Re: [Freesurfer] mgz to dicom or NiFTI
mri_convert will convert from .mgz to nifti (but not to dicom). cheers, Bruce On Tue, 13 May 2008, Stoffers, D. wrote: Dear all, Our imaging techs use a specific artifact correction which requires converting the DICOM images to mgz files. Does anybody know a good tool to convert the mgz files back to DICOM or, even better, to NiFTI? Any suggestions would be really appreciated! Cheers Diederick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] imensions of an mgh file generated by
Hi, I'm just wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] using func2sph-sess w/ FS4
Hello all, I am trying to run func2sph-sess with FreeSurfer 4. When mri_vol2surf tries to run, it looks for a file called h_000.hdr. The version of selxavg I used produced h.nii, but not h_000.hdr. mri_vol2surf won't run without this file (h_000.hdr), and I am not sure how to specify that the needed file is h.nii (if this is, in fact, correct). Is there a way to specify that h.nii should be used? Thank you, ~Sue * * ** *** * * Susan M. Mosher Program in Neuroscience Boston University office phone: 857-364-2214 [EMAIL PROTECTED] * * ** *** * * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using func2sph-sess w/ FS4
I've fixed this problem locally. I've included the script that needs to
change. Copy it to:
$FREESURFER_HOME/fsfast/bin/
doug
Susan Mosher wrote:
Hello all,
I am trying to run func2sph-sess with FreeSurfer 4. When mri_vol2surf
tries to run, it looks for a file called h_000.hdr. The version of
selxavg I used produced h.nii, but not h_000.hdr. mri_vol2surf won't
run without this file (h_000.hdr), and I am not sure how to specify
that the needed file is h.nii (if this is, in fact, correct). Is there
a way to specify that h.nii should be used?
Thank you,
~Sue
* * ** *** * *
Susan M. Mosher
Program in Neuroscience
Boston University
office phone: 857-364-2214
[EMAIL PROTECTED]
* * ** *** * *
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
#! /bin/csh -f
#
# func2sph-sess
#
# with version 1.7, the old vss functions are no longer used.
# Passing -old as an argument will invoke the old func2sphere-sess
# (now called func2sphere-sess-vss).
#
# Original Author: Doug Greve
# CVS Revision Info:
#$Author: greve $
#$Date: 2008/05/13 20:43:35 $
#$Revision: 1.8.2.1 $
#
# Copyright (C) 2002-2007,
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: [EMAIL PROTECTED]
#
set VERSION = '$Id: func2sph-sess,v 1.8.2.1 2008/05/13 20:43:35 greve Exp $';
set inputargs = ($argv);
set analysis= ();
set ScriptOnly = 0;
set umaskarg = ();
set hemilist = ();
set nolog = 0;
set sphdir = sph
set IcoOrder = 7;
set ProjFrac = ();
set ProjFracMin = ();
set ProjFracMax = ();
set ProjFracDelta = ();
set Surface = white;
set SurfaceReg = sphere.reg
set Float2Int = ();
set MapMethod = nnfr; # for surf2surf
set TrgSubject = ico
set Interp = nearest;
set synth = 0;
set fwhm = ();
if($#argv == 0) goto usage_exit;
# look for -old or -vss flag #
foreach a ($argv)
if($a == -old || $a == -vss) then
echo INFO: running old verssion of func2sph-sess
func2sph-sess-vss $argv;
exit $status;
endif
end
# look for version string #
set n = `echo $argv | grep version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
## Look for nolog option ##
set n = `echo $argv | grep nolog | wc -l`
if($n != 0) set nolog = 1;
# Create a log file ##
if(! $nolog) then
set logdir = `pwd`/log;
mkdir -p $logdir
if(! -e $logdir) then
echo ERROR: could not create $logdir
exit 1;
endif
set LF = $logdir/func2sph-sess.log
if(-e $LF) mv $LF $LF.old
else
echo No log file
set LF = /dev/null
endif
echo --
echo func2sph-sess logfile is $LF
echo --
echo fucn2sph-sess log file $LF
echo $VERSION $LF
pwd$LF
echo $0 $LF
echo $inputargs $LF
uname -a $LF
date $LF
which mri_vol2surf $LF
set SessList = `getsesspath $argv`;
if($status || $#SessList == 0) then
echo ERROR: cannot find any sessions | tee -a $LF
exit 1;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
## Get functional subdirectory from the info file ##
set infofile = $analysis/analysis.info
if(! -e $infofile) then
echo ERROR: cannot find $infofile
exit 1;
endif
set fsd = `cat $infofile | awk '{if($1 == fsd) print $2}'`;
set designtype = `cat $infofile | awk '{if($1 == designtype) print $2}'`;
if($#designtype == 0) then
set designtype = `cat $infofile | awk '{if($1 == avgtype) print $2}'`;
endif
### Go through each session ##
set StartDate = `date`;
set nth = 1;
foreach sess ($SessList)
set sessid = `basename $sess`;
echo - | tee -a $LF
echo - | tee -a $LF
echo Session: $sessid $nth/$#SessList | tee -a $LF
echo $StartDate
date | tee -a $LF
@ nth = $nth + 1;
# Make sure the Session Dir exists (redundant) ##
if(! -d $sess) then
echo ERROR: $sess does not exist | tee -a $LF
exit 1;
endif
## Go to the functional subdirectory for the session ##
pushd $sess/$fsd /dev/null
