from:"Doug Greve"

Re: [Freesurfer] mri_preproc

2008-09-18 Thread Doug Greve


/space/barlab_002/users/cibu/dep_LGI does not exist



Cibu Thomas wrote:

Hello 
When I run the mri_preproc command I am getting the message

ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI
But the fsaverage folder is in the path and subjects_dir is set
correctly.
So I am not sure what's wrong with the command
Here's the command I am trying to run

mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage --
hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh


Any help would be greatly appreciated

Thankyou 
Cibu Thomas


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Re: [Freesurfer] mri_convert and image orientation; Analyze format

2008-09-18 Thread Doug Greve

Watson, Christopher wrote:

Hello Freesurfers,
Lately I've been scratching my head about image orientation problems. What I do
here is take the DICOM images and use mri_convert to convert them into SPM
Analyze format. The command I use is:

mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \
"path/to/subj/dir/image" --out_type spm

So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly are Analyze format and not NIfTI (if i'm incorrect please tell me, this would be very important).

Yes, analyze format, but they include the .mat, which has orientation
info but is not part of the analyze spec but spm will read them and act
on them.

There are weird things SPM does concerning image orientation, so it's *very*
important that I get this right (we do functional imaging on surgery
candidates):

*Does mri_convert flip the images in any way?*

No.

That is, if my DICOM images are in radiological convention, will the imageXXX
images still be in radiological convention? I've been searching far and wide
and have hit a wall. With patients, we can see the water pill on the right side
of the forehead easily, but with the EPI functional images for our research
subjects it's pretty much impossible to tell.

Thanks very much,
Chris Watson

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Re: [Freesurfer] frontal lobe volume

2008-09-19 Thread Doug Greve

You can create labels for each of the cortical annotations with 
mris_label2annot, then merge the labels for your lobe together  with 
mri_mergelabels, then run mris_anatomical_stats on the final label. This 
will give cortical volume for your lobe (will exclude white matter).


doug

Tadeu Kubo wrote:


Me too...

Best wishes,
Tadeu Kubo.

On Fri, Sep 19, 2008 at 4:18 AM, dfwang <[EMAIL PROTECTED] 
> wrote:


Dear all,
 
I would like to calculate the frontal lobe volume from the outputs

of freesrufer. Could any body here please tell me the way to do this?
 
Any comments are welcome!
 
Best wishes,

Vincent

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Tadeu Takao Almodovar Kubo



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Re: [Freesurfer] fsaverage across versions

2008-09-22 Thread Doug Greve

Iris, the registration targets were derived differently. With version 4,
we automatically fill in all the ventricles. In verion 3, they were
partially filled in manually. Version 3 creates a surface around the
ventrical making it look like a sulcus, and this affects both the target
and the registration to the target. So, on most of the surface, the
registration will be very close, but it will deviate signifiacntly
around the ventricles/medial wall. I think the fsfast in version 4
should work fine with the anatomicals (including fsaverage) of version 3.

doug

Steinmann, Iris wrote:

Hi,

we have several reconstructed brains, which were processed by freesurfer 3.0.5.
We also kept using the fsaverage data from 3.0.5 in order to be consistent.

We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that
talairach coordinates differ slightly
when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5.

Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother.

We would like to know what constitutes the exact difference between these two
fsaverage datasets and
whether it is possible to use the new version for analysis with the "old" fsaverage data without
getting inconsistent results.

Thanks a lot,
Iris

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Re: [Freesurfer] mri_convert: DICOM to nifti - multiple frames

2008-09-25 Thread Doug Greve

We don't have anything that will do it explicitly. If you have FSL 
installed, you can use fslsplit. Otherwise, you can write your own 
script to convert to spm analyze, then convert each file to nifti 
(nothing is lost as we keep the .mat files around).


doug

Watson, Christopher wrote:


Hi, I'm interested in getting multiple nifti images for each time point, 
similar to this old thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03317.html

i.e., for a scan of 5 minutes and TR = 3, I would like 100 separate nifti 
images. This works fine when I set --out_type spm, but I'd like to start using 
the nifti format. The command I use:

mri_convert.x86_64.dev -dicomread2 i545236.MRDC.1 -ot nifti1 "$SUBJ_DIR/image"

only creates one file - image.nii. Is there a newer version of mri_convert that 
can do what I'm looking for? Here's the info:

$./mri_convert.x86_64.dev --all-info
ProgramName: mri_convert.x86_64.dev  ProgramArguments: --all-info  
ProgramVersion: $Name:  $  TimeStamp: 2008/09/25-14:47:29-GMT  BuildTimeStamp: 
Jun 15 2007 11:06:50  CVS: $Id: mri_convert.c,v 1.144 2007/06/14 03:18:56 greve 
Exp $  User: matlab7  Machine: occipital  Platform: Linux  PlatformVersion: 
2.6.9-55.0.6.ELsmp  CompilerName: GCC  CompilerVersion: 30300


Thanks,
Chris


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Re: [Freesurfer] Volume processing question

2008-09-30 Thread Doug Greve



You can use mri_surf2vol to create a mask. Is that what you mean?

doug


On Tue, 30 Sep 2008, Tommaso De Marco wrote:


Hi,
I'm a freesurfer user beginner. I need to discretize the gray matter in a 
cubic mesh. I have extracted the $h.pial and $h.white surfaces, and I would 
know if it is possible in freesurfer to discretize the volume suttended by 
these surfaces. I have seen that there are some files called $h.volume; what 
kind of information is stored in these files? Is it possible to open them in 
a matlab environment or with tksurfer?


Regards

Tommaso De Marco
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Re: [Freesurfer] convert single-frame dicoms to a multi-frame dicom?

2008-09-30 Thread Doug Greve



I'm sure there are some out there, but we cant do it in FS.

doug



On Mon, 29 Sep 2008, Qianqian Fang wrote:


hi

I know that mri_convert and a few other tools are able to convert
a series of dicom files into a 4D (multi-frame?) nifti file. However,
is there a way, either using freesurfer or other tools you know,
can convert a the dicoms, or a 4D nifti, to a 4D (multi-frame) dicom?

thanks

Qianqian
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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats

2008-10-02 Thread Doug Greve



I've gone through a few iterations re-working this code over the last 
month or so. The aparc+aseg (and wmparc) should respect the ribbon. So, 
voxels within the white surface but labeled as Cortex in aseg should be 
labeled as WhiteMatter in aparc+aseg. Voxels labeled as "None" should 
also be re-labeled as Cortex or WhiteMatter if they fall into those 
places on the ribbon.


There was a bug that was fixed in two stages, one on 8/6/08 and the 
other on 8/28/08. I'm not sure when our last stable version was cut, but 
we'll have a new version with these fixes in a few weeks.


doug



Michael Harms wrote:


Hi Doug,
I was comparing the aseg.mgz and aparc+aseg.mgz segmentations (FS
v4.0.2), and recalled a previous thread on this issue in which you
corrected me on an aspect of how the aparc+aseg.mgz is affected by the
surfaces.


From what I can tell looking at this again, voxels labeled as "None" in

the aseg.mgz are also still ALWAYS labelled as "None" in the aparc
+aseg.mgz, even if those voxels are clearly interior to the final pial
surface.  However, voxels interior to the white surface that are labeled
as "Cortex" in the aseg.mgz get converted to "None" in aparc+aseg.mgz.
That is, it appears that a voxel must be in ribbon.mgz to be eligible
for one of the "ctx" parcellation labels in aparc+aseg.mgz, but not
necessarily all voxels in the ribbon will be labelled as "ctx" (some
will remain labeled as "None", apparently propagated from aseg.mgz).

Do I have this summary correct?

thanks,
Mike H.


On Tue, 2008-07-22 at 14:54 -0400, Doug Greve wrote:
 


Actually, the construction of aparc+aseg and wmparc do use info about
where the surface is to refine the aseg cortical boundaries. This
information is stored in ribbon.mgz (and it overrides the aseg
definition). At some point, we will use the surfaces to directly
refine the aseg boundaries.

doug




Michael Harms wrote: 
   


Hi Chris,
Doug, please correct me if I'm wrong, but the original gm/wm
segmentation contained in aseg.mgz is based on the 3D volume-based
tissue segmentation.  This original segmentation then forms the basis
for all subsequent additional segmentations of either GM or WM in the 3D
volume.  That is, aparc+aseg.mgz and wmparc.mgz make "use" of the
surface based parcellation, but only to decide the most appropriate
label to assign to GM/WM as defined in the already existing volume-based
segmentation that is contained in aseg.mgz.

Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on
the 3D volume segmentation, there is no apriori reason that their
spatial extent will correspond precisely to the more accurate gray and
white mattes surfaces that come out of the surface-based processing
stream. (Although certainly we would hope that the discrepancies don't
become too large).

cheers,
Mike H.

On Thu, 2008-07-17 at 12:00 -0500, [EMAIL PROTECTED] wrote:
 
 


I have sent two images created with the following commands.

tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white 
-segmentation (aparc+aseg.mgz and wmparc.mgz) 
$FREESURFER_HOME/FreesurferColorLUT.txt


The wm segmenations go through the "main surface" and the "orig surface" 
into the gray matter, for example in the rh-supramarginal and 
rh-postcentral. From your last response I am unsure as to which pipeline 
creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) or 
the surface-based pipeline (i.e. ribbon.mgz) or some combination of the 
two. It seems to me that the gm/wm parcellations are created using the 
surface pipeline and then transferred to the closest class-matched voxels 
from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg 
segmentations. I guess the question is how are we getting from the surface 
parcellations back to volume space; is there a binary?
 In a related vein, the value from aseg.stats "surface-based-volume mm3 
lh-cerebral-white-matter" seems to be created with mri_segstats or is it 
from mris_wm_volume? Thanks for all your help!


Chris Bell





On Jul 17 2008, Doug Greve wrote:

   
   


When the volume is created, a decision has to be made at each voxel as
to what to classify it as. This is used when the aseg.mgz and
ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from
these files. When using mri_segstats with --pv, it will take the
volume of a 1mm3 voxel and divide it up so that it can contribute to
more than one region. But there's not a way to put the partial volume
information into the segmentation itself. Not sure why that do not
appear alingned, but we've been recently looking into this for other
reasons. Can you send a pic.?

doug



On Wed, 16 Jul 2008, [EMAIL PROTECTED] wrote:

 
 

I was wondering how the calculations of the wm volume were performed as 
well. The six values below are volume

Re: [Freesurfer] labels to surface

2008-10-03 Thread Doug Greve



Hi Joost, you can load the label into matlab with read_label.m and then 
convert it into the vector you want. Alternatively, there is a new 
version of mri_annotation2label (x64 below) which you can use to create 
a "segmentation" surface in nifti or mgz from an annotation. Then find 
"voxels" that have a value equal to that of the structure you are 
looking for.


doug

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_annotation2label

j janssen wrote:


Hi,

using version 4.0.5. 

i want to convert the lh.Medial_wall.label found in the fsaverage 
label subdir into a mask which consists of 1 x v vector, with value 1 
inside the mask, 0 outside the mask and v=#vertices. should i follow 
mri_label2vol and thereafter mri_vol2surf? i guess i am looking for a 
way to put binary masks on surface data.


thanks,
-joost



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Re: [Freesurfer] difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz

2008-10-06 Thread Doug Greve

one uses ?h.aparc.annot and one uses ?h.aparc.a2005s.annot. These are 
two different parcellations.


Hwee Ling Lee wrote:

 

 


Hi!

 


I hope this finds you well.

What is the difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz?

I tried to extract the label for 1180 but I get nothing from 
aparc+aseg.mgz. I was wondering if the difference in these images 
affect what kind of label I extract.


 


Thanks!

 


Cheers,

HweeLing

 




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Re: [Freesurfer] Fwd: glmfit and surfcluster

2008-10-09 Thread Doug Greve



Hi Joost, can you look at the original sig map thresholded at 1.3 to see 
if there is a cluster of that size?


Hi,

version 4.0.5

after:

mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf 
fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh 
--glmdir stats/newperm_lh/


i got an csd file (attached), "stats/newperm_lh and --glmdir 
stats/newperm_lh/" were ignored (as expected).


i want to use this .csd file to inspect clusters:
mri_surfcluster --in qdec/N83_only_boys.mgh --csd 
stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum 
qdec/summary.txt


which gives the following output (summary.txt is attached):

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $
# $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $
# CreationTime 2008/10/08-08:52:02-GMT
# cmdline mri_surfcluster --in qdec/N83_only_boys.mgh --csd 
stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum q

dec/summary.txt
# cwd /home/neuro/joost/redes/maranon/freesurfer
# sysname  Linux

# hostname fedoraneuro.lim.local
# machine  x86_64
# FixVertexAreaFlag = 1
#
# Input  qdec/N83_only_boys.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi lh
# surface white
# SUBJECTS_DIR /home/neuro/joost/redes/maranon/freesurfer
# Minimum Threshold 1.3
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# Area Threshold0 mm^2
# CSD thresh  1.30
# CSD nreps1000
# CSD simtype  perm
# CSD contrast diff-1-2.txt
# CSD confint  90.00
# Overall max 4.37947 at vertex 3484
# Overall min 1.58841e-06 at vertex 136280
# NClusters  1
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 1
#
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWP
CWPLowCWPHi   NVtxs
  14.3793484  98860.55-34.7   11.5   -6.9  0.00100  
0.0  0.00200  155267

[EMAIL PROTECTED] qdec]$ cd ..
[EMAIL PROTECTED] freesurfer]$ mri_surfcluster --in 
qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig 
stats/cluster_map.mgh --sum qdec/summary.txt

thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $
hemi   = lh
srcid  = qdec/N83_only_boys.mgh paint
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 1.3
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
nth = -1
sumfile  = qdec/summary.txt
subjectsdir= /home/neuro/joost/redes/maranon/freesurfer
FixMNI = 1
- XFM matrix (RAS2RAS) ---
/home/neuro/joost/redes/maranon/freesurfer/fsaverage/mri/transforms/talairach.xfm
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;


Reading source surface 
/home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white

reading group avg surface area 822 cm^2 from file
Reading in average area 
/home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh

Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 4.37947 at vertex 3484
overall min = 1.58841e-06 at vertex 136280
surface nvertices 163842
surface area 65417.097656
surface area 65416.648438
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=1.30 (1.30), thmax=-1.00 (-1), thsignid=0, 
minarea=0.00

Found 1 clusters
Max cluster size 98860.554688
INFO: fixing MNI talairach coordinates
Saving cluster pval stats/cluster_map.mgh


- the cluster size seems way to big.

your thoughts?

- for visualizing the cluster i thought:
loading the --cwsig file (cluster_map.mgh) as an overlay on the 
(inflated) surface of fsaverage and then configure the overlay to set 
the minimal threshold to 1.3.


your thoughts?

thanks!
-joost



On Tue, Oct 7, 2008 at 7:37 PM, Pratap Kunwar 
<[EMAIL PROTECTED] > wrote:



   Hi,

   You have a continuous variable "age" in your fsgd file. As far as i
   know,
   permutation can't have continuous variables.

   Try mc-z that should work.

   pratap

> Hi,
>
> using version 4.0.5
>
> i ran the command:
> mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss
   --surf
> fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/
>
> it worked.
>
> then i did:
>
> mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss
   --surf
> fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3
   stats/newperm_lh
> --glmdir stats/newperm_lh/
>
> output:
>
> gdfReadHeader: reading qdec/qdec.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>

Re: [Freesurfer] tksurfer display tcl error & FS training

2008-10-09 Thread Doug Greve

One method that leaps to mind is to have new RAs analyze a relatively 
small set of data (say 10), then do a vertex-wise paired t-test between 
your gold standard set and the new RA's set.


doug

Derin Cobia wrote:


Nick,

Yes, our tcltktixblt directory was intact and set correctly.  The reason I
thought it was a BLT lib was it came up missing when I ran fs_lib check. 
At any rate, the DefaultDepth is already at 24 in our xorg.conf file and

the problem persists.  Any other thoughts what might be occurring?  Would
you like me to submit my output as well?

Also, any thoughts from anyone with regard to question #2 (see below)? 
Thanks.


-Derin


On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote:

Derin,

To answer your first question, the solution to that particular problem
that you reference was not to install the BLT libs (as they are included
with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and
found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by
changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the
file /etc/X11/xorg.conf file.

Nick

Two questions:

1.  We installed the latest version of 32-bit FS on several workstations
running CentOS 5.1 in our lab.  However, once we ran the CentOS updates
(~280 of them through up2date), tkmedit now fails to open and tksurfer
exhibits behavior exactly as described in this message from the mail
archive:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html
Having attempted to troubleshoot it I discovered that a blt lib was
missing, but even with re-installation of this tksurfer continues to not
display correctly.  I believe it's a tcl problem, but I don't understand
why performing incremental updates to CentOS would break FS.  More
importantly, I'm not sure which of the updates does "the breaking" so I
can just avoid it.  Any ideas?

