Freesurfer June 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
66 discussions

Mean & SD over ROI in a FIR analysis (several timepoints)
by Tommi Raij 10 Jun '05

10 Jun '05

We are trying to calculate mean and SD over all the spatial (vertex) points included in a single functionally defined ROI/label. Bottom line, the biggest problem is that we do not know which tool to use to read all timepoints/frames of the hemodynamic waveforms (of all the vertex points included in the label, one at a time) into matlab. For details, please see below. Problem 1: We tried to use mri_label_vals but this gives only one value per vertex point. However this is a FS-FAST FIR analysis with a time window of 16 frames/TRs (of which two are prestimulus) so we should get 16 values for each vertex point in order to draw a BOLD time course. So we need a reader that will produce the functional stat values for all the time points, separately for all vertices included in the ROI. Problem 2: We would need to subtract the mean prestimulus baseline values from all 16 time points in order to set a (mean) zero baseline. This is necessary to decrease the voxel-to-next-voxel variability that is large in fMRI data. This of course has to be done before calculating the mean and SD values over the ROI. We did use mkcontrast-sess -rmprestim - does this result in that the baseline is already subtracted in the values (for each vertex point separately)? There are typically about 600 single vertex points in a label so saving them manually one by one as ASCII and then combining them is not feasible. As a separate but complicating issue, we have 6 simple contrasts (condition N minus REST, with names such as A-REST, V-REST, etc) and 2 slightly more complicated contrasts (condition 1 plus condition 2 minus condition 3). Loading and overlaying the ROI mean +- SD curves for each contrast separately increases the work load 6-fold. We have multiple subjects in six different conditions, each with multiple ROIs, and 6 simple contrasts, leading to thousands of BOLD waveforms - any practical application should automatically load all 6 contrast HDR waveforms and overlay them in a single window (exactly as sliceview-sess, tkmedit, and tksurfer do when you load time course - except that in these programs the time courses are displayed for only a single voxel at a time). Any suggestions how this could be achieved? Example data/analysis can be found in /space/cognito/5/users/raij/avml_fmri/avml12_session_BRISI07_ISI1TR_BERT There are two analyses here - here we are interested in the FIR analysis: ISI1TR_BERT_ERFIRsm6pf5tpefsub ... and the variables are setenv SUBJECT avml12 setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ Any advice would be greatly appreciated! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129

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Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 10 Jun '05

10 Jun '05

Hi, I downloaded the entire MNI package. Although I see all these MNI files, I still get the same error, file not found. Any clues why this might be? Thanks, Arvind Gururajan On 9 Jun 2005, Bruce Fischl wrote: > just download and install the whole MNI package. Much easier than trying > to install various pieces.... > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > Hello, > > > > I am very new to Freesurfer. Could anybody please tell me which specific > > MNI tool, I need to install? > > > > > >> > >> I tried the following command. > >> > >> ./recon-all -smooth1 ZM > >> ######################################## > >> program versions used > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire > >> mri_convert --version > >> $ > >> strings: rawtominc:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: minctracc:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: mincresample:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: mincaverage:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > >> mri_convert --version > >> $ > >> strings: mritotal:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: nu_correct:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> ####################################### > >> ERROR: Flag ZM unrecognized. > >> -smooth1 ZM > >> > >> > >> The folder ZM has only one orig file in the surf directory. There are no > >> raw data(.COR files). Please let me know your feedback. > >> > >> Sincerely, > >> > >> Arvind Gururajan > > > > _______________________________________________ > > 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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Strip and register check
by Fornito, Alexander 10 Jun '05

10 Jun '05

Hi, A couple of questions; 1 - The skull stripping feature has overstripped some of my brains, and using -wsmore doesn't completely fix the problem. Are there any other options? 2 - I'd like to check my registrations by mapping labels from the average back onto the individual's brain. What's the best way to do this? Thanks, Alex

2 1

(no subject)
by Arvind Gururajan 09 Jun '05

09 Jun '05

Hello, I am very new to Freesurfer. Could anybody please tell me which specific MNI tool, I need to install? > > I tried the following command. > > ./recon-all -smooth1 ZM > ######################################## > program versions used > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ > mri_convert --version > $ > strings: rawtominc:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: minctracc:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: mincresample:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: mincaverage:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > mri_convert --version > $ > strings: mritotal:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > strings: nu_correct:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ####################################### > ERROR: Flag ZM unrecognized. > -smooth1 ZM > > > The folder ZM has only one orig file in the surf directory. There are no > raw data(.COR files). Please let me know your feedback. > > Sincerely, > > Arvind Gururajan