df . | tee -a $LF
## Prepare the script, if need be ##
if($ScriptOnly) then
if(! -d scripts) mkdir scripts
set scriptfile = scripts/run-func2sph-$analysis
rm -f $scriptfile
[Freesurfer] Re: ffx bug
Hi Xiaomin, I finally got around to looking at this, and this is a bug. The "cespct" is not actually a percent, rather it is a fraction of the mean functional. However, the "cesvarpct" is a percent, which makes the group ffx analysis with percent fail. I have fixed this in both dev and stable such that cespct is actually a percent, live on next update. Let me know if this does not fix your problem. doug xiaomin wrote: Hi, I am running the following command for group fixed factor and random factor analysis with and without percent parameter on. Here are the commands: 1) for the no percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -hemis -o . -subject fsaverage mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh 2) for the percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -percent -hemis -o . -subject fsaverage mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh However, the significance between percent and no percent is inconsistent. For testing if the data has problem, I run it with rfx design. The significance between percent and no percent is almost same. (see attached graph) Second, the significance with percent parameter for the fixed factor analysis is very small, which is abnormal. We need to use ffx significant map to define a ROI. The data is here: /autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D epth. Xiaomin Yue Research Fellow NMR center, MGH -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: ffx bug
There were a bunch of voxels with no significance because the ffx noise had essentially been multiplied by 100 (so 100 times more noise than there really was). make sense? xiaomin wrote: Hi Doug, Thanks for fixing it. I will rerun the group analysis and let you know if it works. However, it is still puzzling to me why the significant histogram from the ffx without percent (as attached in my last email) looks so weird. The maximum is too large. Also, the shape of the significant ffx histogram should not be different for percent vs. non-percent. Xiaomin From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Tuesday, May 13, 2008 5:13 PM To: xiaomin Cc: [EMAIL PROTECTED]; 'Roger Tootell'; 'Daphne Holt'; 'Brittany Cassidy'; Free Surfer Subject: Re: ffx bug Hi Xiaomin, I finally got around to looking at this, and this is a bug. The "cespct" is not actually a percent, rather it is a fraction of the mean functional. However, the "cesvarpct" is a percent, which makes the group ffx analysis with percent fail. I have fixed this in both dev and stable such that cespct is actually a percent, live on next update. Let me know if this does not fix your problem. doug xiaomin wrote: Hi, I am running the following command for group fixed factor and random factor analysis with and without percent parameter on. Here are the commands: 1) for the no percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -hemis -o . -subject fsaverage mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh 2) for the percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -percent -hemis -o . -subject fsaverage mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh However, the significance between percent and no percent is inconsistent. For testing if the data has problem, I run it with rfx design. The significance between percent and no percent is almost same. (see attached graph) Second, the significance with percent parameter for the fixed factor analysis is very small, which is abnormal. We need to use ffx significant map to define a ROI. The data is here: /autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D epth. Xiaomin Yue Research Fellow NMR center, MGH -- 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 -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] difference maps
Hello, We are using mri-surfcluster to output ocn files. The default format seems to be volume encoded surface file which seems to be a long array and it is unreadable by MRIread. Is there a way to convert this file into something that is readable by Matlab? Alternately, we want to compare activations from sessions for different conditions for an individual subject. (We only have pilot data on two subjects and trying to form difference maps) Any recommendations? Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question: can't display retinotopy fieldsign data
Hi, sorry for the delay. I've verified the problem with my data here,
though the solution may take a while to find. As a temporary fix, I've
written a matlab script which will conver the field sign map into
something that can be loaded as a simple overlay (attached).
