Re: mris_surfglm
Hi Darren, the ico and average7 are about the same computationally. However, it is more convenient to use average7 it has a surface that you can directly render the results on. With ico, you'd still have to run mri_surf2surf to convert it to another surface. I'm not sure what you're trying to do in terms of the surface registration... doug Darren Weber wrote: Dear Doug et al, surfglm looks good. I have processed 10 controls and 8 patients such that each surface contains a whole cortical surface, without the usual split through the corpus callosum. How would I use the surface registration process? Should I use 'ico' as the average or can I use one of the subjects? Take care, Darren -- Darren Weber, PhD Student Cognitive Neuroscience, School of Psychology Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust. Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877 http://203.3.164.46/~dlw/homepages/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: mri_surfglm!!!
Hi Brian, I just finished that program a few weeks ago. This program allows you to do cross-subject/cross-group analysis of surface data by solving a GLM with ordinary least-squares (OLS). It also allows you to pre-smooth the surface values as well as include covariates (eg, age, gender, etc). Look at the help page (using mri_surfglm --help) for more info. Since it just uses OLS, it cannot do more sophisticated modeling of the variances (eg, modeling different groups with different variances), though we hope to integrate it with FLAME, a program that will be in FSL's next release. Those who do not have mri_surfglm in their bin directory can download it with the most recent snapshot from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/snapshots/ Let me know how it goes. doug Brian Schweinsburg wrote: I was able to answer my own question regarding thickness parameter maps from the other day by poking through the Linux/bin directory. Looking forward to using it. brian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: mri_surfglm!!!
Hi Brian, you probably need to specify a target subject (--trgsubj). I've put a newer version of mri_surfglm at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/. The guts of it have not changed, but it does better command-line error checking. doug Brian C. Schweinsburg wrote: Hi Doug, I was looking forward to a program like this. The help file is excellent! I used the info in it to run an analysis and everything ran okay except the very last part. It gave me an error message when the paint command was listed last (like the the gender-age example in the help file). It said something like it had no surface to paint to (I don't have the exact message because I am not in linux right now). So, I haven't seen the painted on results yet. thanks, brian - Original Message - From: Doug Greve [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, October 02, 2002 7:49 AM Subject: Re: mri_surfglm!!! Hi Brian, I just finished that program a few weeks ago. This program allows you to do cross-subject/cross-group analysis of surface data by solving a GLM with ordinary least-squares (OLS). It also allows you to pre-smooth the surface values as well as include covariates (eg, age, gender, etc). Look at the help page (using mri_surfglm --help) for more info. Since it just uses OLS, it cannot do more sophisticated modeling of the variances (eg, modeling different groups with different variances), though we hope to integrate it with FLAME, a program that will be in FSL's next release. Those who do not have mri_surfglm in their bin directory can download it with the most recent snapshot from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/snapshots/ Let me know how it goes. doug Brian Schweinsburg wrote: I was able to answer my own question regarding thickness parameter maps from the other day by poking through the Linux/bin directory. Looking forward to using it. brian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: spm_to_b
Ah, that is a problem. The IRIX we use to build new binaries is down, so I can't get a new version for you. One work-around (if you don't have a Linux box handy) is to use matlab to read in as analyze and write out as bfloat. If you have a version of FS-FAST (probably in freesurfer_alpha/fsfast), use the fmri_svbfile function in the toolbox to save a volume in bfloat format. doug Bradley Goodyear wrote: Thanks Doug. Those links don't seem to work. In any case, I am running Freesurfer on an SGI. -BRad On Wednesday, July 31, 2002, at 11:35 AM, Doug Greve wrote: Ah, I think you must have an old vesion. You can get a new Linux version of mri_convert from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/ Or an entirely new version of FreeSurfer from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/fsa-20020724/ maybe try the first first to make sure that's the problem. Copy mri_convert.linux into freesurfer_alpha/bin/Linux doug Bradley Goodyear wrote: unknown flag --in_nspmzeropad -Brad On Tuesday, July 30, 2002, at 03:51 PM, Doug Greve wrote: Try the following command-line: mri_convert --in_type spm --in_nspmzeropad 3 NS f_000.bshort --out_type bshort (This should also work for bfloat). doug Bradley Goodyear wrote: My files are NS_001.img, NS_002.img, ..., NS_209.img. Each contains 12 slices at 128x128. mri_convert --in_type spm --out_type bshort NS_001.img f.bshort The result is 12 bshort files, but only one time point per instead of 209. I also tried combining all the .img files into one big spm files, but got the same result. using out_type as bfloat gives an error saying output type not supported -Brad -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: spm_to_b