2.  We are in the process of training new research assistants in how to
use FS.  Typically we have approached this in a more qualitative way by
working side-by-side with them to guide their edits and processing.  I was
wondering if there is a quantitative way of comparing their work that you
(or others) have used when training "new recruits" in FS.  Maybe something
like was done in the Han et al (2006) paper, such as compare their
thickness (or other) maps with someone we know does well with manual
interventions?  In essence, we're trying to think of a rigorous way to
train new people in FS, thanks!

-Derin
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Re: FW: [Freesurfer] Talairach_with_skull.lta accuracy

2008-10-09 Thread Doug Greve

I just added those changes to stable, so it should be in our next stable 
release.


Michael Harms wrote:


At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirming the accuracy of
either the talairach_with_skull.lta and talairach.lta transforms
(respectively).  However, neither of those flags are options in the
current public release of FS 4.0.5.

Doug:  Will the forthcoming FS release have those flags available as
options to tkregister2?  We've found them to be a very helpful addition
to tkregister2, and it sounds like Jeff would as well.

Jeff: In the interim, here are my notes on how to do what you want to
accomplish (N.B.  Doug's improved tkregister2 using the --gca-skull flag
is a more powerful approach because it makes the target the subject
space and thus the surfaces can also be meaningfully displayed via the
--surf option):

mri_convert $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca
RB_gca.mgz --frame 0
(N.B. add --conform option if you want to avoid format conversion within
tkregister2 itself (which slows loading))

tkregister2 --targ RB_gca.mgz --mov nu_noneck.mgz \
  --lta transforms/talairach_with_skull.lta --reg tmp.reg


cheers,
-Mike H.


On Mon, 2008-09-08 at 15:54 -0600, Jeff Sadino wrote:
 


Hello,

I am trying to validate the ICV value by lining up the nu_noneck image with the 
RB image.  These are the commands I am using:


mri_convert nu_noneck.mgz --apply_transform transforms/talairach_with_skull.lta 
nu_noneck5.mgz
tkmedit -f nu_noneck5.mgz &
tkmedit -f /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca &

When I compare these two, they don't line up.  The RB image is all blurry 
(Maybe it's a combination of several subjects and is supposed to be like that). 
 Any suggestions as to how to line up the noneck transformed imaged to the RB 
image is greatly appreciated!

I also attached three files to show what's happening in my transform process.

Thanks,
Jeff



   


Date: Fri, 5 Sep 2008 20:31:55 -0400
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy

can you send this to the list so others can respond? Where did you get the
tmp.reg file? If you have transformed them already you shouldn't need
tkregister2 (or a registration file in general) to compare them.

On Fri, 5 Sep 2008,
Jeff Sadino wrote:

 


Thank you very much for your help.  Your knowledge and quick responses are very 
much appreciated.

I converted my image into transformed space, but it still does not match the RB 
image.  These are the commands I used:

mri_convert nu_noneck.mgz --apply_transform
   


transforms/talairach_with_skull.lta nu_noneckt3.mgz
 


tkregister2 --targ
   


/apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --reg tmp.reg
--lta /data/040002_S04_bakj/mri/transforms/talairach_with_skull.lta --mov
/data/040002_S04_bakj/mri/nu_noneckt3.mgz
 


Again, my main goal is to verify the ICV value, so to do that I need to verify 
that the lta file is transforming the nu_noneck image onto the RB image...I 
think.

What step am I missing?

Thank you
Jeff



   


Date: Fri, 5 Sep 2008 13:09:21 -0400
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
CC: [EMAIL PROTECTED]
Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy

that won't generate a transformed volume, just display it in the
transformed space. That is, the volumes you sent were in their native
space and would have no reason to be aligned. The neck removal seems to
have been fine in both cases.
On Thu, 4 Sep 2008, Jeff Sadino wrote:

 


ps, sorry, I forgot to include my command:


tkregister2 --targ /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca 
--mov /data/${file}/mri/nu_noneck.mgz --lta 
/data/${file}/mri/transforms/talairach_with_skull.lta --reg tmp.reg

I believe this will transform the nu_neck.mgz image via the talairach matrix, 
so that it matches the RB image.

btw, we processed the scans using freesurfer 3, but the tkregister2 that came 
with freesurfer 3 did not include the --lta tag, so I am using the tkregister2 
from freesurfer4.

Thanks!


   


Date: Thu, 4 Sep 2008 21:49:27 -0400
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach_with_skull.lta accuracy

Hi Jeff,

why do you say that one is bad? We don't resample, so neither one will be
aligned with the atlas unless you apply the transform.

We are aware that the eTIV measures have more variability than we would
like, and we're looking into it, but don't have a good solution from only
T1 images.

cheers,
Bruce
On Thu, 4 Sep 2008,
Jeff Sadino wrote:

 


Hello all,

According to aseg.stats, our ICV values fluctuate on the

Re: [Freesurfer] subcortical masks

2008-10-24 Thread Doug Greve


You can use mri_binarize with the --match option  to spec the index, eg:

mri_binarize --i aseg.mgz --match 17 --o hippo.lh.nii

doug

Martin Ystad wrote:

Hi, I'd like to create binary masks in the nifti-format from each of 
the subcortical segmentations in freesurfer, separately (one for 
hippocampus, one for thalamus, and so forth..). Is there any way to do 
this automatically from the command line?


Thanks,
Martin Ystad
Ph.D. candidate,
University of Bergen

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Re: [Freesurfer] Viewing atlas?

2008-10-24 Thread Doug Greve


If you've reconned a subject, you can use the aparc+aseg.mgz volume.

doug

Ryan Scotton wrote:


Hi Freesurfers,

Some associates of mine are working on a pipeline that generates 
cortical parcellations and we are looking to compare its measurements 
to some measurements generated by the freesurfer pipeline.  However, 
our pipeline parcellates broader regions which include several labels 
generated by the FS cortical parcellation process within each of our 
labels.  What we need is to get a general idea of where every label 
generated by FS fits within the context of our broader labeling scheme.


SO, this may be an obvious question, but how might i be able to view 
an atlas image volume with the FS parcellation/labeling scheme applied 
to it in order to get a general idea of how the separate labeling 
schemes match up?


Thanks!

Ryan



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Re: [Freesurfer] convert multiple Analyze to single 4D nifti

2008-10-24 Thread Doug Greve


one way to do it is with mri_concat, something like

mri_concat f???.img --o f.nii.gz

if your individual volumes are f000.img f001.img etc

Kara Dyckman wrote:

I'm not sure.  When I just tried it, it converted to .nii.gz.  Maybe 
it has to do with the version of fsl being used? I'm posting this to 
the freesurfer listserv to see if anyone else has ideas.



Xu Cui wrote:

Thanks Kara.  I tried fslmerge on my images and the result is a 
single .img / .hdr pair, not a nii or nii.gz file.  Do you have any 
clue?  The reason to convert to nii is that fsfast seems to require 
nii file.


Thanks,
Xu

On Thu, Oct 23, 2008 at 2:20 PM, Kara Dyckman 
<[EMAIL PROTECTED] > wrote:


If I remember correctly, you can use the fslmerge command to merge
all the .hdr files into one nifti file.

Try this in the directory where your analyze files are:
fslmerge -t outputname *.hdr

outputname is whatever you want to call your new nifti file

The result will be outputname.nii.gz

Hope that helps!
Kara


Xu Cui wrote:

Does anybody know how to convert a series of Analyze files
into a single nii file?  Each analyze file is a single 3D
volume at a time point; the nii file would be 4d.

Thanks,
Xu

-- 


Xu Cui
Department of Psychiatry and Behavioral Sciences
Stanford University





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Massachusetts General Hospital
Charlestown Navy Yard
149 13th St.
Charlestown, MA  02129
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http://nmr.mgh.harvard.edu/manoachlab




--

Xu Cui
Department of Psychiatry and Behavioral Sciences
Stanford University







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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats

2008-10-24 Thread Doug Greve



They should be exactly the same. If not, it's a bug. I just looked at a 
few of mine, and they are the same.


doug

Kathy Zhang wrote:

Hello, I've recently started a project that involves measuring the 
volume of the hippocampus and other subcortical structures, so I was 
also wondering whether aseg.stats was more accurate or wmparc.stats.  
So far the difference between them appears to be approximately a 
hundred voxels for each right/left hippocampus.


Thank you,
Kathy Zhang '09

On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi <[EMAIL PROTECTED]> wrote:

Hi, for subcortical segmentations, is it then better to use the
volumes in wmparc.stats than those in aseg.stats?



On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
>
> Actually, the construction of aparc+aseg and wmparc do use info
about where
> the surface is to refine the aseg cortical boundaries. This
information is
> stored in ribbon.mgz (and it overrides the aseg definition). At
some point,
> we will use the surfaces to directly refine the aseg boundaries.
>
> doug
>
>
>
>
> Michael Harms wrote:
>
> Hi Chris,
> Doug, please correct me if I'm wrong, but the original gm/wm
> segmentation contained in aseg.mgz is based on the 3D volume-based
> tissue segmentation.  This original segmentation then forms the
basis
> for all subsequent additional segmentations of either GM or WM
in the 3D
> volume.  That is, aparc+aseg.mgz and wmparc.mgz make "use" of the
> surface based parcellation, but only to decide the most appropriate
> label to assign to GM/WM as defined in the already existing
volume-based
> segmentation that is contained in aseg.mgz.
>
> Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still
based on
> the 3D volume segmentation, there is no apriori reason that their
> spatial extent will correspond precisely to the more accurate
gray and
> white mattes surfaces that come out of the surface-based processing
> stream. (Although certainly we would hope that the discrepancies
don't
> become too large).
>
> cheers,
> Mike H.
>
> On Thu, 2008-07-17 at 12:00 -0500, [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> wrote:
>
>
> I have sent two images created with the following commands.
>
> tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface
rh.white
> -segmentation (aparc+aseg.mgz and wmparc.mgz)
> $FREESURFER_HOME/FreesurferColorLUT.txt
>
> The wm segmenations go through the "main surface" and the "orig
surface"
> into the gray matter, for example in the rh-supramarginal and
> rh-postcentral. From your last response I am unsure as to which
pipeline
> creates the wm parcellations, the volume-based pipeline (.i.e
aseg.mgz) or
> the surface-based pipeline (i.e. ribbon.mgz) or some combination
of the
> two. It seems to me that the gm/wm parcellations are created
using the
> surface pipeline and then transferred to the closest
class-matched voxels
> from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg
> segmentations. I guess the question is how are we getting from
the surface
> parcellations back to volume space; is there a binary?
>   In a related vein, the value from aseg.stats
    "surface-based-volume mm3
> lh-cerebral-white-matter" seems to be created with mri_segstats
or is it
> from mris_wm_volume? Thanks for all your help!
>
> Chris Bell
>
>
>
>
>
> On Jul 17 2008, Doug Greve wrote:
>
>
>
> When the volume is created, a decision has to be made at each
voxel as
> to what to classify it as. This is used when the aseg.mgz and
> ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from
> these files. When using mri_segstats with --pv, it will take the
> volume of a 1mm3 voxel and divide it up so that it can contribute to
> more than one region. But there's not a way to put the partial
volume
> information into the segmentation itself. Not sure why that do not
> appear alingned, but we've been recently looking into this for other
> reasons. Can you send a pic.?
>
> doug
>
>
>
> On Wed, 16 Jul 2008, [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
wrote:
>
>
>
> I was wondering how the calculations of the wm volume were
performed as
> well. The six values below

Re: [Freesurfer] optseq psdwin

2008-10-24 Thread Doug Greve

You need to set up the psdwin to span the duration of a hemodynamic 
response to your event as if it were presented in isolation. For a 3sec 
event, you can probably use something like 24 sec (so min=0, max=24). 
Since your TR=2, but your event duration is 3sec, I'd set dpsd=1 (so 
that both the TR and the stimulus duration will be divided equally by 
the dpsd). To control the first-order counter balance, use --focb 100. 
This will cause optseq2 to compute the FOCB matrix fover 100 sequences, 
and keep the one that is closest to the optimum.


doug

Linh Dang wrote:


Hi,

I have 2 questions.

1) How do I calculate psd min, max, and dpsd.  Is there a formula for 
calculating these values?  I have 4 kinds of stimuli, stim duration = 
3s, stim repetition = 25, TR =2 so:


optseq2 --ntp 180 --tr 2 --psdwin [?]  --ev A 3 25 --ev B 3 25 --ev C 
3 25 --ev D 3 25 --o 4types --tsearch 10 --nkeep 4


What should my psd min, max, and dpsd be? 



2) My task is history-dependent.  I would like to control the 
probabilities that stimulus B follows A, C follows A, A follows D... 
Is there a way for me to do that with optseq?


Thank you so much for your help.

Cheers,
Linh




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Re: [Freesurfer] Group Thickness Maps/Looking at outputs from mri_preproc

2008-10-28 Thread Doug Greve

If you go into the qdec output directory, you will find a contrast for
each group (class). In the contrast directory, you will find a file
called gamma.mgh. This will be the average thickness for the group. You
can load it into tksurfer, something like:

tksurfer fsaverage lh inflated -overlay gamma.mgh

doug

Bramen, Jennifer E. wrote:

Dear Freesurfer List

I want to look at the average thickness maps for each of my groups, not just the
statistical maps displayed by qdec. I think I found a tool that can do this. I used
mri_preproc and a list of subjects instead of a single subject, and now have the
output. I do not know to view this output though (_thickness_fsavg.mgh). Can someone explain what this output is and how
I can use it?

The other alternative is make_average_surface for each of my groups. Is that
what I need to be doing? It takes a ong time to run, so I was hoping there was
another way to go.

Thank you

Best regards,

Jennifer Bramen, Ph.D.
Postdoc
David Geffen School of Medicine at UCLA
Developmental Cognitive Neuroimaging 635 Charles Young Drive South
Los Angeles, CA 90095-7332
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Fax: (310)206-5518
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Re: [Freesurfer] Group Thickness Maps/Looking at outputs from mri_preproc

2008-10-29 Thread Doug Greve

There should be multiple contrasts, one of the contrasts should be for
group1, one for group2, and one for the difference (may be
more). Sorry, I can't remember what names they are called off the top
of my head. There will be an Xg.dat file with the design matrix to
show which regressor is which group, and in each contrast directory,
there will be a C.mat file with the contrast vector.

doug

On Wed, 29 Oct 2008, Bramen, Jennifer E. wrote:

When I look in the contrast folder, there is only one gamma.mgh image, but I
have two groups. I am assuming this is the mean thickness, or the mean
difference in thickness between groups. How do I get it to save out one file
for each group? Where is there a good explanation of the output files from qdec?

Thanks

Jen

On Oct 28, 2008, at 4:30 PM, Doug Greve wrote:

If you go into the qdec output directory, you will find a contrast for each
group (class). In the contrast directory, you will find a file called
gamma.mgh. This will be the average thickness for the group. You can load it
into tksurfer, something like:

tksurfer fsaverage lh inflated -overlay gamma.mgh

doug

Bramen, Jennifer E. wrote:

Dear Freesurfer List

The other alternative is make_average_surface for each of my groups. Is that
what I need to be doing? It takes a ong time to run, so I was hoping there was
another way to go.

Thank you

Best regards,

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Re: [Freesurfer] mris_calc

2008-11-01 Thread Doug Greve



You can also use mri_concat, like

mri_concat \
  010130_vc6126/surf/lh.thickness.fsaverage.mgh \
  zmaps/OCplusYC/lh_mean.mgh \
  --paired-diff \
  --o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh

Masking can be done by mri_mask, and thresholding with mri_binarize.

doug


On Fri, 31 Oct 2008, Akram Bakkour wrote:



Hello,
I have two thickness files I want to subtract one from the other, so I did:

on thigpen
source /usr/local/freesurfer/nmr-std-env
cd /space/elvin_005/users/akram/AGING_MASSIVE
setenv SUBJECTS_DIR $PWD
mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \
 -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \
 -src_type w \
 -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \
 -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \
 OAS1__MR1/surf/lh.thickness.fsaverage.mgh

#OAS1__MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache

mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \
010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh 
\


and I get this weird error:
"mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' 
has wrong magic number."


Any ideas what this means, or if there is any way around this?
I suppose I could do this in MATLAB, but I was curious about this magic 
number business.