Instructions for use are below.
doug
help convert_fieldsign
err = convert_fieldsign(infname,outfname)
Loads a field sign (infname) as saved by the void write_fieldsign()
in tksurfer and saves in the given output format. This allows the
field sign map to be loaded as an overlay in tksurfer. This can
also be used to convert a field sign mask.
Eg:
In matlab:
convert_fieldsign('fieldsign-lh','lh.fieldsign.mgh');
convert_fieldsign('fieldsignmask-lh','lh.fieldsignmask.mgh');
In the unix shell:
mri_mask lh.fieldsign.mgh lh.fieldsignmask.mgh lh.fieldsign-masked.mgh
tksurfer subjectname lh inflated \
-overlay lh.fieldsign-masked.mgh -fthresh 0.5
Kai Hwang wrote:
Hello Doug,
Yes fieldsign maps were created by paint-sess without any problem, I
was able to view my fieldsign overlays with surf-sess in stable-3
version, but not version 4.
Kai
Doug Greve 提到:
Did paint-sess complete? Are there field sign maps created?
Elif SIKOGLU wrote:
Hello,
I have the same surf-sess problem as Kai. First I see the inflated
brain and then the view screen turns black and nothing shows up. It
is only for fieldsign map. eccentricity and polar maps look good.
Any suggestions?
Thanks,
Elif
On Thu, Apr 24, 2008 at 1:24 PM, Kai Hwang [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] wrote:
Hello,
I'm trying to use freesurfer to map the visual cortex and get region
borders of V1, V2.. etc.
We used a conventional rotating/expanding wedge paradigm, and I
followed
the steps described in FsFastIndividualRetinotopy Analysis
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis)
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
Everything worked fine till the last step, I can't view the
results with
surf-sess. After I execute the command surf-sess, first a flatten
cortex
appeared, then the view screen turned black and nothing showed up.
Here is what I have in the terminal window
[EMAIL PROTECTED]:~/Subjects surf-sess -s Pilot1 -a VM_retinotopy
-retinotopy
fieldsign -flat
grep: /home/hwang/Subjects/Pilot1/session.info
http://session.info: No such file or directory
-
surf-sess logfile is
/home/hwang/Subjects/log/surf-sess.VM_retinotopy.fs.log
-
--
--
Session: Pilot1
-- lh hemisphere --
/home/hwang/Subjects/Pilot1/bold/VM_retinotopy
--
/home/hwang/Subjects/Pilot1/bold/VM_retinotopy
tksurfer -Pilot1 lh inflated -tcl
/usr/local/freesurfer/lib/tcl/fs-flat.tcl
--
Loading /usr/local/freesurfer/surface_labels.txt
surfer: current subjects dir: /home/hwang/Subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/hwang/Subjects/Pilot1/bold/VM_retinotopy
surfer: Reading header info from
/home/hwang/Subjects/Pilot1/mri/T1.mgz
surfer: vertices=149915, faces=299826
can't find talairach file
'/home/hwang/Subjects/Pilot1/surf/../mri/orig/COR-.info/../transforms/talairach.xfm'
surfer: ### redraw failed: no gl window open
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
tksurfer: fs-flat.tcl: set flags
setdefpatchview: ### position.tcl for Pilot1 does not exist
setdefpatchview: ### setting flatzrot to 90 (default)
setdefpatchview: ### setting flatscale to 1.0 (default)
setdefpatchview: ### setting flatxtrans to 0.0 (default)
setdefpatchview: ### setting flatytrans to 0.0 (default)
readenv.tcl: == read global setenv vars
readenv: set invphaseflag 0
readenv: set fm fieldsign/fieldsignmask-lh
readenv: set angle_offset 0
readenv: set dir /home/hwang/Subjects/Pilot1/bold/VM_retinotopy
readenv: set truncphaseflag 0
readenv: set offset 0.4
readenv: set fmid 0.8
readenv: set fs fieldsign/fieldsign-lh
readenv: set lat
readenv: set fthresh 0.4
readenv: set complexname -imag
readenv: set realname -real
readenv: set eccendir eccen
readenv: set floatstem map
readenv: set hemi lh
readenv: set rgbname map
readenv: set use_vertex_arrays 0
readenv: set nosave 0
readenv: set polardir polar
readenv: set noexit
readenv: set curv lh.curv
readenv: set patchname occip.patch.flat
readenv: set fslope 1.3
readenv: set colscale 0
readenv: set mc () { . /usr/share/mc/bin/mc-wrapper.sh
}
Re: [Freesurfer] using func2sph-sess w/ FS4
