[Freesurfer] phase data overlay using fsaverage
Dear freesurfer experts, I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). I then brought these data into freesurfer using the following: bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2 mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh However, I do not see anything on the sphere (or fsaverage for that matter) ... Can you provide any hints? The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ... Any tips would be a big help! Best wishes, Jason. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Memory allocation problem with mri_robust_template
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the first
step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5
anatomical datasets (our typical load for surface reconstruction). The
problem seems to come when the third dataset is being registered, at which
point recon-all exits with the following error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not
open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version 10.6.0:
Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST 2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine (which
has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template (from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried running
it on version 5 with just 2 anatomical datasets, and it works just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] roisummary-sess from binary mask
Hello, I am trying to get a summary of beta value activation for a hand-drawn binary mask. This mask is a sphere, so it does not correspond to a particular anatomical label or functional contrast. Is there any way to apply roisummary-sess to this type fo binary mask (in nii or mgz format)? If not, can I specify my mask as an roi so that the roisummary-sess function will work? Or is there another command I should be using to get a summary of beta values for a particular mask? Thank you, Emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Three starting questions
Dear FreeSurfer community, You were very helpful for my last question, thank you. Now I have three basic questions. 1. I would like to check the segmentation by loading T1.mgz and aseg.mgz as an -aux volume, so that I can switch between them. How can I do this? (tkmedit subject T1.mgz -aux aseg.mgz gives some king of black and white segmentation instead of colorful one). 2. When I press View - View configuration, I have three options there (Single view, Multiple orientations, and Mosaic). How can I view just 3 orientations or 2 (e.g. sagittal and transverse)? 3. Do MacOS users have problems with mouse? When I try to edit segmentation or surfaces with Edit Tools, my mouse doesn't seem to work. I mean, when I click on the pixel with any of three buttons, nothing changes. I saw similar problem on the mailing list, but there was no answer. Thank you for your time, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tksurfer error
Dear freesurfer community, I am currently trying to view one of the surfaces generated by recon-all command in tksurfer but when I enter the command: tksurfer LuceHR_FS_SURF lh inflated.nofix I receive a series of errors that look like this: Received X error! Error code : 1 Request code : 147 Minor code : 181 Error text : 'BadRequest (invalid request code or no such operation)' Subsequently the surface window does not display what I would believe is the surface I am trying to view and then the only way I can exit the tksurfer environment is by exiting the terminal that I invoked it in. Any ideas or solutions? Thank you very much, Evan Luther ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Abblocked Setup
Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what I understand from your first e-mail, this is the opposite of what we want. I tried looking at the surface-based analysis using tksurfer, but since there is no constrast file for abblocked, I specified all contrasts, but how do you differentiate if you have more than one? tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call I think perhaps it would be better for us to switch to the block design to make things simpler? Thanks!! Chindhuri sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] about option -show-edits in version 5.0.0
Hi, I am trying to develop a custom software to run freesurfer, make edits if necessary(user intervention) and rerun the freesurfer from appropriate staring point and also, track/record the user interventions. My prime concern is the tracking of user intervention part, and I came across -show-edits option. But I could not find proper documentation on how we can retrieve desired info using this option. Is it possible to track any sort of user intervention by running -show-edits option with recon-all? If so how can one perform that? Thanks in advance. Binod ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Slice Order
Hi Rita, I would not automatically assume that regarding slice ordering with interleaved acquisitions, as I don't think that there is necessarily any standard that different manufacturers are committed to following. It is actually a non-trivial issue -- e.g., how do scanner choices regarding acquisition mode, image numbering, and direction of graphical slice prescription all relate to each other. You might be able to check with an engineer/technician for your particular platform and confirm how it is done on that platform for your chosen protocol, acquisition parameters, and way of doing slice prescription. But probably easiest to just figure it out empirically by acquiring 4-5 slices (select an even or odd number to match your desired protocol) with a large slice gap and a long TR (e.g., 10 sec), and having the subject rotate his/her head far to the left following the collection of the first slice. The slice acquired first temporally is then easily identified as the non- rotated slice. cheers, -MH On Tue, 2011-02-08 at 11:41 -0500, Rita Loiotile wrote: If my BOLD scan has 30 slices in interleaved series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surfaces to voxelspace
Dear freesurfer experts, I would like to display freesurfer surfaces in the voxelspace of the original subject image using matlab. Which coordinate transformation do I have to apply to get the vertex-coordinates to the RAS space and finally to the original voxelspace of the subject? (i guess for RAS2Vox I can use the matrix I can obtain with mri_info ... but I cannot find a way from vertex-coordinates to RAS) Thank you for any hint Best Regards Steffen Bollmann ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem with mri_robust_template
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to
the first image. Since 5.0 we use the mri_robust_template tool (as it
can ignore outlier regions and produces more accurate registrations, see
Reuter et al Neuroimage 2010 ..robust registration), but it is more
memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template
uses a lot of memory. I tested that tool in the longitudinal stream
where I successfully ran it on 10 images on a 4 gig machine (those
images are probably smaller than yours).
So you have the following options:
1. use only the best 2 input images. This has been recommended in the
past, 5 inputs are usually not improving anything (see old emails on
this list from Bruce)
2. pass the flag -flirt-motioncor to recon-all and it will revert back
to using flirt (but accuracy of the registration might suffer, since the
inputs are full head images with potentially a lot of differences in
jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that
fits into the memory. They will be converted to uchar anyway in the
conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the
first step of recon-all ('recon-all -autorecon1 -subjid ...') when
using 5 anatomical datasets (our typical load for surface
reconstruction). The problem seems to come when the third dataset is
being registered, at which point recon-all exits with the following
error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th
slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could
not open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version
10.6.0: Wed Nov 10 18:13:17 PST 2010;
root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST
2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine
(which has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template
(from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried
running it on version 5 with just 2 anatomical datasets, and it works
just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Three starting questions
Dear Tanja, Concerning your question 3 do the following: In the System Preferences - Keyboard Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed On 09 Feb, 2011, at 00:07, tetian...@gmail.com wrote: Dear FreeSurfer community, You were very helpful for my last question, thank you. Now I have three basic questions. 1. I would like to check the segmentation by loading T1.mgz and aseg.mgz as an -aux volume, so that I can switch between them. How can I do this? (tkmedit subject T1.mgz -aux aseg.mgz gives some king of black and white segmentation instead of colorful one). 2. When I press View - View configuration, I have three options there (Single view, Multiple orientations, and Mosaic). How can I view just 3 orientations or 2 (e.g. sagittal and transverse)? 3. Do MacOS users have problems with mouse? When I try to edit segmentation or surfaces with Edit Tools, my mouse doesn't seem to work. I mean, when I click on the pixel with any of three buttons, nothing changes. I saw similar problem on the mailing list, but there was no answer. Thank you for your time, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
