and thmax flags wrong? thanks so much, emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fmri conjunction/correlation map
Hi all, I have a few questions on two related topics. Topic 1, conjunction analysis: Thank you Doug for your response pointing out the mergecontrasts tool. I have 2 questions for anyone who may have used this in the past. First, do I specify the two contrasts to merge using the contrast flag twice? Ex: -contrast [name] [thresh] [tail] -contrast [name] [thresh] [tail] or do I specify both contrasts under a single tag? Additionally, this is a memory task and the encoding and retrieval runs were analyzed separately (same analysis type, but same coding in paradigm files and different sessions parent directories) so will it be possible to indicate to the program where the encoding contrast to be merged with the retrieval contrast is? Or will I have to rearrange my directories, recode my paradigm files, and make new contrasts? probably the latter huh? Topic 2, correlation analysis: As an alternative to a conjunction analysis, is it possible to use freesurfer to perform a voxel-by-voxel group level correlation analysis of encoding versus retrieval runs for a memory task perhaps obtaining a map of r-values or sigs or r values representing the correlation of the time courses from corresponding voxels from the two runs? what freesurfer tools would do this? Thanks in advance, Cameron Oh, you want a conjunction I think. Corrlation means something else. Try mergecontrasts-sess doug Cameron Ellis wrote: Hi Doug, We would like to compare, voxel by voxel, the activity between two back-to-back runs, one encoding run and one retrieval run for a memory task. Ideally what we have in mind would be to view, on the inflated surface, a map of voxels that were above a certain threshold during both encoding and retrieval. Could we somehow make a whole brain functional mask from the encoding run an apply this to the retrieval run? Cameron I'm not sure what you are trying to do. sound like you have two values per voxel for each subject that you want to correlate, but you can't really correlate two values. I think I'm missing something ... doug Cameron Ellis wrote: Does anyone have an answer to this question? Hello, I am looking for a way to perform voxel-wise, within-subject correlations of two activation maps (in talairach space). The two existing maps reflect encoding and retrieval runs of a memory task. The idea would be to generate a correlation map across all subjects, to identify clusters where there was a positive or negative correlation between encoding and retrieval activation. I've seen this done with SPM but not Freesurfer. Any suggestions? (Perhaps this would involve glmfit?) Many thanks, Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mri_surfcluster problem
Sorry, it did fall thru the cr cks. Can you try running it with --no-adjust? When you give it a sign (ie, --pos), it assumes that the input values and threshold are -log10(p) and then adjusts the threshold for a single-tailed (signed) test, which means that it subtracts log10(2) = 0.3 from the threshold. So it's really using 0.5-0.3=0.2 as the threshold. Hope that made sense ... doug Emily Cooper wrote: hi, sorry to bother the mailinglist again, but i haven't received a response to this question. i just wanted to make sure that it hadn't slipped through the cracks. any help would be very much appreciated, emily On 6/1/07, Emily Cooper [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: hi, i am having a strange problem with mri_surfcluster. i give it the following command line: mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt and i get this result in the summary: # Cluster Growing Summary (mri_surfcluster ) # $Id: mri_surfcluster.c,v 1.26.2.4 http://1.26.2.4 2006/07/13 17:50:28 greve Exp $ # $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ # CreationTime 2007/06/01-19:04:15-GMT # cmdline mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt # cwd /disks/gpfs/fmri/emily.permutations/correlation.permutations # sysname Linux # hostname andrew.bsd.uchicago.edu http://andrew.bsd.uchicago.edu # machine i686 # FixVertexAreaFlag = 1 # # Input /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/ecooper/subjects # Minimum Threshold 0.5 # Maximum Threshold 1 # Threshold Signpos # AdjustThreshWhenOneTail 1 # Area Threshold6 mm^2 # Overall max 0.632052 at vertex 5494 # Overall min 0.12689 at vertex 750 # NClusters 2 # Total Cortical Surface Area 70394.7 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 10.6325494 85426.29-50.2 -16.0 -7.2 161181 20.2239300 23.61-31.7 -26.79.968 the problem is that this is just entirely incorrect. when i view the input dataset in tksurfer, it's clear just from scanning over the vertices that 161181 out of 163842 total of them do not have intensity values between .5 and 1 (thmin and thmx), let alone in a giant cluster together. furthermore, when i make a historgram of a text file containing these intensity values, it shows that the majority of them are less than .5, and thus shouldn't be recognized as part of a cluster based on my specifications in the mri_surfcluster command: $breaks [1] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 [13] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 $counts [1]10 205 1320 3881 7834 12333 16777 20168 21369 20405 17219 13789 [13] 10453 7479 4897 2988 1599 737 2838114 1 $intensities [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $density [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $mids [1] -0.075 -0.025 0.025 0.075 0.125 0.175 0.225 0.275 0.325 0.375 [11] 0.425 0.475 0.525 0.575 0.625 0.675 0.725 0.775 0.825 0.875 [21] 0.925 0.975 any ideas as to what is going wrong here? am i using the thmin and thmax flags wrong? thanks so much, emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center
[Freesurfer] w file to label
Hello, I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way. What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new label, and 3.) removing the component labels that went into it. # entered in bash shell # generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh # merge labels cat Subject_Lists/bw-group-error-5 | while read subject; do mri_surfcluster --in $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5 --sign pos --subject $subject --hemi lh --surf orig --annot aparc --minarea 1 --sum $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab $subject/label/rACC_lh_pos_0_ASce68 ; cd $subject/label; mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/\-i rACC/g') -o rACC_lh_pos_0_ASce68.label; rm rACC_lh_pos_0_ASce68-0*.label; cd $SUBJECTS_DIR; done #check in tksurfer surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh -fthresh 1 It seems to work, but if there is a more direct way, it may be better just because there is potential room for error the way I am doing it. Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