Thanks!
Happy Halloween!
A




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Re: [Freesurfer] mris_calc

2008-11-01 Thread Doug Greve



I just modified fscalc.fsl to take surfaces. This is a front-end to
FSL's fslmaths command. You give it the exact same arguments, but the
files can be of any format. If the underlying data are on a surface,
then add --surf subject hemi, and it will reshape the surface to fit
in nifti (as long as the largest prime factor of the number of
verticies is less than 2^15, but that was probably obvious).

doug

On Fri, 31 Oct 2008, Akram Bakkour wrote:



Hello,
I have two thickness files I want to subtract one from the other, so I did:

on thigpen
source /usr/local/freesurfer/nmr-std-env
cd /space/elvin_005/users/akram/AGING_MASSIVE
setenv SUBJECTS_DIR $PWD
mris_surface_stats -mask fsaverage/label/lh.cort_thick.label \
 -surf_name $SUBJECTS_DIR/fsaverage/surf/lh.white \
 -src_type w \
 -out_name $SUBJECTS_DIR/zmaps/OCplusYC/lh_std.mgh \
 -mean $SUBJECTS_DIR/zmaps/OCplusYC/lh_mean.mgh \
 OAS1__MR1/surf/lh.thickness.fsaverage.mgh

#OAS1__MR1/surf/lh.thickness.fsaverage.mgh were generated using -qcache

mris_calc mris_calc -o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh \
010130_vc6126/surf/lh.thickness.fsaverage.mgh sub zmaps/OCplusYC/lh_mean.mgh 
\


and I get this weird error:
"mris_calc: curvature file '010130_vc6126/surf/lh.thickness.fsaverage.mgh' 
has wrong magic number."


Any ideas what this means, or if there is any way around this?
I suppose I could do this in MATLAB, but I was curious about this magic 
number business.

Thanks!
Happy Halloween!
A




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MGH-NMR Center
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Re: [Freesurfer] Error Log

2008-11-01 Thread Doug Greve


It creates a file called ".xdebug_tkmedit", not sure if it puts all
the commands there, though.

doug

On Sat, 1 Nov 2008, Kellen Mobilia wrote:


Hi
Would anyone happen to know the location where Freesurfer hides its error
logs? Especially for the "medit tool. Are the located in the local
Freesurfer directory or are they located somewhere else, like in the
individual; subject folder? Any help would be awesome. Also what would be
even better, if anyone knows of a command log that keeps a record of all the
commands the medit tools is executing in the background, it probably doesn't
exist but it is worth a shot.
I am running Freesurfer on a Linux.
Thanks
Kellen



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Re: [Freesurfer] Extraction mean curvature values

2008-11-02 Thread Doug Greve



Do you mean one for each subject? If you output a cluster number
volume (--ocn) from mri_surfcluster, then you can pass the ocn to
mri_segstats  as a segmentation, and pass the mri_glmfit input (--y)
as --in, then save the result as an ascii file with --avgwf.

doug


On Wed, 29 Oct 2008, Carl Schultz wrote:


Dear all,

I compared the mean curvature between two groups using the mri_glmfit
command and the Monte carlo simulation. Is there a possibility to
extract the smoothed average curvature values of the significant
clusters for all subjects?


Thank you in advance

Best regards

Christoph Schultz
University of Jena
Department of Psychiatry
Germany

Universitätsklinikum Jena
Körperschaft des öffentlichen Rechts und Teilkörperschaft der
Friedrich-Schiller-Universität Jena
Bachstraße 18, 07743 Jena
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Medizinischer Vorstand: Prof. Dr. Klaus Höffken;
Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer
Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse
Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221;
Gerichtsstand Jena
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Re: [Freesurfer] diffusion unpacksdcmdir error-wrong run!

2008-11-03 Thread Doug Greve

Can you try specifying "-run 15" instead of "-run 015"? Not sure that 
will make a diff, but it might.


doug

[EMAIL PROTECTED] wrote:


Hi,

 Running the following command line :

unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015
dti NII ajb_cerv_1a_dti.nii -unpackerr

I encountered an error of the wrong run being unpacked.  Instead of 15 as
designated, 13 appears to have unpacked.  This is data from our CD backup.
This does not seems to be related to environment, because I originally
tried to unpack in STD environment with same results, though all the
original analysis was done in stable3 in 2004 when the scans were
collected.  The logfile is following after bugr.

Thanks in advance!
Jake

BUGR:

FREESURFER_HOME: /usr/local/freesurfer/stable3

Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717

RedHat release: CentOS release 5 (Final)

Kernel info: Linux 2.6.18-8.1.15.el5 i686

NMR Center info (/space/freesurfer exists):

 machine: striatum

 SUBJECTS_DIR: /space/sake/3/users/inverse/subjects

 PWD: /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti






Log file created by unpacksdcmdir
$Id: unpacksdcmdir,v 1.12 2006/01/24 18:04:33 greve Exp $
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/unpack.log
/autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti
Mon Nov  3 14:19:09 EST 2008
-src /media/AJB_CERV1A/07311357 -targ
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015
dti NII ajb_cerv_1a_dti.nii -unpackerr
dicomdir /media/AJB_CERV1A/07311357
Scanning source directory ...
INFO: summary file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile
INFO: status file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status
INFO: scanning path to Siemens DICOM DIR:
  /media/AJB_CERV1A/07311357
INFO: Found 1758 files in /media/AJB_CERV1A/07311357
INFO: counting Siemens Files
$Id: mri_parse_sdcmdir.c,v 1.13.2.1 2006/05/15 21:42:35 greve Exp $
cwd /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti
cmdline --sortbyrun --d /media/AJB_CERV1A/07311357 --o
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile
--status
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status
sysname  Linux
hostname striatum
machine  i686
user jake
INFO: found 1756 Siemens Files
INFO: scanning info from Siemens Files
INFO: status file is
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status
0   2   4   6   8  10  12  14  16  18  20  22  24  26  28  30  32  34  36
38  40  42  44  46  48  50  52  54  56  58  60  62  64  66  68  70  72 
74  76  78  80  82  84  86  88  90  92  94  96  98 100

INFO: found 1756 Siemens files
syngo MR 2004A 4VA25A
Sorting
Assigning Run Numbers
RunNo = 0
RunNo = 1
RunNo = 2
RunNo = 3
RunNo = 4
RunNo = 5
RunNo = 6
RunNo = 7
RunNo = 8
RunNo = 9
RunNo = 10
RunNo = 11
RunNo = 12
RunNo = 13
RunNo = 14
WARNING: Run 11 appears to be truncated
 Files Found: 78, Files Expected (lRep+1): 126
FileName/media/AJB_CERV1A/07311357/58851927
Identification
NumarisVersyngo MR 2004A 4VA25A
ScannerModel  Allegra
PatientName   ajb_cerv_1a
Date and time
StudyDate 20040731
StudyTime 121222.984000
SeriesTime130908.562000
AcqTime   130848.812487
Acquisition parameters
PulseSeq  epfid2d1_64
Protocol  ge_functionals
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  30
InversionTime 30
RepetitionTime2500
PhEncFOV  200
ReadoutFOV200
Image information
RunNo 10
SeriesNo  11
ImageNo   1
NImageRows384
NImageCols384
NFrames   78
SliceArraylSize   30
IsMosaic  1
ImgPos581.7606 607.9159  80.1682
VolRes  3.1250   3.1250   5.
VolDim 64  64  30
Vc -0.9896  -0.0181  -0.1426
Vr  0.0368  -0.9909  -0.1294
Vs -0.1389  -0.1333   0.9813
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1
WARNING: Run 15 appears to be truncated
 Files Found: 70, Files Expected (lRep+1): 1
FileName/media/AJB_CERV1A/07311357/58844259
Identification
NumarisVersyngo MR 2004A 4VA25A
ScannerModel  Allegra
PatientName   ajb_cerv_1a
Date and time
StudyDate 20040731
StudyTime 121222.984000
SeriesTime134037.953000
AcqTime   134005.220012
Acquisition par

Re: [Freesurfer] Subcortical Segmentation

2008-11-03 Thread Doug Greve


What is your tkmedit command line?

Alexa Nardelli wrote:

Hi, I am new to freesurfer and to automated segmentation in general  
and I am having a problem using tkmedit's segmentation. I am able to  
open my images with freesurfer but I am having problems with the  
segmenation function. I am not sure I am even properly using it? I  
have gone through the tutorial with the tutorial data however I 
cannot  do the same things with my own data. Any hints or procedures 
to follow?


Thanks

Alexa
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Re: [Freesurfer] segmentation region export

2008-11-04 Thread Doug Greve


They are in aseg.mgz, you can extract them into a nifti file with

mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii

251 is the code for CC Posterior (found in 
$FREESURFER_HOME/FreeSurferColorLUT.txt)


doug


vin wrote:


hi,

I am trying to export segmented regions as NIFTI, and it works for the 
regions like Thalamus whole.  But when freesurfer finished autorecon, 
than it showed lot of sub regions for example :  Thalamic sub regions 
and also CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus 
Callosum) and...Mid anterior and Anterior.


How I can get these sub regions. In which files they are stored, and 
How I can extract them as NIFTI format.


any suggestion would be great !!

thank you very much ,

vin



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Re: [Freesurfer] Image deidentification

2008-11-04 Thread Doug Greve

nifti generally does not have the capability to save patient info. I 
might if the software that created it has a nifti extension (FreeSurfer 
does not, yet). There is a comment field in the nifti header, so it is 
possible it could be there, but unlikely (it would not be with a 
FreeSurfer program). A crude check is to run the unix strings program on 
the nifti file and see if there is anything there.


doug

Keller, Corey J. wrote:


Hi freesurfers,

 I have been unable to find a program/method to view the header file on some
nifty files made from mri_convert with MPRAGE scans. I want to make sure the
files we are creating do not have patient information in the headers. Is there
an easy way to check this? Thanks.

 Best,
 Corey


Corey Keller
Epilepsy Unit
Clinical Research Coordinator
Massachusetts General Hospital
Wang 735, 55 Fruit Street
Boston, MA 02114 
Phone  802.578.6292

Email   [EMAIL PROTECTED]
  [EMAIL PROTECTED]



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Re: [Freesurfer] thickness measurement

2008-11-04 Thread Doug Greve


SurfArea is the surface area of the parcellation in mm^2.

GrayVol is the volume of gray matter in the parc (basically thickness 
time area) in mm^3


ThickAvg is the average thickness (use this for your thickness study)

MeanCurv is the average mean curvature.

GausCurv is the average gaussian curvature.

doug

asaf achiron wrote:



Dear Group,

in the 
lh.aparc.stats

i can find this variables:



SurfAreaGrayVol ThickAvg
MeanCurvGausCurv
what is the difference between them?

for the thickness is use the thick avg, right?

thank you

Asaf



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Re: [Freesurfer] fslcalc.fsl

2008-11-07 Thread Doug Greve



How many vertices does that subject have and is there a prime factor
less than 2^15?

doug



On Thu, 6 Nov 2008, Akram Bakkour wrote:



Hello,
Thanks for adapting fslcal.fsl to work on surfaces Doug. This is very 
helpful. It was working for me until today.


I'm working on thigpen.

setenv SUBJECTS_DIR /space/brich_004/users/akram/HRDEV_processing

mri_surf2surf --srcsubject 03222007_4TT_clindem47 --sval  \ 
03222007_4TT_clindem47/surf/rh.thickness --trgsubject HRDEV197_1mm \

--tval 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --hemi rh

mri_surf2surf --s HRDEV197_1mm --sval \
03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --tval \
03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh --fwhm 15 \
--hemi r

mri_surf2surf --s HRDEV197_1mm --sval HRDEV197_1mm/surf/rh.thickness --tval 
HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh --fwhm 15 --hemi rh


fscalc.fsl HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh -sub \
03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh \
HRDEV197_1mm/surf/tp1_min_tp2.thickness.mgh --surf HRDEV197_1mm rh

I get the following error:
** ERROR: nifti_convert_nhdr2nim: bad dim[1]
** ERROR (nifti_image_read): cannot create nifti image from header 
'HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1.nii.gz'
** ERROR: nifti_image_open(HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1): bad 
header info

Error: failed to open file HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1
Cannot open volume HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1 for reading!

It's weird, because I did exactly the same thing with a different subject tp1 
and tp2 two days ago and it worked great!

Thanks for the help!
Akram.




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Re: [Freesurfer] optseq2 question

2008-11-13 Thread Doug Greve



Hongchuan Zhang wrote:

> Hi, list,
> I am new to optseq2 so I really need advices to my questions. We have
> an experiment of 2 factors with36 trials for each factor, and another
> 24 null trials. So in total we have 96 trials. We also have 3 random
> jitters which make our trials could last for either 4.6, 5 or 5.4
> seconds. The total session time is thus 480 seconds. Since our TR is 2
> seconds, the ntp = 240.
> My questions are:
> (1) How can I set the psdwin? My intuition is that dPSD should be
> divided by both TR and trial duration. That means we can only have a
> dPSD = 0.2. Would that be too small? I observed that by doing this the
> largest psdmaxis only 2 seconds.

That is not too small, but if you are going to analyze your data with an
FIR model, then it will kill your power. If you are going to assume a
shape (eg, gamma function or diff of gammas), then it is fine.

> (2) What should I do if I want to break the session into two parts?
> The previous optseq version seems to allow one specify the runs for
> each sesssion. But I did not find this option in optseq2. Can I just
> use half the trials to get two sequences and use themfor thetwo parts?

Yes, spec --nkeep 2

doug

> Thanks! Your suggestionis appreciated.
> Hongchuan
> 2008-11-03
> 
> Hongchuan Zhang, Ph.D.
> Postdoctoral Research Associate
> Developmental Cognitive Neuroscience Laboratory
> Northwestern University
> 2240 North Campus Drive
> Frances Searle Building, Room 2-356
> Evanston, Illinois, 60208
> phone: (847)467-1549
> e-mail: hongchuan-zhang at northwestern.edu
>
>
>
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Re: [Freesurfer] mri_convert --conform spatial changes

2008-11-13 Thread Doug Greve


Use mri_vol2vol, something like:

mri_vol2vol --mov ribbon.mgz --targ rawavg.mgz --regheader --o 
ribbon-in-rawavg.nii  --interp nearest


doug

Arthur Mikhno wrote:

Hi, 

I am trying to convert the ribbon (amongst other mgz files) from a 
freesurfer run to the native space ANALYZE file I initially imported 
into freesurfer. I need to do this to create a cortical ribbon mask as 
a pre-processing step for normalization (with another package). 
However, every mgz file in the mri/ folder, after conversion, has a 
slightly different spatial distribution after conversion. Although, 
when I convert 001.mgz and rawavg.mgz the resultant image matches the 
image I imported exactly. By spatial distribution I mean, minor 
cortical fold shifts (up down, left right) and individual minor 
rotations in the cortical folds, some minor internal translations. 

I think I tracked the problem down to the conform step, when 
rawavg.mgz gets conformed (mri_convert --conform) to 1x1x1mm and saved 
as orig.mgz. 

I need to ensure a spatially correct cortical ribbon in the native 
space data. Is there any way to un-conform ? or some way to say, 
convert orig.mgz BACK to rawavg.mgz?


For reference, this is the command I am using to convert .mgz to 
ANALYZE (.hdr, .img):
mri_convert --out_orientation LSP -rl native_mri.img orig.mgz 
converted_native_mri.img


I would really appreciate any help as this is my LAST roadblock!

Thanks in advance,
-Arthur



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Re: [Freesurfer] Qdec problem?

2008-11-13 Thread Doug Greve

There are two things you can do here. One is to create your own design 
matrix in a text file and pass it to mri_glmfit with the --X (instead of 
using an fsgd file). If you want to stay with the fsgd, then you can 
spec DODS (this will set up one regressor for MMSE instead of two).


doug


Martin Kavec wrote:


Hi,

I am trying to run a group analysis on cortical thickness between patients and 
controls. In the qdec.dat I set a MMSE for all the controls 0.0. Now, 
whenever I try to covariate thickness against age and MMSE, the qdec 
complains that there is no spectrum in MMSE values. I tried to set MMSE for 
one of controls to 0.1 and the analysis goes fine. After thinking for a 
while, I started to wonder whether I shouldn't calculate thickness difference 
first, but I am not finding the receipt on the web anymore.


Thanks in advance,

Martin
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Re: [Freesurfer] A problem on groupanalysis

2008-11-13 Thread Doug Greve


Have you looked at my presentation on group analysis? The slides are here:

http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/freesurfer.groupanalysis.pdf

There's a very similar design on slides 23 and 24.

doug



Zhangyuanchao wrote:

> Dear Mr or Ms,
> I have read the FreeSurfer Tutorial: Group Analysis, but there are
> still something I do not quite understand. I want to make comparison
> of lgi between two groups, namely, normal control groupand patient
> group. I want to regress out gender and age.For example,if I have 4
> subjects:nc1 male age=30,nc2 female age=31,patient1 male age=32,
> patient2 female age=30, how should I create the FSGD file?How should I
> design the constrast vector? What kind of test does Freesurfer
> use,F-test or t-test to detect difference regionof thickness orlgion
> the surface? What should I do if I want to use t-test to detect the
> difference between two groups? How should I set the option of the
> command mri_glmfit --sim nulltype nsim thresh csdbasename if I want to
> set the p-value threshold 0.05?
> Sorry for the trouble!
> Thank you very much!
> Yuanchao Zhang
>
> 
> 雅虎邮箱，您的终生邮箱！ 
>
>
>
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Re: [Freesurfer] mri_convert

2008-11-14 Thread Doug Greve

All those commands will do the same thing. When you pass mri_convert a 
single dicom file, it looks at all the files in that directory and finds 
all the dicoms that have the same series number, and puts them into one 
volume.