Ah, I think you must have an old vesion. You can get a new Linux version of mri_convert from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/ Or an entirely new version of FreeSurfer from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/fsa-20020724/ maybe try the first first to make sure that's the problem. Copy mri_convert.linux into freesurfer_alpha/bin/Linux doug Bradley Goodyear wrote: unknown flag --in_nspmzeropad -Brad On Tuesday, July 30, 2002, at 03:51 PM, Doug Greve wrote: Try the following command-line: mri_convert --in_type spm --in_nspmzeropad 3 NS f_000.bshort --out_type bshort (This should also work for bfloat). doug Bradley Goodyear wrote: My files are NS_001.img, NS_002.img, ..., NS_209.img. Each contains 12 slices at 128x128. mri_convert --in_type spm --out_type bshort NS_001.img f.bshort The result is 12 bshort files, but only one time point per instead of 209. I also tried combining all the .img files into one big spm files, but got the same result. using out_type as bfloat gives an error saying output type not supported -Brad -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: spm_to_b
Use mri_convert. Here's an example for an spm functional volume spm001.img, spm002.img ... mri_convert spm001.img --in_type spm spm_000.bfloat This should create the spm bfloat volume. doug Bradley Goodyear wrote: Which parameter from the .HDR file does spm_to_b use as the number of volumes (i.e., time points)? whenever I try running spm_to_b it only outputs 1 volumes per slice. -Brad -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: Matlab window problems with FS-FAST
Hi Nick, what does the -tty do? Is that new to version 6? Will it work for version 5? doug Nicholas Knouf wrote: Hi there, I've got a question, this time about FS-FAST (if this isn't the appropriate place to ask these questions, feel free to let me know). I'm running the latest version of the FS-FAST software (with fsfast directory fsfast-20020510). When running commands that use Matlab (such as selxavg-sess), the script runs matlab and opens up a command window, instead of running within the terminal window. I found that by modifying the script file to run $MATALB -tty instead of $MATLAB -display iconic, matlab ran as expected in the terminal window. Unfortunately, there are a ton of scripts that I would have to change to get this to work correctly with my hack, and I'm sure that that is not the desired effect. What can I do to get matlab to start properly? I'm running matlab version 6.1.0.450 (R12.1) and the sawfish window manager on a modified version of RedHat linux, if that's of any help. Thanks for your help, Nick Knouf Lab Manager, Kanwisher Lab -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: SPM and Freesurfer
It looks like mri_convert cannot find information about the orientation of the volume. The analyze format does not have fields in the header for this information, but SPM usually adds a .mat file. It does not look like fs_sub.img has a fs_sub.mat, so mri_convert is guessing (incorrectly) what the direction cosines are. You can fix this in multiple ways: (1) get the proper .mat file (2) get a new copy of mri_convert from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer, and re-run mri_convert specifying the direction cosines on the command-line using the --in_X_direction, where X is i, j, or k corresponding to col, row, and slice doug Felix Blankenburg wrote: Dear Bruce, Doug and Xiangchuan and others, First of all thank you very much for your help. The processing of the surfaces works now very well. But I got a few problems with the overlay of the SPM99 results. After conversion of the 'analyze' data (t-maps and epis) with mri_convert the bshort and bfloat images looked very warped. It seems that the program is not able to compute the correct dimensions i. e. does not read the header information's. After making a functional directory, creating the analyse.dat, register.dat in the image subdirectory and the SPM t-map (changing the write filtered to float type) it seems that the conversion of the functional data leads to the described problem. Enclosed is the log-file for the conversion of the data: mri_convert fs_sub.img sub --out_type bfloat reading from fs_sub.img... INFO: analyzeRead(): found 1 files for fs_sub.img INFO: analyzeRead(): min = 0, max = 4.3109 TR=0.00, te=0.00, flip angle=0.00 warning: volume may be incorrectly oriented warning: input volume axes are not orthogonal i_ras = (1, 1, 1) j_ras = (0, 0.5, 0) k_ras = (0, 0, 0.5) warning: output volume axes are not orthogonal i_ras = (1, 1, 1) j_ras = (0, 0.5, 0) k_ras = (0, 0, 0.5) writing to sub... INFO: bvolumeWrite: stem = sub Does anyone know the problem and have a solution for this or could help me with a step to step documentation how to overlay SPM results onto the brain surfaces. Thank you very much in advance, Felix Dr. med. Felix Blankenburg Dept. of Neurology Charité, Humboldt-University Schumannstr. 20/21 10117 Berlin, Germany Phone: ++49-30-450 560 194 Fax: ++49-30-450 560 952 http://www.charite.de/ch/neuro/forschung/teams/klinisch/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: off-by-1/2s...