Hi Doug, Thanks, that worked for func2sph-sess. I am running into a similar problem with sphsmooth-sess and tried making a change to the references to bfloat and hdr files to refer them to .nii (lines 130 and 135), but I got the following error: ./sphsmooth-sess -s MAD014 -analysis MAD_gamma_MADpilot2 -smoothsteps 8 -outsphdir sphsm8 -- sphsmooth-sess logfile is /autofs/space/baobab_002/users/MAD/fMRI_sess/log/sphsmooth-sess.log -- lh rh hemisphere Tue May 13 19:16:25 EDT 2008 nvertices = 0 ERROR: could not compute ico order Which are the specific h-files that: set i0 = $instem_000.bfloat; and set i0 = $instem_000.hdr; refer to? Can I just specficy these manually in my copy of sphsmooth-sess? Thank you, ~Sue On Tue, 13 May 2008, Doug Greve wrote: Date: Tue, 13 May 2008 16:45:07 -0400 From: Doug Greve [EMAIL PROTECTED] To: Susan Mosher [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using func2sph-sess w/ FS4 I've fixed this problem locally. I've included the script that needs to change. Copy it to: $FREESURFER_HOME/fsfast/bin/ doug Susan Mosher wrote: Hello all, I am trying to run func2sph-sess with FreeSurfer 4. When mri_vol2surf tries to run, it looks for a file called h_000.hdr. The version of selxavg I used produced h.nii, but not h_000.hdr. mri_vol2surf won't run without this file (h_000.hdr), and I am not sure how to specify that the needed file is h.nii (if this is, in fact, correct). Is there a way to specify that h.nii should be used? Thank you, ~Sue * * ** *** * * Susan M. Mosher Program in Neuroscience Boston University office phone: 857-364-2214 [EMAIL PROTECTED] * * ** *** * * ___ 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 [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 * * ** *** * * Susan M. Mosher Program in Neuroscience Boston University office phone: 857-364-2214 [EMAIL PROTECTED] * * ** *** * * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: ffx bug
Sorry, It's not "live" yet -- meaning that the stable version has not been updated yet. Usually, this happens overnight. You can tell by running: ls -l $FREESURFER_HOME/fsfast/toolbox/fast_selxavg.m doug xiaomin wrote: Hi Doug, The significance of ffx with percent is still very small from -0.0249 to 0.0682, which is similar to what I got before. I am using stable 4. Xiaomin From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Tuesday, May 13, 2008 5:32 PM To: xiaomin Cc: 'Roger Tootell'; 'Daphne Holt'; 'Brittany Cassidy'; 'Free Surfer' Subject: Re: ffx bug There were a bunch of voxels with no significance because the ffx noise had essentially been multiplied by 100 (so 100 times more noise than there really was). make sense? xiaomin wrote: Hi Doug, Thanks for fixing it. I will rerun the group analysis and let you know if it works. However, it is still puzzling to me why the significant histogram from the ffx without percent (as attached in my last email) looks so weird. The maximum is too large. Also, the shape of the significant ffx histogram should not be different for percent vs. non-percent. Xiaomin From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Tuesday, May 13, 2008 5:13 PM To: xiaomin Cc: [EMAIL PROTECTED]; 'Roger Tootell'; 'Daphne Holt'; 'Brittany Cassidy'; Free Surfer Subject: Re: ffx bug Hi Xiaomin, I finally got around to looking at this, and this is a bug. The "cespct" is not actually a percent, rather it is a fraction of the mean functional. However, the "cesvarpct" is a percent, which makes the group ffx analysis with percent fail. I have fixed this in both dev and stable such that cespct is actually a percent, live on next update. Let me know if this does not fix your problem. doug xiaomin wrote: Hi, I am running the following command for group fixed factor and random factor analysis with and without percent parameter on. Here are the commands: 1) for the no percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -hemis -o . -subject fsaverage mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh 2) for the percent: isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -percent -hemis -o . -subject fsaverage mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh However, the significance between percent and no percent is inconsistent. For testing if the data has problem, I run it with rfx design. The significance between percent and no percent is almost same. (see attached graph) Second, the significance with percent parameter for the fixed factor analysis is very small, which is abnormal. We need to use ffx significant map to define a ROI. The data is here: /autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D epth. Xiaomin Yue Research Fellow NMR center, MGH -- 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 -- 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 -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Dimensions of an mgh file generated by mris_preproc
Hi, I'm wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Why? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