Alexa Nardelli wrote:


Hi,

I have a question regarding converting files to mgz format from  
siemens (dicom). Per each image I have 144 IMA files (i.e. for one  
subject I have files from .001.IMA to .144.IMA) and I am wondering 
how  to convert those into 1 mgz file. The only way I seem to find is 
to  use the command:


mri_convert filename.001.ima subjectname/mri/orig/001.mgz

mri_convert filename.002.ima subjectname/mri/orig/002.mgz

...


mri_convert filename.144.ima subjectname/mri/orig/144.mgz

While this is painful and time consuming I also worry that in my 
quest  to find the hippocampal volumes, Freesurfer will not read these 
files  as one volume.


Is this the correct way to convert these files? Or is there another  
easier way?


Thanks

Alexa
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Re: [Freesurfer] Configure thresholds in overlay options

2008-11-18 Thread Doug Greve

In general, this is a bit of a mess. The way that I do it is to use 
piecewise and set the min and mid to the same thing (this is what linear 
opaque was supposed to do). This way, anything that is over threshold 
has color, everything else is transparent. BTW, everything over the mid 
will be opaque. Values between min and mid will be semi-transparent. 
Some people like to much around with the min and mid to improve the look 
of the image, but really you want anything over threshold to be opaque.


doug

Juranek, Jenifer wrote:


Hi,
Running FSv405 on RHEL5. 
Is any descriptive information available for threshold options in the configure overlay display gui?

Specifically the bases for linear, linear opaque, and piecewise thresholds?
Visually, the three options appear dramatically different. Are there specific 
datatypes each overlay option is designed to handle?

Many thanks for any information you can provide,
Jenifer

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Re: [Freesurfer] mri_surf2surf - Error

2008-11-18 Thread Doug Greve

did you create a subject called "average"? This is done with 
make_average_subject. Alternatively, we distribute an average subject 
called fsaverage, so you can just use that instead if you want.


doug

Alexandru Hanganu wrote:


Dear Freesurfer Users,
We have a little problem with mri_surf2surf. Our goal is to determine 
the statistical data - t-test, ANOVA, for a group of subjects. So 
initially we made the recon-all, autorecon1,2,3 and -qcache for all 
subjects. After that we created the FSGD file and mris_preproc - in 
order to create ?h.thickness.mgh file. Now in order to initiate the  
mri_glmfit step we have to create the ?h.thickness.sm10..mgh file with 
the mri_surf2surf command.


We used this command line:

mri_surf2surf --hemi lh \
--s average \
--sval lh.thickness.mgh \
--fwhm 10 \
--tval lh.thickness.sm10.mgh


and we receive the Error:
– /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open 
file

Could you please tell us where might be the mistake ? What step is needed to 
create the lh.sphere.reg file. Thank you very much for your help.

Best regards,
Dr. Alexandru Hanganu
___
 


Department of Neurology,
Schleswig-Holstein University Hospital, Kiel Campus
Arnold-Heller-Str. 3, building no. 41
D-24105 Kiel, Germany.




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Re: [Freesurfer] Issues with FreeSurfer and Slicer3

2008-11-19 Thread Doug Greve

from a freesurfer standpoint, it looks like you've done the right 
thing. Sorry, can't help out much on slicer. It is possible that slicer 
is expecting an integer data set, so you can try


mri_convert FSParcel_FSorient.mgz FSParcel_FSorient.int.mgz  
--out_data_type int


doug


joel bruss wrote:

I must have posted this to an incorrect address before so I'll try 
this again:


Hello-

I'm running freesurfer-Linux-centos4-
stable-pub-v4.0.5 on Suse 11.

I've used the output of FreeSurfer, specifically wmparc.mgz to create 
a 32-bit volume to which I've applied edits.  The two commands I used 
were:


mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o 
wmparc-in-native.mgz --regheader --interp nearest


mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz 
wmparc_in_native_analyze


(The new Analzye set was renamed FSParcel.hdr/img)


After making the appropriate edits, I wanted to put this file back 
into mgz format/freesurfer space so I ran:


mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz

mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o 
FSParcel_FSorient.mgz --regheader --interp nearest


(I assumed that a target of wmparc would be most appropriate sinc 
that's what I started with but I've tried aseg as well)



I've been playing around with Slicer and trying load the file as a 
label file to which I create (I believe) vtk models.  If I convert 
wmparc to an Analyze set and then back to FreeSurfer mgz without any 
edits, I get an exact copy, as would be expected.  If I make any 
alterations to the file and follow my steps, Slicer gripes that it 
can't parse the header.  No matter what dims I use, I get pixels 
scattered across the screen and it appears that the volume is 
scrunched to 1 slice.  If I run tkregister (as mri_vol2vol suggests)


tkregister2 --mov FSParcel_FSorient.mgz --targ 
$SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg


everything looks fine.  I find the Slicer documentation a bit lacking 
and don't know who to turn to.  Is there something inherently wrong 
with my commands or is there a way to write header params to the mgz 
file so that Slicer will just work?


-Joel



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Re: [Freesurfer] stats in freesurfer

2008-11-20 Thread Doug Greve




Lúcia Garrido wrote:


Dear all,

I have a few questions about stats in freesurfer that I'd be very grateful
if you could answer.

1. Is it possible to reduce the search from the whole brain to a smaller
region of interest to apply corrections for multiple comparisons? For
example, if I'm interested in differences in the fusiform gyrus, can I
restrict the FDR correction to the fusiform?
 



Yes, click in the fusiform, click on the "Mark Label" button (or 
tools->Labels->Mark Selected Label), then check the "Only Marked" button 
next to the FDR, then "Set Threshold Using FDR", the "Apply".


Not sure about the others.


2. Is it important to control for any global measure when comparing
cortical thickness? For example when comparing grey matter volume, it's
good practice to control for the intracranial volume. In case of cortical
thickness (and other dependent measures in freesurfer), do you know how
these are affected by the intracranial volume (or other measures) and how
these could be controlled?

3. Finally, I posted a question a few days ago about comparing volume
using freesurfer. I'm sorry for insisting on this but I still haven't
found any response. My question was whether it's possible to compare
volume maps in freesurfer. I'm using an older version (4.0.4) and my
impression is that the most recent version might have this feature, but
this is unclear to me. I'd be very grateful if you could let me know if
this is the case. And if there's any way in which I can compare volumes
usig data pre-processed using the version I have.

Thank you very much!

Best wishes,

Lucia



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Re: [Freesurfer] cortical labeling issue

2008-11-21 Thread Doug Greve

The cortical segmentation from the aseg does not often line up very well 
as it is only based on a voxel/volume analysis. The aseg is not informed 
by the surface analysis.


doug

[EMAIL PROTECTED] wrote:


Hello all-

I'm having some trouble with sessions in which the pial surface is not
matching up with the cortical segmentation. Subjects were run on a 1.5T
Vision scanner and we're using an average of 3 MPRAGEs. Does anyone have
any suggestions on how to troubleshoot this issue? I've attached a
snapshot illustrating this problem.

Thanks,
Tessa


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Re: [Freesurfer] fs-fast smoothing

2008-11-25 Thread Doug Greve

Hi Scott, you should skip steps 2-6 (that is the old stream). Instead, 
run isxconcat-sess after #1, then smooth on the surface either in 
isxconcat-sess or with mri_surf2surf before running mri_glmfit.


doug


Scott Gorlin wrote:


Hi,

I'd like some clarification on the recommended procedure for smoothing 
functional data across the cortical surface in FS-FAST.


I've managed to get it working using the following procedure:

1) analyze my data using selxavg3-sess in the native space, without 
smoothing

2) resample the averages into the spherical space using func2sph-sess
3) smooth these averages using sphsmooth-sess (which required several 
edits to work with .nii files)

4) recreate the contrasts in the smoothed sph space with stxgrinder-sess
5) paint the analysis onto the surface with paint-sess (which also 
required edits for .niis)

6) view with surf-sess (which I had to edit to read the subject properly)

Surely there's a simpler way to accomplish this?  I'm particularly 
confused because the online documentation says that selxavg3 replaces 
stxgrinder, but it seems stxgrinder has to be called to make contrasts 
in non-native space (and uses different code to produce the contrasts 
than selxavg).   Plus, the revision date for stxgrinder is more recent!


Then, it seems odd that isxconcat will reproject the data for a group 
analysis if it's already sampled on the surface via func2sph.


Thanks,
Scott
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Re: [Freesurfer] Segmentation Volume Data

2008-11-25 Thread Doug Greve

The aseg.stats is computed with a partial volume correction at the 
boundaries of the structures, tkmedit just counts voxels.


Yuan Xu wrote:


Hi FreeSurfer:

 

 when I compare a brain structure volume count on the aseg.stats 
files with a volume of same structure measured using tkmedit 
"Segmentation Label Volume Count" feature to display on TkMedit Tools 
window. They are closer but not the same, usually about 3 to 10% 
difference. Why?


 


Thanks,

 


Yuan



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Re: [Freesurfer] fs-fast smoothing

2008-11-25 Thread Doug Greve

Oh, in that case the easiest thing to do is to smooth the raw data on 
the surface. If you have a development version of freesurfer, you can do 
this with preproc-sess using the -surf-fwhm option


doug

Scott Gorlin wrote:


Thanks Doug, though I'm still a bit confused:

I'd like to see the smoothed results on the individuals, not just the 
group - so it seems isxconcat-sess wouldn't be appropriate.


Are you suggesting running mri_surf2surf directly on the contrast 
sig.nii files?  Is smoothing a significance map the equivalent of 
smoothing the data, then recreating the significance in the sphere 
space?  This didn't seem true to me, which is why I tried to recreate 
the significance maps as below.


Thanks,
-S



Doug Greve wrote:

Hi Scott, you should skip steps 2-6 (that is the old stream). 
Instead, run isxconcat-sess after #1, then smooth on the surface 
either in isxconcat-sess or with mri_surf2surf before running 
mri_glmfit.


doug


Scott Gorlin wrote:


Hi,

I'd like some clarification on the recommended procedure for 
smoothing functional data across the cortical surface in FS-FAST.


I've managed to get it working using the following procedure:

1) analyze my data using selxavg3-sess in the native space, without 
smoothing

2) resample the averages into the spherical space using func2sph-sess
3) smooth these averages using sphsmooth-sess (which required 
several edits to work with .nii files)
4) recreate the contrasts in the smoothed sph space with 
stxgrinder-sess
5) paint the analysis onto the surface with paint-sess (which also 
required edits for .niis)
6) view with surf-sess (which I had to edit to read the subject 
properly)


Surely there's a simpler way to accomplish this?  I'm particularly 
confused because the online documentation says that selxavg3 
replaces stxgrinder, but it seems stxgrinder has to be called to 
make contrasts in non-native space (and uses different code to 
produce the contrasts than selxavg).   Plus, the revision date for 
stxgrinder is more recent!


Then, it seems odd that isxconcat will reproject the data for a 
group analysis if it's already sampled on the surface via func2sph.


Thanks,
Scott
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Re: [Freesurfer] 2D to 3D registration

2008-11-26 Thread Doug Greve

Hi Susie, I have a tool that works very well on this type of thing, but
I am not quite ready to release it (a few more weeks). It will be
greatly facilitated if you acquired a whole-brain image during your scan
(this can include the MPRAGE itself). If not, then you'll have to do
some hand registration to get it close (if you collect more data of this
type, make sure to get a whole-brain scan -- virtually anything will do,
including a single time point from an epi).

doug

Susie Heo wrote:

Hello,
I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE.

Is Freesurfer capable of finding and applying the appropriate transformation?
Specific suggestions would be greatly appreciated.

Best,
Susie

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Re: [Freesurfer] mri_label2vol

2008-11-30 Thread Doug Greve



what is your command line?


On Fri, 28 Nov 2008, Steinmann, Iris wrote:


Hi Freesurfers,

there is a little problem: I load fsaverage in tkmedit and marked with 
tools-'Configure-Brush-Info...' an area in the volume, then I saved it as a 
label (newarea.label).
I want to create a binary mask with this newarea.label and used mri_label2vol, 
to have 1 where the label is and 0 where it is not. But it doesnt work...I just 
get a file (I tried it with nii and bfloat) with only 0 everywere. Is something 
wrong in my workflow?
I hope somebody have an idea...
best greetings

Iris



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Re: [Freesurfer] question on tksurfer tcl

2008-12-02 Thread Doug Greve


try just running tksurfer with the -label-outline option.

j janssen wrote:


Hi,

using version 4.0.5

my goal: to display in tksurfer an inflated brain with curvature and 
an *outlined* label, using a tcl-script.


there are probably numerous ways, i did:

 tksurfer "subject" rh inflated -gray -tcl tksurf.tcl

where tksurf.tcl contains:

make_lateral_view
rotate_brain_x -90
redraw
labl_load "label-file"
set gaLinkedVars(redrawlockflag) 0
SendLinkedVarGroup redrawlock
set gaLinkedVars(labelstyle) 1
SendLinkedVarGroup view
save_tiff "tiff_file.tiff"

all works except for the label to be outlined. any suggestions?

thanks!
-joost



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Re: [Freesurfer] How to compare left vs right hemi (flip RL)

2008-12-02 Thread Doug Greve

We don't have a good way to do this yet. I've have been working on one 
but have dropped the ball. Some people will analyzed both the 
correctly-oriented data and left-right reversed for each subject, but 
this is not the best way to do it.


doug

Frederic Andersson wrote:


Hi,

Is there any way to compare left vs right hemisphere (surface morpho. 
and functional data). I mean, is there any function to flip one 
hemisphere in order to compare it with the other one?


Thanks,

Frederic Andersson


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Re: [Freesurfer] Using qdec to compare groups of twins?

2008-12-02 Thread Doug Greve

Do you just want to do a paired analysis? Do you want to include other 
covariates?


Burmicz, Ryzarda wrote:



Hello,

Could you please advise as to whether or not the following analysis is 
suitable?


I would like to compare groups of monozygotic twins (MZ concordant vs. 
MZ control ; MZ discordant affected twin vs. unaffected twin) using 
qdec. This is not as straightforward as group comparisons usually are 
because I cannot make the assumption of all data being independent as 
twin pairs are, obviously, related to one another.


To get around this issue I have started a qdec analysis and added a 
category 'pair' in which twin pairs share a category as follows 
(qdec.table.dat), in order to indicate that they have shared genetic 
and environmental influence:


subject no
subjid  pairdiagnosis   age gender
1   a   MZ_Discord_Well ... ...
2   a   MZ_Discord_Ill 
3   b   MZ_Discord_Ill 
4   b   MZ_Discord_Well
5   c   MZ_Discord_Well
6   c   MZ_Discord_Ill 
7   h   MZ_Discord_Well
8   h   MZ_Discord_Ill 
9   l   MZ_Discord_Well
10  l   MZ_Discord_Ill 
11  m   MZ_Discord_Well
12  m   MZ_Discord_Ill 
13  n   MZ_Discord_Well
14  n   MZ_Discord_Ill 
15  p   MZ_Discord_Well
16  p   MZ_Discord_Ill 
17  s   MZ_Discord_Well
18  s   MZ_Discord_Ill 
19  t   MZ_Discord_Well
20  t   MZ_Discord_Ill 


I would appreciate if you could suggest a more robust way around this.

Many thanks,

Rysia



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Re: [Freesurfer] Error with motion-correction session(ms-sess)

2008-12-02 Thread Doug Greve

Looks like matlab is having trouble running from the shell. I have no 
idea what causes this, you may have to ask your system administrator for 
help.


doug

 wrote:


Hi, Mr or Ms

My name is Kenta in Japan. I'm undergraduate student.
Please help me!
I've tried some things to solve the error with mc-sess.
But I could not solve this error.

The mc-sess processing didn't completely run and  following message 
showed up.


I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5.
If you want some information about this error or another things, let 
me know.


==
->> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2008-12-02 
20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- 
can't fully enable headless mode.

==

Yours sincerely.

Kenta



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Re: [Freesurfer] Possible to constrain FDR to a label in the volume?

2008-12-02 Thread Doug Greve

Yea, there's not a mask to label. There is a mask to brain, but I'm not 
sure if you can substitute your own mask for it. I just tried to run it, 
and could not get FDR to work at all in tkmedit. Is it working for you 
at all?


doug

Dan Dillon wrote:


Dear FreeSurfers,

 

I've created a basal ganglia label and am wondering if it's possible 
to constrain the FDR calculation to that label? Based on earlier 
messages it seems like tksurfer has a "marked label only" option for 
FDR, but I haven't been able to find something similar in tkmedit. Any 
help greatly appreciated.


 


Thanks!

 


Dan Dillon, Ph.D.

