Fwd: Re: [Freesurfer] Average Volume
-- Forwarded message --
From: Rafael Huber <[EMAIL PROTECTED]>
Date: 11.09.2007 09:19
Subject: Re: Re: [Freesurfer] Average Volume
To: Doug Greve <[EMAIL PROTECTED]>
Hy Doug,
Thank you for your help. I tried to do it with your advice, but when i
runned "mri_concat --i SUBJECTS*/surf/lh.volume.mgz --o lh.volume
--mean" i always got an error message called "ERROR: dimension
mismatch between SUBJECT1/surf/lh.volume.mgz and
SUBJECT2/surf/lh.volume.mgz". I created all the volume.mgz files in
the same way in matlab. Do you have an idea? Thanks in advance.
Best Regards Rafael
2007/9/4, Doug Greve <[EMAIL PROTECTED]>:
>
> Try following the instructions for doing a thickness study, ie, run
> mris_preproc specifying lh.volume.mgz as the measure, then run either
> mri_glmfit with --osgm or run mri_concat with --mean.
>
> doug
>
>
>
>
> On Mon, 3 Sep 2007, Rafael Huber wrote:
>
> > Our goal is to get a file of average volume. As i understand the make
> > average command it takes the whole information of e.g. ?h.thickness
> > out of every /surf folder of every subject and creates an average
> > ?h.thickness file and saves it to /average/surf. i try to do the same
> > with the ?h.volume.mgz files, which we created with the matlab command
> > you proposed us. we made it as far that we have two ?h.volume.mgz
> > files in each subjects surf folder and we would like to continue the
> > group analyses process.
> >
> >
> > Hi Rafael,
> >
> > sorry, I don't understand. What do you mean " Problems appeared later
> > on, because we didn't find a difference in the average folder compared
> > to using the command without lh.volume.mgz files in the surf folder."
> > What problems? What kind of differences are you looking for and how?
> >
> > Bruce
> >
> >
> > On Mon, 3 Sep 2007, Rafael Huber wrote:
> >
> > Dear freesurfer users
> >
> > Do you have an idea how to create an average ?h.volume file?
> >
> > Our goal is to create a file with average volumes for our subjects, to
> > follow the group analysis. We know that the idea of using a volume
> > measure isn't implemented in the freesurfer software. We runned the
> > make_average_subject command in hope to find something like an
> > ?h.volume file in the average folder as there are files for the other
> > measures like thickness, area, curvature.
> > Before we runned the make_average command we followed the advice of
> > Bruce Fischl to create .mgh files in matlab with the following
> > command:
> >
> > [thickness, f] = read_curv('lh.thickness') ;
> > [area, f] = read_curv('lh.area') ;
> > volume = thickness .* area;
> > save_mgh(volume, 'lh.volume.mgz', eye(4));
> >
> > This functioned very well and we got our lh.volume.mgz files in the
> > surf folder. Problems appeared later on, because we didn't find a
> > difference in the average folder compared to using the command without
> > lh.volume.mgz files in the surf folder. We're now not sure if we
> > should continue like normal, or what exactly to do. Has somebody an
> > idea.
> >
> > Best regards
> >
> > Rafael Huber
> > ___
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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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--
Rafael Huber
Student
Division of Neuropsychology
Institute of Psychology
University of Zurich
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RE: [Freesurfer] parcellation problem
that type of pattern usually means you loaded the wrong hemisphere (e.g. the lh.aparc.annot on the rh.inflated or visa versa) On Mon, 10 Sep 2007, Wang, Xin wrote: the following error is reported when I run the tksurfer and load annotation. I attach a image of parcellation. Thank you. Xin Talairach transform /home/xwang/bin/freesurfer/subjects/amputation/APN01R650/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /home/xwang/bin/freesurfer/subjects/APN01R650_f/mri/transforms/talairach.xfm surfer: Reading header info from /home/xwang/bin/freesurfer/subjects/APN01R650_f/mri/T1.mgz surfer: vertices=130570, faces=261136 Talairach transform /home/xwang/bin/freesurfer/subjects/amputation/APN01R650/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /home/xwang/bin/freesurfer/subjects/APN01R650_f/surf/../mri/transforms/talairach.xfm From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 9/10/2007 2:31 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] parcellation problem can you send us an image to show what you mean by "completely messed up"? On Mon, 10 Sep 2007, Wang, Xin wrote: Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of talairach transform and white matter surface did not mess up the parcellation. Could anyone tell me what is wrong? Thank you in advance, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?h.volume files
Dear Freesurfer users I computed ?.volume files by using several commands sent by Bruce. Instead of using the save_mgh.m command, which not really worked because there was a dimension mismatch later when using mri_concat, we used write_curv.m. I need the number of faces in the surface to write ?h.volume files. Where can I get these numbers? Is it the file called f created in the Matlab current directory after running read_curv multiplying area times thickness, and write_curv? Thanks in advance Best regards Juergen Haenggi - 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] ?h.volume files
read_curv will return that also:
[thickness_vector, nfaces] = read_curv('lh.thickness') ;
I'm a bit worried that you have a dimension mismatch. That shouldn't
happen.
Bruce
On Tue, 11 Sep 2007, Juergen Haenggi,
Psychological Institute wrote:
Dear Freesurfer users
I computed ?.volume files by using several commands sent by Bruce. Instead of
using the save_mgh.m command, which not really worked because there was a
dimension mismatch later when using mri_concat, we used write_curv.m. I need
the number of faces in the surface to write ?h.volume files. Where can I get
these numbers? Is it the file called f created in the Matlab current
directory after running read_curv multiplying area times thickness, and
write_curv?
Thanks in advance
Best regards
Juergen Haenggi
-
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)
-
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[Freesurfer] Segmentation Probability Values
Hello FreeSurfers- At any point in the recon-all processing stream does a voxel by voxel map of segmentation probability values get generated? If not, are that at all obtainable through post-processing methods? -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Segmentation Probability Values
Hi Jim, I haven't tried this in a long time, but when I was writing the aseg stuff I implemented something in mri_ca_label to write out the probabilities at each step of the ICM. Run mri_ca_label with "-write_probs " and it will write out sprintf(output_fname, "%s03d.mgz", fname, iteration_number) is that clear? Not sure it works, but it did at some point :). Note that in the usual way these are monotonically related to probabilities rather than the actual probabilities themselves. cheers, Bruce On Tue, 11 Sep 2007, James N. Porter wrote: Hello FreeSurfers- At any point in the recon-all processing stream does a voxel by voxel map of segmentation probability values get generated? If not, are that at all obtainable through post-processing methods? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