Ahh, if this is true, then there may be no inconsistency between mri_tesselate and the other routines! Bruce Fischl wrote: it's not just for historical reasons. The orig surface is generated by covering the faces of each white matter voxel (that doesn't neighbor white) with vertices, so their natural location is between slices. Bruce On Thu, 14 Mar 2002, Doug Greve wrote: Hi Blaise, the problem may be that the vertex is between slices. When you use the goto vertex option in tkmedit, the cursor will go to the closest point to that vertex. If the vertex is between slices, it won't interpolate. The RAS reported in the control panel will then be that of the cursor. For historical reasons, all the orig vertices are placed between slices (ie, they will all have 0.5 in the x,y, and z coords). doug Blaise YVERT wrote: I am refering to the Volume RAS prompted in tkmedit. Blaise. How are you measuring the RAS coords? doug Blaise YVERT wrote: Dear All, First of all, I'd like to thank the whole team of Harvard NMR center for making available freesurfer. Indeed, although this mailing list is mostly used to report bugs and problems, please know that fs is a great tool ! Now, to follow up the discussion introduced by Al Kim, it seems that the coordinates in *.asc files are slightly shifted with respect to the RAS coordinates, namely : Xras = Xasc - 0.5 Yras = Yasc + 0.5 Zras = Zasc - 0.5 Could anyone confirm this ? Best wishes, Blaise. -- -- INSERM U280 151 Cours Albert Thomas, F-69424 Lyon cedex 03, France. Tel : +33 4 72 68 19 27 Fax : +33 4 72 68 19 02 URL : http://www.lyon151.inserm.fr/unites/280_tout.html -- -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
Re: mri_convert -- GET NEW VERSION!!
Hi All, thanks to Al's diligence, I have tracked down a bug in the most recent version of mri_convert, the one that I mentioned a few weeks ago that could be downloaded from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer. There was a problem with the way it was reading the SPM mat file. This does not apply to older versions, only the one that was on the FTP site above. I have placed new Linux and SunOS versions at the FTP site with which you should immediate replace the previous version. let me know how it goes doug Albert Kim wrote: Dear all, I'm having trouble with the use of mri_convert to convert my SPM/Analyse structural volume to COR format. (mri_convert foo.img /Subjects/E12246/mri/orig/) The resulting orig image, when viewed in MEDIT, is flipped: the second volume index increases from posterior to anterior the third volume index increases from inferior to superior (i'm not sure whether the first index is flipped, bcs it is left-right) This problem does not occur when I use Setup Structural Scan Parameters from the GUI to read the iamge, and then CONVERT/AVERAGE. Does anybody know if there is a problem here? Here is a copy of the output from mri_convert mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img Subjects/E12246C/mri/orig/ # mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img Subjects/E12246C/mri/orig/ mri_convert Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img Subjects/E12246C/mri/orig/ reading from Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img... INFO: analyzeRead(): found 1 files for Subjects/E12246C/mri/orig/SPM/E12246_struct124O.img INFO: analyzeRead(): min = 0, max = 258 TR=0.00, te=0.00, flip angle=0.00 warning: volume may be incorrectly oriented warning: input volume axes are not orthogonal i_ras = (1, 0.613839, 0.613839) j_ras = (0, 0, 1.16364) k_ras = (0, 1.16364, 0) changing data type... reslicing (interpolate)... writing to Subjects/E12246C/mri/orig/... Thanks Al Kim Department of Psychology University of Washington, Box 351525 Seattle, WA. 98195, USA E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