Post-doctoral Fellow

Affective Neuroscience Lab

Dept. of Psychology, Harvard University

Phone: (617) 495-1889

E-mail: [EMAIL PROTECTED] 



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Re: [Freesurfer] missing information in volume headers

2008-12-04 Thread Doug Greve

It was likely converted thru an intermediate format that did not retain 
those values (eg, nifti or analyze) before being imported into freesurfer.


Jared Price wrote:


Dear freesurfer gurus,
I noticed something unusual in some of our data today.  When the 
command mri_info was run on some of the orig.mgz volumes the values 
listed for echo time and flip angle in some of the scans were 0.00, 
even though there was a listing for repetition time.  What could have 
caused this?  Could misinformation in the header cause variation in 
the freesurfer processing of that scan?

Cheers,
Jared
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Re: [Freesurfer] vertex wise correction for multiple comparisons using permutation

2008-12-04 Thread Doug Greve



Yes, the max stat is stored in the CSD, and it's purpose is to enable 
voxel-wise correction, but I've never gotten around to it (and this is 
the 1st request:). You might be able to program something in matlab 
pretty quickly. You can use FS's load_csd.m to load the CSD file, and 
MRIread() to load the overlay.


doug



Lúcia Garrido wrote:


Dear Freesurfers,

I'd like to correct for multiple comparisons vertex-wise instead of
cluster-wise. Is it possible to do this using permutation (and not FDR)?
I've seen in an e-mail from last year that the values of maximum statistic
stored in the CSD file could be used for this purpose, and I'd be very
grateful if you could let me know how.

Many thanks,

Lucia

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Re: [Freesurfer] Statistic analysing for a mask

2008-12-08 Thread Doug Greve


Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.

doug

Alexandru Hanganu wrote:


Dear Freesurfer users,

We have an MNI mask and we want to apply this mask on a group of 
subjects for small volume correction.

so we did the following steps:

1. cd $SUBJECTS_DIR/fsaverage/surf
fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg 
TT_avg152T1_to_fsaverage.dat


2. cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf --mov /path/to/ROI5.nii --reg 
TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest 
--hemi lh  --out lh.fsaverage.ROI5.mgh


3. cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval 
lh.thickness --tval lh.thickness.fsaverage.mgh

.
.
.
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237
nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits = 
2.31875

Saving target data



4. Next step was just for verifying, but we received an error (maybe 
it's not so important):

cd $SUBJECTS_DIR/subjid/surf
mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh 
--in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt


Loading 
/usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh

Loading lh.thickness.fsaverage.mgh
ERROR: dimension mismatch between input volume and seg

We want to determine the statistics only for this mask for the whole 
group of subjects (qdec, or mri_glmfit).
If the mapping of our subjects thickness data was good, what should we 
do next in order to achieve our goal ?


Thank you.

Best regards,
Dr. Alexandru Hanganu
___
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Schleswig-Holstein University Hospital, Kiel Campus
Arnold-Heller-Str. 3, building no. 41
D-24105 Kiel, Germany.



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Re: [Freesurfer] mri_volcluster

2008-12-08 Thread Doug Greve

I would probably use --ocn with mri_volcluster to create a single volume 
in which each voxel value is the cluster number it belongs to. Then 
split them out like:


mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh

doug

Gregory Dierksen wrote:



Hi,

I'm trying to use the mri_volcluster command to make label files from 
a single volume of binary voxel clusters.  Once I have split the 
volume into individual label files I want to convter the label files 
back into individual cluster volumes (I am trying to use mri_label2vol 
to do this). The commands I've been using are:


 mri_volcluster --in microbleeds-reslice.mgz --allowdiag --thmin .5 
--labelbase ../scripts/clusters/testing/cluster


mri_label2vol --label ../scripts/clusters/testing/cluster-0001.label 
--temp orig-flip-reslice.mgz --o cluster-0001.mgz


(NOTE: the -reslice is because these volumes have been resliced from 
0.4492, 0.4492, 6. sized voxels to conform to 1 mm^3 sized voxels; 
the dimensions of the image were altered as well, from 384 x 512 x 23 
voxels to 173 x 230 x 138 voxels)


When I view cluster-0001.mgz with tkmedit the result is a 3D 
checkerboard like pattern with no two voxels having common edges 
(despite the original cluster in microbleeds-reslice.mgz being a solid 
cluster of 90 mm^3). What I wanted to see was that each cluster could 
be reconstructed in a single volume (i.e. cluster-0001.mgz, 
cluster-0002.mgz, etc with each volume containing only one cluster).


Also, when I use mri_cor2label and then mri_label2vol to switch 
between label files and volumes files, the clusters (despite not being 
split up like I want) are solid and do not display this checkerboard 
effect...leading me to think that its an issue with mri_volcluster.


Any help you can offer would be great.  Thanks.

Greg



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Re: [Freesurfer] Statistic analysing for a mask

2008-12-08 Thread Doug Greve

what's your cmd? You need to make sure to add --in lh.thickness to get 
thickness in the summary file


Alexandru Hanganu wrote:

Thank you Nick, and Doug for your answers. I used both "--reshape" 
flag and "--noreshape" flag and the results after "mri_segstats" were 
in both cases:

.
.
.
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation
  0 0   134504  134504
  1 1   29338  29338

Reporting on   2 segmentations

So I understand that these are the thickness data of the mask I used. 
Are these data in mm ? Because when using "mris_anatomical_stats" 
command line to see the thickness - the data is in mm, and is very 
different.


Sincerely,
Alex.



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Re: [Freesurfer] register.dat

2008-12-09 Thread Doug Greve



Try looking at the docs on

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

esp the fscoords.{pdf,ppt}

doug


Julien Dubois wrote:


Hi

I need one piece of info that I can't seem to find anywhere (after 1h
of searching).

What exactly do the numbers in register.dat correspond to (I know for
the first four rows, but the last four rows are still a "mystery")?

Can I manually temper with that info (if I know I translated an image
by hand before coregistration, for example)?

Thank you very much in advance
- Julien Dubois
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[Freesurfer] Docs for FSGD Files

2008-12-09 Thread Doug Greve



Hi Y'all, I've completed some new documentation on the FreeSurfer Group 
Descriptor (FSGD) files. They can be found in these locations:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat
https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss

Please let me know if you have questions (or find typos:).

doug



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[Freesurfer] Paired Analysis with FreeSurfer

2008-12-10 Thread Doug Greve



I just created another wiki page to document how to perform a paired 
statistical analysis in FreeSurfer (someone was asking me about it, but 
I lost the email). The page is here:


https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

It is admittedly a little rough, so let me know if you find typos or 
have questions.


doug


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Re: [Freesurfer] I cannot get tutorial data

2008-12-10 Thread Doug Greve


Sorry, try it now.

doug

 wrote:


Hi, Mr. and Mrs

I want Tutorial file of fsfast.
But I didin't get it from the following pass.

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz


If you know about that please let me know.
Thank you for your help.

Best regards,
Kenta
 






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Re: [Freesurfer] Discrepancy between sig.nii and .w files

2008-12-11 Thread Doug Greve

I just noticed this about a week ago and have not been able to track it 
down. The w file (or anything created by mri_vol2surf, which is run by 
paint-sess) is the gold standard. When tksurfer loads in a 
volume/registration, it is slightly off. I'm working on why.


doug

Jesse Friedman wrote:


Hi,

I'm using paint-sess to create .w files from a contrast's sig map (I need
the .w files for use with MNE).

When I view the sig.nii file in tksurfer, the activation differs subtly
but noticeably from the .w files.

For example, I'll run a command like:
paint-sess -analysis EC -contrast eVc -offset 5 -s subjects/RMCON005

When I load RMCON005/bold/EC/eVc/sig-5-lh.w into tksurfer, the activation
is slightly different than when I load RMCON005/bold/EC/eVc/sig.nii and
view that hemisphere at that offset.

Is this discrepancy to be expected? If so, is there a way to create .w
files that have identical activation to the sig.nii file?

--
Jesse Friedman, B.A.
Massachusetts General Hospital
Martinos Center, Manoach Lab
Psychiatric Neuroimaging
149 13th Street #2613
Charlestown, MA 02129
Phone: (617) 726-1908
Fax: (617) 726-4078
jes...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Some questions about my analysis

2008-12-11 Thread Doug Greve




Christian Scheel wrote:


Dear all,

I have got several questions about the analysis of my data. Maybe you 
can help me out:


1) Regarding the different levels of smoothing (FWHM) in Qdec are 
there already some 'standards' that one should usually stick to? My 
results look better when I set the smoothing level to 15 or even 20, 
but is it really appropriate to use such high levels of smoothing?


As with all smoothing, there is no real standard, but it is not unusual 
to use 15 or 20. Surface smoothing is much more forgiving that volume 
smoothing in  terms of mis-localization of activation. In fMRI 
volumetric analysis, it is not unusual to see 10-20mm smoothing.




2) In Qdec is there a possibilty to set something like an 'Extent 
threshold' in order to display only clusters of a certain size and 
hide all clusters that are smaller?


This is not possible in Qdec yet. Outside of qdec, there is 
mri_surfcluster which will do this. We will be adding it into qdec.




3) Am I correct that the best way to get the total gray and white 
matter volume is

a) for the gray matter volume:
mris_volume ?h.pial
minus
mris_volume ?h.white
b) for the white matter volume:
mris_wm_volume subject ?h


I'll leave this for others.



I read that the values for white and gray matter in the aseg.stats are 
not that accurate, but what about the GrayVol value in the 
?h.aparc.stats files? I was a bit surprised that the sum of these 
GrayVol values is not the same as the total gray matter volume 
calculated with mris_volume (although it comes quite close)


4) All of recon-all has been run with Freesurfer 4.02 for all subjects 
- is it OK to use Freesurfer 4.05 or 4.10 for the analysis?



I'll leave this for others.

5) I have tried loading my data into the qdec version shipped with 
Freesurfer 4.05 and noticed that now there is an option to chose 
between DODS and DOSS. In my study I wish to compare the thickness of 
a group of patients and a group of controls accounting for gender and 
age. Did I understand Dougs freshly updated wiki page correctly and 
can I use DOSS in case I assume that age has the same effect on 
patients and controls (so same slope) and they are only starting at 
different thickness levels? And when chosing DOSS is age really still 
in the calculation as a covariate? I was surprised to see that I can 
only chose the question 'Does the average thickness, accounting for 
gender, differ between patient and control' but not 'accounting for 
gender and age'.


Yes, if you believe that the slope is the same for patients and 
controls, you can use DOSS. Age is used as a covariate, and the question 
text should be changed to reflect this.




6) I would like to have a look at the local gyrification index aswell 
but still need to buy Matlab for it. Do I also need some extra 
toolboxes to run the lgi calculation - or do I just need the core 
programm?


I'll leave this for others.

doug



Any help is greatly appreciated.

Best wishes,
Christian Scheel


---
University of Cologne
Department of Psychiatry
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Re: [Freesurfer] spatial AR1

2008-12-11 Thread Doug Greve

it is automatically computed by mri_glmfit and used to compute the fwhm 
(saved in fwhm.dat). I'm working on an RFT-based correction for multiple 
comparisons correction, and that requires fwhm. You also need it if you 
are going to use the monte-carlo-based simulation.


doug

Michael Harms wrote:


Hello,
What is the role of the spatial AR1 that is automatically computed as
part of a QDEC analysis?

thanks,
Mike H.


 



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Re: [Freesurfer] .mat/.hdr and orientation

2008-12-15 Thread Doug Greve

I would have thought that that mri_convert cmd (with .img) would have 
worked. what went wrong?


Susie Heo wrote:


Hello,
I am hoping that someone can help me to solve my orientation/angle acquisition 
problem:

1)  I have an EPI oblique slice in Analyze format with incorrect 
orientation/angle acquisition information in the .hdr file (no .mat file)
2)  I have a distorted image of the same slice in Analyze format with the 
correct orientation/angle information in the .hdr/.mat files
3)  I would like to change the .hdr/(.mat?) file of 1) to conform to the 
orientation/angle specs of 2).

I have tried:
1)  Replacing 1).hdr w/ 2).hdr--incorrect orientation; image off center; same 
as if kept 1).hdr
2)  Replacing 1).hdr w/ 2).hdr and 2).mat--correct slice angle, image flipped -y and possibly -x? 
3)  mri_convert   --iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 where  = 1).img, 2).hdr, 2).mat --lost slice angle, correct orientation


Any tips?  What exactly do the .hdr and .mat files contain?

Susie


 
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Re: [Freesurfer] make_average

2008-12-15 Thread Doug Greve

Hi Petr, when you list your subjects, just use the subject's name. It 
looks like you put path specifiers in there, ie, "./1013" shoudl be 
simply "1013"


doug

p.s.bjer...@studmed.uio.no wrote:


Hi,

Trying to make an average of about 60 subjects. The problem is that the
proper files are not produced. In average/mri/ I only have the
mni305.cor.mgz and the folder "transforms". There should more.

During processing I can see the following repeating at some point: "tail:
cannot open `+3´ for reading: No such file or directory". Not sure what +3
means...

Further, in the end of output (also in the make_average_volume.log,
attached) we have the ERROR: failure writing /./..//.mgh
where  is the first of the subjects in the "list". If I try to remove
it and rerun, it only complain about the next in line...

Don´t know what to do here...:)

Petr



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Re: [Freesurfer] reg-feat2anat failed

2008-12-15 Thread Doug Greve

Hi Xin, the problem is that neither the sform nor the qform are valid. 
Did the message below not appear when you ran tkmedit?


WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:


Hello, Freesurfer group,
I am registering the fMRI results to surface using reg-feat2anat (v 
1.26.2.1 2007/08/15) and tkregister2. The automatic registration 
catastrophically failed in the subject space, but worked fine in the 
standard space. The orientations of example_func.nii.gz in the subject 
space are flipped in any view. I use the tkmedit to view the 
example_func, and found the orientation is wrong. It seems Freesurfer 
can not read nifti header correctly. I attach the reg-feat2anat log 
file and an example_func.nii.gz.  
I found the following message from Freesurfer email list.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
Does Freesurfer have a solution for this type of problems by now?

Thank you in advance,

Xin



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Re: [Freesurfer] reg-feat2anat failed

2008-12-15 Thread Doug Greve

There is a flag in the nifti header saying whether the qform or sform 
are valid, and it looks like your scripts do not set this flag. You can 
use mri_convert (the freesurfer program). This will create valid files 
that can be read into any program.

doug

Wang, Xin wrote:

Thank you very much for your quick reply, Dr. Greve. I asked our 
institutional MRI center for correct information on qform and sform 
since the header of nifti files are created by their scripts. But I do 
not know what they can do to fix this problem. I will appreciate if 
you have any further suggestion on how to do the registration without 
the information on qform and sform in case I can not get them. Does 
convert to ANALYZE format or manually correct in tkregister2 work?

Thank you again,

Xin 

-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed

Hi Xin, the problem is that neither the sform nor the qform are valid.
Did the message below not appear when you ran tkmedit?

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug

Wang, Xin wrote:

> Hello, Freesurfer group,
> I am registering the fMRI results to surface using reg-feat2anat (v
> 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> catastrophically failed in the subject space, but worked fine in the
> standard space. The orientations of example_func.nii.gz in the subject
> space are flipped in any view. I use the tkmedit to view the
> example_func, and found the orientation is wrong. It seems Freesurfer
> can not read nifti header correctly. I attach the reg-feat2anat log
> file and an example_func.nii.gz. 
> I found the following message from Freesurfer email list.

> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> Does Freesurfer have a solution for this type of problems by now?
>
> Thank you in advance,
>
> Xin
>
>
>
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Re: [Freesurfer] mri_convert 3D set to a single 4D ?

2008-12-15 Thread Doug Greve


There are two things you can do,

mri_concat spm_*.img --o 4d.img

you can also  do it with mri_convert, but I don't think  it buys you 
anything over using mri_concat.


doug

Siddharth Srivastava wrote:


hi everyone,
   is it possible to combine, using mri_convert, a set of
3D spm/analyze files into a 4D analyze file  ? can anyone help
me out with the syntax, if possible?
thanks,
sid.



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Re: [Freesurfer] mri_convert 3D set to a single 4D ?

2008-12-15 Thread Doug Greve

mri_convert will fail in the same way.  But it should have worked. Can 
you point me to the dir and give me read perms?


Siddharth Srivastava wrote:


Hi Doug,
 Thanks for the reply. I tried mri_concat as you 
suggested,  and got the following:


WARNING: analyzeRead(): matfile spmfile1-0003.mat 
exists but could not read ...

  may not be matlab4 mat file ... proceeding without it.
-
INFO: could not find spmfile1-0003.mat file for 
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped 
(default).
INFO: if not valid, please provide the information in to>spmfile1-0003.mat file

-

These files are the outputs from spm_reslice command, and i looked at 
the contents of the
mat files: they have 2 entries: "M" and "mat", and store the same 
matrix. Do you think
mri_concat may be getting confused by 2 entries in the mat file? Is 
there any flag i can

use (eg --it analyze ) to make it run?
I would also be interested in using the mri_convert option as an 
alternative. can you (or anyone)

help me with the command line flags?

regards,
sid.


