Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Re: [Freesurfer] dlcompat binaries needed.
by Nick Schmansky 13 Jun '05

13 Jun '05

Mark, Creating empty directories for the subjects and fsl/bin was the right solution to the warning messages you were seeing. I need to add stub directories with READMEs to the directory structure. The FreeSurferEnv.csh file (which I am guessing you 'source' in your .cshrc file) has some text on the environment variables it references, including SUBJECTS_DIR and FSL_DIR, which pertain to your question (remember to set these before sourcing FreeSurferEnv.csh). Here's a snippet from that file: ############################################################################# # Name: FreeSurferEnv.csh # Purpose: sets up the environment to run FreeSurfer and FS-FAST # Usage: # 1. Create an environment variable called FREESURFER_HOME and set it # to the directory in which FreeSurfer is installed. # 2. From a csh or tcsh shell or (.login): # source FreeSurferEnv.csh # 3. There are environment variables that should point to locations # of software or data used by FreeSurfer. If set prior # to sourcing, they will not be changed, but will otherwise be # set to default locations: # FSFAST_HOME # SUBJECTS_DIR # MINC_BIN_DIR # MINC_LIB_DIR # FSL_DIR # 4. If NO_MINC is set (to anything), then all the MINC stuff is ignored. # 5. If NO_FSFAST is set (to anything), then the startup.m stuff is # ignored # 6. The script will print the final settings for the above variables # as well as any warnings about missing directories. If # FS_FREESURFERENV_NO_OUTPUT is set, then no normal output will # be made (only error messages). # # The most convenient way to use this script is to write another # script that sets FREESURFER_HOME and possibly SUBJECTS_DIR for # your set-up, as well as NO_MINC, NO_FSFAST, or # FS_FREESURFERENV_NO_OUTPUT as appropriate, and then source this # script. Nick On Sat, 2005-06-11 at 00:21 -0400, Mark Pinsk wrote: > Hi Nick, > > Thanks for the Tiger installation. I just installed it on my ibook > just to see if it worked, and so far so good. I was able to get the > csurf GUI to pop up, so I'll have to run thru a subject on my G5 > desktop in the next few weeks after I get back from HBM. > > 1 question: > When I sourced my .cshrc file it could not find a 'subjects' directory > and a 'fsl/bin' directory within the freesurfer folder. > I went ahead and just created empty folders with those names so that > it wouldn't complain. > But for future reference, where can I define the location of my > subjects folder and of my FSL installation if they aren't within the > freesurfer folder? > > Thanks ! > Mark > > > On 6/10/05, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Mark, > > > > I don't think dlcompat is required to run freesurfer. I am able to run it > > on a tiger machine without it. > > > > There is a new freesurfer build for Tiger just posted on the ftp site. Its > > a .dmg file, which is a compressed installation package. After download, a > > .mpkg file will appear, and clicking on that will begin the installation. > > > > The 'full' installation includes freesurfer binaries, support libraries and > > the MINC toolkit, all newly created on tiger from source. All install in > > /usr/pubsw/packages, thus Administrator access is required. The install > > location is not relocatable, as freesurfer depends on some fixed paths. A > > Fink installation is not necessary, as the support-libs packages includes > > everything freesurfer needs: jpeg, tiff, glut, tcl/tk, tix, blt and gsl. > > > > The full install file is at: > > > > ftp://surfer.nmr.mgh.harvard.edu > > and the file is called freesurfer-Darwin-tiger-full.dmg > > > > > > This is a work-in-progress, so I'd appreciate any comments, especially if > > it works for you. > > > > Nick > > > > > > > > On Fri, 2005-06-10 at 16:11 -0400, Mark Pinsk wrote: > > > > > > Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger > > machine. > > > > Turns out that Fink is not longer offering the dlcompat library for > > download. > > > > Can anyone wrap those binaries up and send them to me, or post them > > for download by any chance? > > > > thanks so much! > > Mark > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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

10 Jun '05

Hi Nick, I am running it on Linux platform. I followed the same instruction described here. http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 I am not sure, if I created the symbolic link correctly. ln -s 5.8.0 perl - ln: `perl': File exists [ Same output even the first time] Also, there are no tools in the path, I manually created current/bin and current/lib. Is there a way to fix this, can I moved all the tools to these two directories? Your help is really appreciated. Arvind Gururajan On 10 Jun 2005, Nick Schmansky wrote: > Arvind, > > Hi. On what platform are you running? Linux? > > Did you follow the special installation instructions, involving making > the symbolic links? Lastly, are the tools in your path? > > If you are feeling brave, an alternative to installing the binaries is > to compile the MNI package from source on your platform, and install > those binaries. Instructions to do this are here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > and the gzip file is here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > Nick > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > 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 > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

dlcompat binaries needed.
by Mark Pinsk 10 Jun '05

10 Jun '05

Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger machine. Turns out that Fink is not longer offering the dlcompat library for download. Can anyone wrap those binaries up and send them to me, or post them for download by any chance? thanks so much! Mark

2 1

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

2 1

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 >

2 1

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

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