2 1

can left and right surfaces be flipped?
by peggy christidis 09 Jun '05

09 Jun '05

Hi there, I just finished creating a surface (with lots of time consuming manual editing) for someone who just informed me that he got the right-left orientation wrong on the volume I was given, and that it needs to be reversed (grrrrr....) Is there any way to do this in FreeSurfer without having to redo the surfaces? Thanks again, Peggy

4 6

control points and monkey brain
by peggy christidis 09 Jun '05

09 Jun '05

Hey everyone, Someone has given me a monkey volume (it's actually the average of 4 volumes and the gray-white matter contrast is pretty good) and I need to make a surface from it. I've never dealt with non-human datasets, but I did read in the freesurfer mailing archives that control points must always be added to a monkey T1 volume in order to get a decent wm segmentation. I ran recon-all stage1 and I got a first pass surface, and indeed I need to add control points because there is alot of white matter in the frontal lobes that is not being included in the segmentation. So I selected some control points (in the T1 volume, within the white matter), and then I ran this command: recon-all stage1 -usecontrolpoints -subjid monkey_surf I looked at the output and it doesn't seem to have helped at all. The segmentation still doesn't include the wm where the control points were added. What am I doing wrong? I've attached a jpg file to illustrate my problem. Thanks, Peggy

2 1

TIV and associated label
by Elizabeth Fenstermacher 09 Jun '05

09 Jun '05

Hello All, I was hoping to add a column for TIV in the calc_vols script I've been using to calculate the volumes of various ROIs. Is there an associated label for the TIV or is that something that would need to be created? Thanks! Eliz

1 0

Inflate from original surface files
by Arvind Gururajan 09 Jun '05

09 Jun '05

Hello, We have already generated a number of original surface files (.orig) in our lab. We were wondering if there is a way to generate the smooth and the inflated surface from the existing .orig files? Could you provide us a seperate tool to do this conversion? Sincerely, Arvind Gururajan

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RE: [Freesurfer] recon-all-nmr -disable-autoseg
by Fornito, Alexander 08 Jun '05

08 Jun '05

I can't find any usage or help for parcellate_subject, and if I simply run parcellate_subject [subjname], I get the following message: CSURF_DIR: Undefined variable. Any clues? Thanks, A. -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 6/9/2005 1:10 AM To: Bruce Fischl Cc: Fornito, Alexander; Elizabeth Fenstermacher; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg I think it looks in the average7 directory for a few labels (central sulc, calc, ...), then maps them to your subject through the registration. The intent was that you could then look at these labels to make sure they were in about the right place. doug Bruce Fischl wrote: > the labels are deprecated since we have the cortical parcellation. And > yes, run parcellate_subject and it will create *.annot files in the > label dir. > cheers, > Bruce > > On Wed, 8 Jun 2005, Fornito, Alexander wrote: > >> That worked, thanks, Doug. >> To expand on the labels issue, from my understanding, the labels are >> used to check that the registration worked, and that these are >> automatically created. >> I don't have any files in my labels directory. >> Do you need to run parcellate_subject to get them? >> Is there any documentation on parcellate_subject? I tried to run it >> and got the message: >> CSURF_DIR: Undefined variable. >> >> as an aside, where is the average7 surface. I though it might be in >> /usr/local/freesurfer/average/, but I don't seem to be able to open >> any of the files in there with tksurfer. >> Thanks again, >> Alex >> >> >> >> -----Original Message----- >> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Wed 6/8/2005 11:08 AM >> To: Elizabeth Fenstermacher >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg >> use the one in dev not std env >> >> >> Elizabeth Fenstermacher wrote: >> >>> >>> Hello All, >>> >>> I have a number of jobs that I will be running through recon-all-nmr >>> -stage1 in the next few days. I tried using the -disable-autoseg >>> flag, but it seems not to work as the jobs I submitted this morning >>> have now run for 50 minutes. >>> >>> The command line as I typed it was >>> >>> pbsubmit -c "recon-all-nmr -stage1 -subjid $s -nuintensitycor >>> -usenuintensitycor -disable-autoseg" >>> >>> perhaps I've misplaced the flag? If anyone has any insight as to why >>> it seems to be persitting in running the autoseg I would appreciate it. >>> >>> Thanks! >>> Eliz >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

freesurfer course
by Kerr, Catherine E. 08 Jun '05

08 Jun '05

Someone told me there was going to be a freesurfer course at the NMR center in July. Is it possible to register? Who would have this information? Thanks

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Freesurfer June 2005