On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


There are two things you can do,

mri_concat spm_*.img --o 4d.img

you can also  do it with mri_convert, but I don't think  it buys
you anything over using mri_concat.

doug

Siddharth Srivastava wrote:


hi everyone,
   is it possible to combine, using mri_convert,
a set of
3D spm/analyze files into a 4D analyze file  ? can anyone help
me out with the syntax, if possible?
thanks,
sid.



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Re: [Freesurfer] func2roi-sess command issue

2008-12-15 Thread Doug Greve

it's only positive for the contrast that you have specified. the roi 
summary reports the HRF amplitudes for each condition. When you compute 
the contrast of those, you should get the right sign.


doug

Dave Brohawn wrote:


Hello,

In the stable 3 environment, I ran the func2roi-sess command. This is what
was included:

func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh
-maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos
-maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR

I then ran this summary generating command:

roisummary-sess -roidef dACC99_rh -analysis EMerror -sf
Subject_files/MTHFRn18-list -d $SUBJECTS_DIR -sumfile
$SUBJECTS_DIR/dACC999_rh.txt

I've viewed the summary file, and found that there are negative values
listed for some of the conditions time points (e.g conditon 1, 2 sec after
stimulus onset).

How can this be if I included the masktail pos flag? I thought that only
captured positive activation.

If there is a way to solve this issue and capture only positive
activation, please post when you can.

Thank you,

Dave Brohawn
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Re: [Freesurfer] tkregister2 error

2008-12-17 Thread Doug Greve

it wants the number of dimensions to be either 3 or 4, even if the size 
of those dims is only 1. You'll probably have to edit the header, though 
I'm not sure how to do that.


Susie Heo wrote:


Hello,
When I try to use the Freesurfer command 'tkregister2' (or 'mri_convert', or 
any Freesurfer command for that matter) to read in my nifti files created using 
SPM, I receive the error message:
"niiRead(): 2 dimensions in ../rsH794_1.nii; unsupported
ERROR: could not read ../rsH794_1.nii as 24"

Does anyone know what the problem is and how to fix it?

Susie


 
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Re: [Freesurfer] Transformation from volume index to vertex index

2008-12-19 Thread Doug Greve



if you have the voxel index (col, row, slice) then you can:

V2R = [
 -1.00.00.0  128.0
  0.00.01.0 -128.0
  0.0   -1.00.0  128.0
  0.00.00.01.0 ]

crs = [col row slice]';

xyz = V2R[crs+1; 1];

then find the vertex whose xyz coors are closest to xyz



Yunjie Tong wrote:


Hi freesurfer experts,

I have a single subject anatomical data in freesurfer. If I know the  
volume index of a point on the surface of the cortex ( from T1.mgz in  
TkMedit), how can I find out the corresponding vertex index or the  
vertex RAS in TkSurfer. Thanks. BTW, I am using matlab.


Thanks,

Yunjie
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Re: [Freesurfer] Thanks for the answers

2008-12-22 Thread Doug Greve


make sure you're not using a 0-based index with matlab

Yunjie Tong wrote:


Hi Doug and Bruce,

Thanks for your answers. One more question, why the vertex RAS of the 
same spot on the brain given in TkSurfer is not the ones I read by 
Matlab program freesurfer_read_surf?


The commands I am using are:

[vertex_coords, faces] = 
freesurfer_read_surf('tutorial_subjs/subject/surf/lh.inflated');


tksurfer subject lh inflated

Thanks,


YJ



if you have the voxel index (col, row, slice) then you can:

V2R = [
-1.00.00.0  128.0
 0.00.01.0 -128.0
 0.0   -1.00.0  128.0
 0.00.00.01.0 ]

crs = [col row slice]';

xyz = V2R[crs+1; 1];

then find the vertex whose xyz coors are closest to xyz



Yunjie Tong wrote:


Hi freesurfer experts,




I have a single subject anatomical data in freesurfer. If I know the 
 volume index of a point on the surface of the cortex ( from T1.mgz 
in  TkMedit), how can I find out the corresponding vertex index or 
the  vertex RAS in TkSurfer. Thanks. BTW, I am using matlab.




Thanks,




Yunjie



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Re: [Freesurfer] (no subject)

2008-12-22 Thread Doug Greve

how are you defining your ROI? Below is some info Im putting together on 
segmentations, parcellations, and labels. It's still pretty raw, but it 
might be useful to you.



Segmentation
 - each voxel has an index
 - index into lookup table (LUT), eg FreeSurferColorLUT.txt
 - only one index per voxel
 - surface or volume
 - binary segmentation (mask) - 0 and 1
Parcellation/Annotation
 - surface only ("surface annotation" is redundant)
 - each vertex has a name
 - inconvenient
 - cross-reference to FreeSurferColorLUT.txt
Label
 - a single segmentation/parcellation
 - surface or volume
 - text file with a list of 5 numbers for each vertex/voxel
 - 1. VertexNo (0-based, ignored for volume labels)
   2. X coordinate of voxel/vertex in tkreg space
   3. Y coordinate of voxel/vertex in tkreg space
   4. Z coordinate of voxel/vertex in tkreg space
   5. Statistic (not used by all programs)

Color Table:
 - List of segmentations/parcellations
 - Each row has 6 columns:
   1. Index
   2. Name (no spaces)
   3. Red   (0-255)
   4. Green (0-255)
   5. Blue  (0-255)
   6. Statistic

Convert a set of labels into an annotation/parcellation:
mris_label2annot

Convert an annotation/parcellation to a set of surface labels:
mri_annotation2label

Convert an annotation/parcellation to a surface segmentation:
mri_annotation2label (name misleading)

Convert a single ROI in a volume or surface segmentation into a volume
or surface label:
mri_cor2label (surface or volume labels, name misleading)

Convert a set of volume labels into a volume segmentation:
mri_label2vol

Convert a set of surface labels to a surface segmentation:
No single program. Use mri_label2annot, then mri_annotation2label

Convert a label on one subject to a label on another subject:
mri_label2label (surface or volume labels)

Convert a surface segmentation to an annotation:
mris_seg2annot

Merge two or more labels together:
mri_mergelabels

Create a label from a bounding box:
bblabel

Merge an annotation/parcellation with a volume segmentation to create
a new volume segmentation: mri_aparc2aseg

Create a binary segmentation (mask) from a segmentation:
mri_binarize (use --match)

Create surface labels from thresholded surface activation maps:
mri_surfcluster

Create an annotation/parcellation from thresholded surface activation maps:
mri_surfcluster

Create a surface segmentation from thresholded surface activation maps:
mri_surfcluster

Create volume labels from thresholded volume activation maps:
mri_volcluster

Create a volume segmentation of activation clusters:
mri_volcluster




Gabriel GLZ wrote:


hello
 
in the case that i have a ROI and i don't know wich voxeles are in 
there, or the coordenates of those voxeles, i want to create a 
specific label that only contains those voxeles, how can i do that??'
 
 
 






Acceso muy fácil al uso compartido de fotos con Fotos de Windows 
Live™. Arrastrar y colocar 





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[Freesurfer] surface cluster area bug

2008-12-22 Thread Doug Greve



Hi Y'all, I've recently found an error in the way that mri_surfcluster 
reports the area of a  cluster when using a group surface such as 
fsaverage. The bottom line is that the area reported is about 25% too 
big. However, the cluster-wise p-values reported by mri_surfcluster 
based on simulations from mri_glmfit ARE NOT AFFECTED. Volume clustering 
is unaffected.


I have fixed this bug in the Martinos Center "dev" environment. Part of 
this fix is to make old versions of mri_glmfit simulation incompatible 
with new versions of mri_surfcluster (and vice versa) for surfaces (ie, 
mri_surfcluster will exit with an error or will crash -- either way, it 
will not complete), as this could generate erroneous p-values. We will 
be propagating the fix to our stable version after the holidays, and 
make new distributions available.


More info and updates can be found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface

As always, sorry for the bug.

doug

ps. On the brighter side, I discovered this bug while implementing 
gaussian random field (GRF) corrections for multiple comparisons, so 
soon you will be able to run GRF in seconds instead of running monte 
carlo simulations over a weekend.






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Re: [Freesurfer] unpacking err runs

2009-01-05 Thread Doug Greve


Try adding  -unpackerr

Adrienne McCallister wrote:


Hello,

I am unpacking recent functional data and during a function run we 
needed to stop it early and so now when I view it in unpacksdcmdir, it 
has a err next to the run. Since those runs are typically skipped when 
unpacking, is it possible to override that and download the file 
anyway? Any help would be appreciated.


Sincerely,

Adrienne



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Re: [Freesurfer] Problem with post-spm registered data

2009-01-05 Thread Doug Greve

Hi Dave, I'm not sure where to begin with this. Can you give more info? 
In particular, you might look at 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues 
efficiently.


doug

Dave Brohawn wrote:


Hello,

Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in
tkmedit seemed to be shifted inferiorly in the coronal view by a wide
margin (an inch or so), leaving no functional activation in the top of the
cortex, even when set at an extremely low threshold.

When running the fMRI scan, we checked our slice prescription and ensured
the area of view covered the entire cortex. We also checked the raw data
output during the scan in the viewing window, and functional activity was
present.

After running the unpacking and recon-all processes, I ran the pre-proc
command and spm-register, and viewed the output using tkregister2. The
registered functional data matched up beautifully with the underlying
anatomy, and went right to the top of the cortex in the coronal view.

We ran our analysis using the appropriate paradigm files (has worked
without fail for our previous subjects) and there is no functional
activity in the top inch or so of the cortex whatsoever.

Please let me know if you have an answer to how this could have happened.

Dave Brohawn
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Re: [Freesurfer] vertex/talairach coordinates

2009-01-05 Thread Doug Greve


yes, it is

Bruce Fischl wrote:

actually Doug can confirm, but I think the average surface RAS are 
already Talairach coords

On Wed, 24 Dec 2008, Nick Schmansky wrote:


Corey,

I'm not 100% sure how to do this but a starting point is to use
mris_info on the surface file you are getting coordinates from, like:

mris_info rh.inflated

and get the surfaceRAS to talaraiched surfaceRAS matrix, and use that in
matlab to do your conversions.  Of course I'd check a few of them
against what you see in tksurfer.

Nick

On Tue, 2008-12-23 at 12:34 -0500, Keller, Corey J. wrote:


Hi Freesurfers,

  I have a list of 50 vertices picked from an average subject's 
inflated brain
in mne_analyze and would like to find the talairach coordinates for 
each of
these vertices. Is there a more efficient way to do this than to 
load tksurfer

and find these vertices by hand? Thanks again.

-Corey

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Re: [Freesurfer] questions about region-wise analysis data

2009-01-05 Thread Doug Greve




Siddharth Srivastava wrote:


Hi all,
 I am trying to understand the --surf flag in the mri_glmfit
command, and the 2 parameters that follow it. The tutorial mentions
--surf average lh .
1) what should "average" contain? should it point to the average of
the population, of fsaverage, or is it just a flag?


This is the name of the average subject as created by 
make_average_subject. If you did not make an average subject, then use 
fsaverage.



2) lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files.


Just the hemisphere



If i am doing a group analysis of a measure (say, thickness), and i have
smoothed thickness maps registered to a population specific template in
a subdir, how should i specify --surf and subsequebt parameters?


The input is specified with with --y. The --surf just tells glmfit that 
it is a surface so that it can compute the FWHM appropriately.




Further, i also get an error saying --C command not found (for the 
contrast vector).

why is this happenning?


Can't say without the cmd line, but I'm guessing you have a rouge space 
in your script




best regards,
sid.

On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky 
mailto:ni...@nmr.mgh.harvard.edu>> wrote:


Sid,

A group analysis can be performed from the command-line using
mri_glmfit
directly.  See this tutorial:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

You can use a different average subject, other than fsaverage,
although
it doesnt improve an analysis to use a subject from your group.  Also,
you can create a symlink from $FREESURFER_HOME/subjects/fsaverage to
your SUBJECTS_DIRS, to spare having to copy the data.

Nick


On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote:
> Hi Nick,
>  Thanks, It was my mistake. It works exactly as you say.
> I still have to look at qdec documentation, but could i ask if it is
> possible to perform the group analysis in a batch mode, without
> the GUI, i.e ?
>
> regarding the movement of data, the first time i did it, i got a
> screen full
> of memory addresses and corresponding routines, followed by a
crash (
> exit from wish, back to shell). I am not able to replicate it, seems
> to work
> now.
>
> Also, is it possible to register everything to a different surface,
> other
> that fsaverage.. for example to one of the subjects? Can this be
> located
> outside the relative paths reachable via $SUBJECTS_DIR ? In
fact, can
> fsaverage be located outside? For the processing i did, i had to
copy
> the fsaverage as one of the subjects, so that it can be located
> within
> the current context of $SUBJECTS_DIR .
>
> Thanks again, for the timely help.
> sid.
>
>
> On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky
> mailto:ni...@nmr.mgh.harvard.edu>>
wrote:
> Sid,
>
> The .mgh files, in the case of the commands you ran, store
> surface data
> corresponding to the 'fsaverage' subject.  So you would
first
> load the
> inflated surface for fsaverage (tksurfer fsaverage lh
> inflated), then
> you would use the Load Overlay menu option to load the .mgh
> file(s) you
> created.  You probably will have to adjust the color
> thresholds (View-
> >Configure->Overlay).  For the lgi data, you can use:
>
> recon-all -s subj -qcache -measure pial_lgi
>
> which will sample the subjects lgi data to the fsaverage
> surface, at
> which point you could average that (although typically a
> statistical
> analysis is performed on the set of subjects sampled to
> fsaverage, see
> out group analysis slides and tutorial pages).
>
> You should be able to move subject data around to other
> directories
> without any problems.  Does tksurfer really halt after that
> 'not in
> scripts dir' message?  That is a common message and not an
> error.  Can
> you open tksurfer for the sample bert subject?
>
> Nick
>
>
>
>
> On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava
wrote:
> > Hi Nick,
> >  I finally got a chance to use the sequence of
> command
> > that you had provided below. In continuation of this
thread:
> >
> > a) The output of using the command mentioned in reply 2)
> below
> > is an MGH file (and not faces/vertices combination)?
How is
> it
> > possible to get a smoothed surface
> > that i can

Re: [Freesurfer] reg-feat2anat failed

2009-01-06 Thread Doug Greve

Hi Xin, I'm not sure what's going wrong here, I think I need more info. 
Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?


doug


Wang, Xin wrote:


hello, Freesurfer group,

I try to use registration.mat files of FSL/FEAT routines, instead of 
anat2example_func.bat, to register the orig.mgz and 
example_func.nii.gz with the thinking that using initial_highres in 
FEAT may improve the reg. However, tkregister2 catastrophically failed 
to register two brains when I use --fsl flag. Modifying header of 
example_func with mri_convert does not solve the problem. I will 
appreciate any suggestion on using .mat file for registration.


second question: what is the best registration of example_func and 
orig.mgz? In another word, what should I check besides things in the 
FS tutorial when I check/modify the registration in tkregister2? Is 
there golden reference points I can use?


Thank you in advance for any suggestion.

Xin wang



-Original Message-----
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:26 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed

There is a flag in the nifti header saying whether the qform or sform
are valid, and it looks like your scripts do not set this flag. You can
use mri_convert (the freesurfer program). This will create valid files
that can be read into any program.

doug

Wang, Xin wrote:

> Thank you very much for your quick reply, Dr. Greve. I asked our
> institutional MRI center for correct information on qform and sform
> since the header of nifti files are created by their scripts. But I do
> not know what they can do to fix this problem. I will appreciate if
> you have any further suggestion on how to do the registration without
> the information on qform and sform in case I can not get them. Does
> convert to ANALYZE format or manually correct in tkregister2 work?
>
> Thank you again,
>
> Xin
>
>
> -Original Message-
> From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 12/15/2008 1:09 PM
> To: Wang, Xin
> Cc: freesurfer
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
> Hi Xin, the problem is that neither the sform nor the qform are valid.
> Did the message below not appear when you ran tkmedit?
>
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
>
> Fix that, and everything will work fine.
>
> doug
>
>
> Wang, Xin wrote:
>
> > Hello, Freesurfer group,
> > I am registering the fMRI results to surface using reg-feat2anat (v
> > 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> > catastrophically failed in the subject space, but worked fine in the
> > standard space. The orientations of example_func.nii.gz in the subject
> > space are flipped in any view. I use the tkmedit to view the
> > example_func, and found the orientation is wrong. It seems Freesurfer
> > can not read nifti header correctly. I attach the reg-feat2anat log
> > file and an example_func.nii.gz.
> > I found the following message from Freesurfer email list.
> > 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html

> > Does Freesurfer have a solution for this type of problems by now?
> >
> > Thank you in advance,
> >
> > Xin
> >
> 
>

> >
> >___
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> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> 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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Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

2009-01-06 Thread Doug Greve



You can use feat2surf (or mri_vol2surf directly), this will create 
something like lh.zstat1.mgh. You can then use

lhz1 = MRIread('lh.zstat1.mgh');

doug


Yunjie Tong wrote:

Hi 

I was able to view the statistical maps (from FSL) on the subject's 
surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I would 
like to see the same image in Matlab. I could show the subject's 
surface as well as the the cortical parcellation in Matlab by 
modifying the functions freesurfer_read_surf.m and read_annotation.m. 
I do not know how to overlap the statistical map onto the surface 
then. Is there any Matlab function I can use? Thanks.


Best,

Yunjie




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Re: [Freesurfer] Problem with post-spm registered data

2009-01-06 Thread Doug Greve

There is no gold standard. Mainly just visualizing it with the surfaces 
and making sure the surfaces line up with the bright and dark folds in 
the EPI, as it says in the tutorial.

doug

Wang, Xin wrote:

Sorry for asking same question here again. I asked Dung before holiday 
about the criteria of good registration of fMRI and thickness map. 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html
I paste my question again: what is the best registration of 
example_func and orig.mgz? In another word, what should I check 
besides things in the FS tutorial when I check/modify the registration 
in tkregister2? Is there golden reference points I can use?

I will appreciate if Dave could give more explanation or references of 
"beautiful match between functional and structural images".  

Thank you in advance.

Xin Wang

----
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:03 PM
To: Dave Brohawn
Cc: jroff...@partners.org; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with post-spm registered data

Hi Dave, I'm not sure where to begin with this. Can you give more info?
In particular, you might look at
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues
efficiently.

doug

Dave Brohawn wrote:

>Hello,
>
>Josh Roffman and I recently ran an fMRI scan. Our subject's data 
viewed in

>tkmedit seemed to be shifted inferiorly in the coronal view by a wide
>margin (an inch or so), leaving no functional activation in the top 
of the

>cortex, even when set at an extremely low threshold.
>
>When running the fMRI scan, we checked our slice prescription and ensured
>the area of view covered the entire cortex. We also checked the raw data
>output during the scan in the viewing window, and functional activity was
>present.
>
>After running the unpacking and recon-all processes, I ran the pre-proc
>command and spm-register, and viewed the output using tkregister2. The
>registered functional data matched up beautifully with the underlying
>anatomy, and went right to the top of the cortex in the coronal view.
>
>We ran our analysis using the appropriate paradigm files (has worked
>without fail for our previous subjects) and there is no functional
>activity in the top inch or so of the cortex whatsoever.
>
>Please let me know if you have an answer to how this could have happened.
>
>Dave Brohawn
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>
>
> 
>

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Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

2009-01-06 Thread Doug Greve

you'll only get the vertices. If you multiple those dims together, 
you'll get the number of vertices in the subject's surface, so just 
reshape it to 1d


doug

Yunjie Tong wrote:


Thanks Doug,

However, I do not know how to interpret the data. For example, my 
lhz1.vol has dimensions of 1x9022x17. What does that mean? I am 
looking for the vertex and faces, with which I could display them in 
Matlab using patch. Do I miss something? Thanks.


Best,

YJ


On Jan 6, 2009, at 12:44 PM, Doug Greve wrote:



You can use feat2surf (or mri_vol2surf directly), this will create 
something like lh.zstat1.mgh. You can then use

lhz1 = MRIread('lh.zstat1.mgh');

doug


Yunjie Tong wrote:

Hi 

I was able to view the statistical maps (from FSL) on the subject's 
surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I 
would like to see the same image in Matlab. I could show the 
subject's surface as well as the the cortical parcellation in Matlab 
by modifying the functions freesurfer_read_surf.m 
and read_annotation.m. I do not know how to overlap the statistical 
map onto the surface then. Is there any Matlab function I can use? 
Thanks.


Best,

Yunjie




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Re: [Freesurfer] Parameter comparison in native vs. template space

2009-01-06 Thread Doug Greve




Christine Ecker wrote:


I would like to export cortical thickness measures and compare the data
across subjects in a vertex-by-vertex fashion.

Please could you confirm that similar functions such as mri_glmfit are based
on the parameters in template space e.g. lh.thickness.fsaverage.mgh and not
on the parameters in native space e.g. lh.thickness.
 


yes


So for a group comparison I would have to export the files in template space
(e.g. lh.thickness.fsaverage.mgh) and could then map the output back onto
the template?
 

not sure what you mean, the thickness.fsaverage.mgh is already in the 
template space



Also, why are the parameters not the same in native and template space?
 


Not sure what you mean. Can you give an example?


Finally, in order to compare groups on the basis of the parcellated regions
(e.g. lh.aparc.stats). Are parameters such as area, volume, curvature etc
comparable across groups or would they still have to be corrected for
whole-brain volume?
 

If you are going to correct for brain or head size, then you'd do it for 
volume, thickness, and surface area measures, but not necessarily curvature.


doug


I would be very grateful if you could help me further.

Thank you!

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Re: [Freesurfer] How can I convert an individual subject's mask to the group average space

2009-03-22 Thread Doug Greve


On Sun, 22 Mar 2009, Avram Holmes wrote:


All,

I have generated a mask of the cingulate regions for each of my participants 
from their aparc+aseg.mgz files (see attached image) and I would like see how 
these masks overlay with the group average brain I have generated for my 
study. Is there a simple way to transform a mask from an individual subjects 
space to the group average volume space? I made my group average with the 
make_average_subject command.


You can create a mask of the cingulate with mri_binarize --match XXX,
then convert that into the average space with mri_vol2vol (for
command-line ops see how the aseg is done in make_average_subject),
then concatenate all of your masks together with mri_concat, adding
--mean to compute the mean. The value at each voxel will then be the
fraction of your subjects that had a cingualte mask at that voxel. You
can display this as an overlay, or you can threshold it to turn it
back into a mask.

In a related question is it possible to generate a group average 
aparc+aseg.mgz file? I can see the surface labels in the average and the 
aseg.mgz cortical labels. However, I don't know of a way to generate the 
aparc+aseg.mgz file.


I did write software to do this, but it turned into a real
mess. Cortex is so thin and the location of the indivdual cortical
regions so variable, that the final map ended up with all kinds of
strange holes (a good advertisement against talairach!). If you just
want it for display, you should be able to run "mri_aparc2aseg --s
avgsubject --volmask", but this won't reflect the actual labels from
your group of subjects.

doug



Thanks for any help you can offer,
Avram




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RE: [Freesurfer] merging rh and lh surfaces

2009-03-22 Thread Doug Greve

you can get something like what you want with

cd $SUBJECTS_DIR/subject
mri_binarize --i mri/ribbon.mgz --min .0001 --o mri/tmp.mgh
mri_tessellate mri/tmp.mgh 1 surf/lh.both
mris_smooth -nw surf/lh.both surf/lh.smboth
tksurfer subject lh smboth

Note that eventhough you call it "lh" it has both hemis. "lh" is just
to fool freesurfer into thinking it is a hemi.

doug

On Sun, 22 Mar 2009, Bruce Fischl wrote:

I see. Sorry, we don't have any easy-to-use tools for creating a single pial 
surface. You could change the value in the filled.mgz so that lh and rh are 
the same and try tesselating/deforming it. I've done this in the past, but 
you have to mess around a bit to get it to work.

cheers,
Bruce

On Fri, 20 Mar 2009 s...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 I am trying to create a volume conductor of human brain for FEM based
 source reconstruction. A nice surface of full pial (and other compartments
 like WM) layer is supposed to generate 3D FEM mesh by means of a meshing
 tool.

 Cheers,
 Seok

>  can you tell us why you want such a thing? I have generated them before,
>  but mostly for special-purpose applications. It's not something we
>  routinely do
>  On Fri, 20 Mar 2009 p...@netfilter.com.br wrote:
> 
> >  I think Bruce or Douglas can explain better.
> > 
> >  However, the reason for both hemispheres being separated is that you

> >  need to mantain an S2 topological space.
> > 
> > 
> >  Sent from my Nokia phone @E71

> >  -Original Message-
> >  From: s...@nmr.mgh.harvard.edu
> >  Sent:  19/03/2009 19:07:48
> >  Subject:  [Freesurfer] merging rh and lh surfaces
> > 
> >  Hi,
> > 
> >  I would like to have a single surf file that composed of both right 
> >  and

> >  left pial surf. Is there a way to do it in freesurfer?
> > 
> >  Best.

> >  seok
> > 
> > 
> > 
> 
> 
> 

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Re: [Freesurfer] determining sizes of clusters on surface data

2009-04-02 Thread Doug Greve



Sorry, I have not used this toolbox much. Maybe Don can chime in.

doug


On Fri, 3 Apr 2009, Zhong Jidan wrote:


Hi,

I was trying to figure out if there is any way to determine the exact
size at which clusters becomes significant given a specified
significance on the surface data.

Then i found there is a subject talking about this:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.html

In that talk,Don Hagler mentioned Keith Worsley's "Random Field
Theory" method 
(http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m)
can be used to directly (in seconds) estimate the cluster size
thresholds given:
..total surface area
..number of vertices
..fwhm smoothness.
function [cluster_threshold,peak_threshold] =
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval);
*> % alpha: corrected p-value
*>* % {default = 0.05}
*>* % pval: uncorrected p-value
*>* % {default = 0.001}

*I tried this function, and it does give me a cluster size with mm^2,
say 100 mm^2.  But I don't know whether this is the right thing to do.

As I'm doing some statistical analysis using GLM, so I also try the
method from Keith Worsley's statistical toolbox, then I can get the
cluster's No. of vertices and the corrected p-value(alpha=0.05) for
the cluster.

Here is one example:

 clusid  nverts  resels P
---
  1  2205  18.2781  2.1299e-06
  2   208  1.421050.013359
  3   127  1.155330.026747
  458   1.04430.036658
  5 5 0.519762 0.20884
  6   105 0.464429  0.2571

The thing I don't understand is , if we are looking for a cluster size
threshold, then we can say that, the clusters above that threshold
size is what we want to keep. And also, the p-value of the clusters
above that threshold size should
be below alpha we set, say 0.05. But when checking the tale above, the
first four clusters' p- value is smaller than 0.05, then we should
keep it. But according to the no. of vertices, we can caculate the
cluster size in mm^2. Then the 4th
cluster size is obviously below 100mm^2, the threshold we found using
the function fs_calc_cluster_thresh. Oppositely, the 6th cluster has a
large no. of vertices and its cluster size is above 100mm^2, while
it's
not kept because its p value is above 0.05.

I know what happened here is because of the 'resels', but it really
confuse me which one is the right one. Since you said we can use the
function, then why is the result  conflicted with each other?

Could you tell me what's wrong here or what did I miss ?

Thanks
a lot,

Jidan



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RE: [Freesurfer] Measuring cortical thickness with high resolution data

2009-04-06 Thread Doug Greve



Falk,  it looks like that file was somehow converted to DOS. try:

dos2unix recon-all
chmod a+x recon-all

then re-run

doug


On Mon, 6 Apr 2009, Falk Lüsebrink wrote:


Hi Nick,

I tried using your modified recon-all today but as soon as I try to process any 
data I receive following error message:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].

Also it doesn't matter at all which flags I add to recon-all or if I don't use 
any flags at all, the error is the same. The unmodified recon-all performs well.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

There are no plans in the near future, but in the long term we'd like to remove 
the dependence on conforming the data.

It just occurred to me that you could have the best of both worlds:
first run your data through the normal stream (conforming) up through 
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same 
resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask, 
which would save hours of work.  If i get few minutes i will try this.

You can copy that recon-all over top your existing v4.x freesurfer installation 
(attached again for the list).

Nick


On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:

Hi Nick,

Thank you very much. I'll have to look into that and try to process some other 
volumes which might work a bit better, with less manual intervention.

Are there any plans to improve Freesurfer in the (near) future so that hires 
data can be processed within the currently available stream?

Regards,
Falk

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 01, 2009 7:53 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Measuring cortical thickness with high
resolution data

Falk,

Attached is a modified recon-all script where I've added a -hires switch to 
force the stream to not conform the data to 1mm^3, and to not use the atlases.

Note that you should add the -clean flag to delete any work that had been done 
prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).

However, in working with the .8mm data that you sent me, working with hires 
data will require quite a bit of manual intervention due to the fact that the 
atlases normally used cannot be used.  The first problem occurs in 
skull-stripping, where quite a bit of dura and skull remains, and seems to have 
intensity values close to gray matter.  This would have to be manually erased 
on each of the slices.  If it is not erased (I did not do this because of the 
amount of time required), then the wm.mgz file, which is what is tessellated to 
create the initial surface, will be very wrong (it tessellates the garbage 
surrounding the gray matter).

See also Bruce's prior posting on the problems of working with hires data in 
freesurfer.

Nick


On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:

Hi Freesurfers,



Iÿÿm trying to evaluate the usefulness of high resolution scans
acquired at 7T with an isometric voxel size of .6mm for the
measurement of cortical thickness. The inhomogeneities are taken
care of by dividing the scans with another scan of another sequence,
so they are not an issue anymore.



My problem is that Freesurfer usually conforms the voxel size to 1mm
which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for
the recon-all process to avoid the conformation and to skip the
subcortical segmentation, but another problem arises while using
these flags.



The error I receive is occurring after the WM Segmentation and
states as follows:



#

#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009



 cp wm.mgz wm.seg.mgz





 mri_segment -keep brain.mgz wm.seg.mgz



preserving editing changes in output volume...

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

computing class statistics for intensity windows...

WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]

GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]

setting bottom of white matter range to 77.9

setting top of gray matter range to 89.4

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

using local geometry to label remaining ambiguous voxels...



reclassifying voxels using Gaussian border classifier...



removing voxels with positive offset direction...

smoothing T1 volume with sigma = 0.250

removing 1-dimensional structures...

thickening thin strands

20 segments, 4813 filled

10270 bright non-wm voxels segmented.

5589 diagonally connected voxels added...

wh

Re: [Freesurfer] Masking brainmask based on surfaces

2009-04-06 Thread Doug Greve



I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,

tkmedit subject orig.mgz -seg ribbon.mgz

aparc+aseg is suppossed to inherit the cortex from ribbon.mgz

doug




On Mon, 6 Apr 2009, Martin Kavec wrote:


Hi Dough,

this data were analyzed using 4.0.4. So indeed it not the latest, which I am
running normally. From which version has this been fixed, so I can check,
before re-runing. From which point should I rerun the analysis.

Thanks,

Martin

On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:

This looks like a problem we had with an older version. What version of
freesurfer are you running?

Martin Kavec wrote:

Hi,

I am trying to mask a non-brain tissue left by watershed based on the
cortical surfaces. I found that all what I need to be left is in
aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and
used FSL to binarize aparc+aseg and mask the brainmask. I found that at
many places the results is too conservative and too much of the GM is
missing, see the attached images, and particularly the temporal lobes.

Is there a better approach to what I am trying to do and what could be
the explanation to the results I get.

Thanks,

Martin






--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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Re: [Freesurfer] Masking brainmask based on surfaces

2009-04-06 Thread Doug Greve



but you are using aparc+aseg to generate the mask, so if aparc+aseg is
perfect, the mask should be as well. Do the mask and aparc+aseg match?



On Mon, 6 Apr 2009, Martin Kavec wrote:


Doug,

ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces ?h.white.

Thanks,

Martin

On Monday 06 April 2009 22:17:18 Doug Greve wrote:

I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,

tkmedit subject orig.mgz -seg ribbon.mgz

aparc+aseg is suppossed to inherit the cortex from ribbon.mgz

doug

On Mon, 6 Apr 2009, Martin Kavec wrote:

Hi Dough,

this data were analyzed using 4.0.4. So indeed it not the latest, which I
am running normally. From which version has this been fixed, so I can
check, before re-runing. From which point should I rerun the analysis.

Thanks,

Martin

On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:

This looks like a problem we had with an older version. What version of
freesurfer are you running?

Martin Kavec wrote:

Hi,

I am trying to mask a non-brain tissue left by watershed based on the
cortical surfaces. I found that all what I need to be left is in
aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz
and used FSL to binarize aparc+aseg and mask the brainmask. I found
that at many places the results is too conservative and too much of the
GM is missing, see the attached images, and particularly the temporal
lobes.

Is there a better approach to what I am trying to do and what could be
the explanation to the results I get.

Thanks,

Martin






--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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RE: [Freesurfer] tksurfer Load Group Descriptor File error

2009-04-07 Thread Doug Greve



Are you loading the one created by mri_glmfit (in the output
directory)?

doug



On Mon, 6 Apr 2009, Jeff Sadino wrote:



Thank you for the advice Sid.  I added those lines, and now my errors 
disappear, but I still get a blank screen where there should be a scatterplot.  
Is this a graphics issue with my hardware, or do I need to do something 
differently?

This is my fsgd file:
GroupDescriptorFile 1
Title try1
MeasurementName thickness
Class nc circle red
Variables Age
Input 060017_HG01 nc .5
Input 060023_F01 nc .8
Input 060024_HG01 nc .1
Input 060025_HG01 nc .5
...
...

The screen that pops up has thickness on the y-axis, but a range of only 0-1 and Age on 
x-axis with range 0-1.  My ages were "real" (50.8, 40.8, 50.1, etc.), but I 
changed them to between 0 and 1 to see if that helped, but no good.

Thanks in advance for your help,
Jeff Sadino

Date: Thu, 12 Mar 2009 18:52:45 -0700
Subject: Re: [Freesurfer] tksurfer Load Group Descriptor File error
From: sid...@gmail.com
To: jsad...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

Class ctrl should be followed by marker and color specification (Class ctrl 
circle red, for e.g). ditto
for cd .

sid.

On Thu, Mar 12, 2009 at 6:37 PM, Jeff Sadino  wrote:






Hello,

Can someone help me get scatterplots of my data?  I am using freesurfer 3.0.5.  
I have ran these commands:

mris_preproc  --fsgd try1.fsgd --target fsaverage --hemi lh --meas thickness 
--out lh.try1.mgh

mri_surf2surf  --hemi lh --s fsaverage --sval lh.try1.mgh --fwhm 10 --tval 
lh.try1.fw.mgh
mri_glmfit  --y lh.try1.fw.mgh --fsgd try1.fsgd dods --C try1.mtx --surf 
fsaverage lh --glmdir lh.try1.dir
tksurfer fsaverage lh inflated -annot aparc.atlas2005_simple -overlay 
lh.try1.dir/try1.mtx/sig.mgh


Then selected a vertex, then File->Load Group Descriptor File and selected 
try1.fsgd, but I get this error:

WARNING: Marker for class ctrl was invalid.
WARNING: Color for class ctrl was invalid.
WARNING: Marker for class cd was invalid.

WARNING: Color for class cd was invalid.

This is try1.fsgd:

GroupDescriptorFile 1
Title try1
MeasurementName thickness
Class ctrl
Class cd
Variables Age
Input 040004_P02 ctrl 55.18
Input 050046_S02 ctrl 37.45

...
...
Input 070073_S01 cd 20.54
Input 070114_OGM01 cd 46.03



I also tried with lh.try1.dir/y.fsgd, but get a similar error:

INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR

INFO: ignoring tag SynthSeed
INFO: gdfRead: reshaping
WARNING: Marker for class ctrl was invalid.
WARNING: Color for class ctrl was invalid.
WARNING: Marker for class cd was invalid.
WARNING: Color for class cd was invalid.


y.fsgd looks like this:

GroupDescriptorFile 1
Title try1
MeasurementName external
Tessellation surface
PlotFile /data/Jeff/glmtut/pass5/try1/lh.try1.fw.mgh
DesignMatFile fsgd.X.mat dods
ResidualFWHM 22.331472

Class ctrl
Class cd
Variables Age
Input 040004_P02 ctrl 55.18
Input 050046_S02 ctrl 37.45
...
...
Input 070073_S01 cd 20.54
Input 070114_OGM01 cd 46.03
Creator  mri_glmfit
SUBJECTS_DIR /share/apps/freesurfer/subjects

SynthSeed1237057379

In both cases, a graph pops up, but it is blank.  Thank you in advance for your 
suggestions,
Jeff Sadino

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Re: [Freesurfer] mri_glmfit-sim bug?

2009-05-31 Thread Doug Greve



Is this for a permutation test? Sorry, this is my fault. I've put a
new version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
that should fix the problem. Can you test it out?

thanks

doug



On Mon, 1 Jun 2009, Georg Homola wrote:


Hi All (and especially Doug, again)!

As one of the final steps I run mri_glmfit-sim for clusterwise correction
(of my random effects analysis btw.). It always worked well and I also
didn't change the command line recently, but since I updated Freesurfer to
the latest version (4.3.1) it quits with:

ERROR: you must supply --fwhm with --sim, even if it is 0

There is no flag like --fwhm for mri_glmfit-sim and when I try
--fwhm-override it won't change anything. Am I missing something?

Thanks
Georg



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Re: [Freesurfer] Re: 'Max' in sig.cluster.summary

2009-06-04 Thread Doug Greve


The sig.mgh is the input that creates the sig.cluster.mgh (and the
summary table).

doug


On Thu, 4 Jun 2009, Judith Segall wrote:


Doug.

Again, I am only asking about the sig.cluster.summary. This was a thickness
study, where monte-carlo simulations where used to correct for multiple
comparisons.  Why would the *max in column 2 of the sig.cluster.summary* be
derived from the sig.mgh and not the sig.cluster.mgh? Since, this report is
generated at the same time as the sig.cluster.mgh. (ClusterNo  *Max*
VtxMax   Size(mm^2)  TalX   TalY   TalZCWP  CWPLowCWPHiNVtxs
 Annot)

I only used the scatter plot as example as to why I has a question about how
to interpret the sig.cluster.summary.

- Judith


On Thu, Jun 4, 2009 at 11:51 AM, Douglas N Greve
wrote:



The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load
the FSGD and look at the scatter plot, the y-axis will be the thickness
value (assuming you're doing a thickness study:).

doug


Judith Segall wrote:


Doug and freesufer list.

 When I load the sig map in tksurfer i know that the CWP is displayed as
the -log(10)p; however, I am not asking about visualization or the CWP. The
newest version of the wiki does a great job in explaining the p values.  I
am only asking about the sig.cluster.summary report. It makes since that
"The Max is the vertex-wise maximum and is bounded below by the vertex-wise
threshold." But then what units is it in?

When I was not sure what the second column was I turned to visualization.
After, loading both the sig.cluster.mgh and the group descriptor file in
tksurfer and  then selecting a vertex in the region with the most
significance, which is  based off of the CWP, it displays a scatter plot.
The scatter plot does not have a label for the y-axis; however, the highest
point on the y-axis is similar to the max, in column 2,  of the
sig.cluster.summary report.  On the older wiki, there was a paragraph
describing how the y was thickness. But, the sig.cluster.summary report does
not have any labels for the second column. But, since the value was similar
to the y-axis I began to interpret it as thickness, but wanted to clarify
with the freesurfer team.

- Judith


On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve <
gr...@nmr.mgh.harvard.edu > wrote:

   It is the maximum vertex-wise -log10(p) found in the cluster. Why
   do you think otherwise? You should be able to load the sig map
   into tksurfer and go to that vertex to find out.

   doug

   Judith Segall wrote:

   Thanks, for you responses Doug and Pratap. But, both of your
   responses need more clarification, because I believe that we
   are not all referring to the same 'max'.

   Doug:

I understand that when I display the sig.cluster.mgh that the
   a CWP value of 0.0001 would be displayed as a 4 by the color
   bar in tksurfer, since it is the -log10(p). However, in this
   case, which is about the cluster growing summary, the
   -log10(p) of the CWP does not equal the Max. Max is -3.312 and
   the CWP is 0.08250. Or an additional example form another
   sig.cluster.summary, where the Max is -4.310 and the CWP is
   0.0192.
   ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ
CWP  CWPLowCWPHiNVtxs   Annot
 1   -4.310   40526376.78-12.0  -66.1
  5.40.01920  0.01750   0.02100   706  lingual

   In Pratap's email his answer to my question of what is the max
   in the CWP is,  "Yes thickness. The MAX indicates the maximum
   -log10(pvalue) in that cluster." Which, is stating that it is
   both the thickness and the pvalue. I really think that it is
   thickness measure, but need some clarification from mgh.

   So, is the Max in column 2 of the cluster growing summary
   report, from monte carlo simulations, thickness?

   Thanks,

   Judith S.

   On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve
   mailto:gr...@nmr.mgh.harvard.edu>
   >> wrote:

  It will be whatever you used as input. In this case, it is the
  -log10(p) value of the maximum in the cluster (not the
   thickness
  value).

  doug


  Pratap Kunwar wrote:

  Hi Judith,

  Yes thickness. The MAX indicates the maximum
   -log10(pvalue) in
  that cluster.

Hi all. After looking over our monte-carlo
results, I a
  simple question
  about the sig.cluster.summary output.

  Is the " Max" in column 2 below a measurement of
   thickness?
  thickness, is the correct interpretation the following:
  the most
  significant
  cluster is in the laterorbitofrontal region.

Re: [Freesurfer] export skull stripped images

2009-06-04 Thread Doug Greve



just

mri_convert brainmask.mgz brainmask.nii

doug





On Thu, 4 Jun 2009, Jose Luis Cantero Lorente wrote:


Dear Freesurfers,

is it feasible to save to nii the MR images after stripping the skull in 
Freesurfer? If so, please let me know how to do it.

Thanks in advance.

Best,
Jose

---
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Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cellular Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Spain -

Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] label2vol

2009-06-17 Thread Doug Greve



You can mri_convert the output specifying the output type as -odt
short. Sorry, don't have any easy way to change the slicing.

doug




On Wed, 10 Jun 2009, xfore...@ucla.edu wrote:


Dear Freesurfer experts,


I'm trying to convert the annotation file into (binary Analyze file),
I tried the command mri_label2vol and it seems to worked fine,
but I find out that the output file is in 32bit/vox resolution, and the 
program
I want to use to open the file doesn't support that and crashes everytime I 
try to open it. I was wondering if there's anyway to make the output file 16 
bit/vox instead? also the output file is in COR, is there anyway I can make 
it Axial?



Best,
Andy
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Re: [Freesurfer] Partial Volume Correction and wmparc.stats

2009-06-17 Thread Doug Greve



yes, it is



On Thu, 11 Jun 2009, Nasim Maleki wrote:


Dear Freesurfer developers,

I'm wondering whether the wmparc.stats is computed with a partial volume 
correction at the boundaries of the structures.


Thank you,
Nasim
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Questions on ROI Comparisons

2009-06-17 Thread Doug Greve



(1) probably using mri_segstats with "--annot fsaverage lh aparc" and
specifying the --y input to mri_glmfit as the "--i invol" and specify
a "--avgwf" output to get all the subjects.

(2) Yes, you would expected it. I'm not sure what it means if you
don't see it. Maybe a bug somewhere.

(3) You can smooth it with mri_surf2surf or mris_fwhm and specify a
label to smooth in. This will be similar to the full-brain
smoothing except at the edges.

doug


On Fri, 12 Jun 2009, Bruce Fischl wrote:

I'll leave 1-3 for Doug and Nick. As for 4, this is a QA step to make sure 
nothing failed in the spherical registration, or the segmentation/surface 
reconstruction in that region.


cheers
Bruce

On Thu, 11 Jun 2009 nmal...@mclean.harvard.edu wrote:




 Dear all,
  
 1-Is there a way to use mris_anatomical_stats
 to calculate mean ROI values on the re-sampled and smoothed individual
 subject data that is produced in the pre-processing step, rather than
 mapping the ROI back to each subjects’ space? If so what is the
 command?
  
 2-If you define a ROI where there is
 statistically significant difference (between 2 groups) at the group level
 on your average subject and then map the ROI back to each subject’s
 space and measure the mean value of say thickness in that ROI, should you
 expect to find the same significant difference between the groups that you
 are comparing? What does it mean if you don’t for some ROIs?
  
 3- Is there a way to smooth the vertices in a ROI similar to
 what is done at the preprocessing level?

 4- There is a comment
 on wiki (qdec, ROI analysis) that indicates the usefulness of mapping
 the ROI back to each ubject's space to 'check the integirty
 of your reults'. Could you please elaborate more on this? 
  
 Thank you,
 Nasim





--
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] Co-vary

2009-06-17 Thread Doug Greve



In this case you would have six regressors:
1. control-offset
2. hiv-offset
3. control-age
4. hiv-age
5. control-ed
6. hiv-ed

If you want to test group thickness "regressing out" the effect of age
and ed, then you would just set the contrast to:

1 -1 0 0 0 0 0

Note that this will test it at age=0 and ed=0, which you may or may
not want to do. Ideally, you would test them at some age/ed in the
range of your sample. A lot of people simply demean each covariate,
but this can bias the results depending upon who you add or
remove. Better to choose an age/ed level independent of your sample.

doug



On Sat, 13 Jun 2009, Jeff Sadino wrote:



Hello Freesurfers,

My apologies for this very basic question more about statistics than 
freesurfer, but I have not found an answer anywhere on the wikis, or the web 
(maybe it is too basic :-) )  I am interested in age-related effects of hiv and 
I wanted to covary for age and education in mri_glmfit.  For example, if my 
fsgd file is:

class control
class hiv
variables age ed
input subj1 control 40 13
input subj2 hiv 35 12
...
...

and I use dods, is my contrast matrix the place where I would tell it to 
covary?  Something like:
0 0-1 1   1 11 1
(y-int) (age slope)   (covary for age)   (covary for ed)

As always, thank you for your help,
Jeff

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Re: [Freesurfer] [Fwd: fsaverage to average7]

2009-06-18 Thread Doug Greve



This cmd is not going to work. I don't think we have a way to convert
between the two. Sorry,

doug





On Wed, 17 Jun 2009, Yigal Agam wrote:


Hi all,

Is there a way to convert results that I have on fsaverage to average7? I 
need to do that to be compatible with some average7 results that go into the 
same paper. When I use mri_surf2surf, activation is displaced. Any advice 
would be appreciated.


This is what I've done:
mri_surf2surf --srcsubject fsaverage --trgsubject average7 --sval [fsaverage 
file]--hemi lh --tval [average7 file]


Thanks,
Yigal


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Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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Re: [Freesurfer] from dicom to mgz

2009-07-17 Thread Doug Greve


we often have problems reading philips dicoms, not sure why.

doug




On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote:


Hi,

I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom 
files as the one attached to this message. However, Freesurfer reports that 
this file is not a dicom. It seems weird to me since it can be opened with 
MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is 
another Freesurfer command to covert these dicoms to mgz from the command line?

Thanks in advance.

Best,
Jose
---
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Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Spain -

Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/en/



--
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] thickness map

2009-08-19 Thread Doug Greve


Yes, this is what our group analysis tools do. You can find tutorials
on the wiki. You'll probably start with mris_preproc.

doug



On Thu, 20 Aug 2009, Feng-Xian Yan wrote:

> Hi,
>
>  Thank you for your responses before.
>
>
>
>  I have another problem want to solve. I check the number of vertex for all
> subjects, but I found that the number of vertex for each subjects and each
> hemispheres is different. Because I want to compare cortical thickness using
> vertex-by-vertex, I would to obtain the same vertex number.
>
> Therefore, have something to do to obtain the same vertex number, i.e.
> template the cortical thickness at each vertex for each subject on the
> fsaverage surface, or other methods?
>
>
>
> How can I do? Would you get me a hand?
>
>
>
> Thank you in advance!
>
>
>
> Feng-Xian
>
>
>
>
> 2009/8/18 Feng-Xian Yan 
>
>>
>> Thank s for your response.
>>
>> So, the coordinates are MNI coordinates, not Talairach coordinates.
>>
>>
>>
>> Thank you in advance.
>>
>>
>>
>> Feng-Xian
>>
>>
>>
>> 2009/8/18 Douglas N Greve 
>>
>>> The values in the asc file are in MNI305 space. You can see this in
>>> tksurfer with View->Configure->Information and select the mni305 button.
>>>
>>> Feng-Xian Yan wrote:
>>>

 Thank you for your response.

 So, you mean that I have to do "mris_convert" two times. One for
 lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates in
 lh.white.tal.asc file corresponds to the cortical thickness value in
 lh.thickness.asc file.


 But, the Tal coordinates in lh.white.tal.asc is difference from the
 result in the tksurfer tool box. That is to say, when I open this subject 
 by
 tksurfer, I look at the coordinate of the vertex Tal in the tksurfer tool
 box, and the coordinate is difference from the coordinates that obtain from
 the command ?mris_convert ?c lh.thickness lh.white lh.thickness.asc?.


 What do have some problems?


 Thank you in advance!


 Feng-Xian


  2009/8/18 Douglas N Greve >>> gr...@nmr.mgh.harvard.edu>>

You have convert the thickness file (lh.thickness) to ascii like
you did
with the surface (with mris_convert). You will then have two
files, and
the second file will have the thickness values.

doug

Feng-Xian Yan wrote:
   >
   > Hi,
   >
   > Sorry, I don't know what you mean. I know each lines is a vertex and
   > represent a Tal coordinate, but each lines only contain xyz, but not
   > contain cortical thickness value of these coordinates. That is
to say,
   > the following is
   >
   > Tal x Tal y Tal z
   >
   > -13.424789 -125.068245 12.671550 0
   >
   > What?s wrong do I think?
   >
   > Thank you in advance.
   >
   > Feng-Xian
   >
   > 2009/8/18 Douglas N Greve >>>
> >>
   >
   > Just convert the lh.thickness to ascii as well. Each line of the
   > xyz coords corresponds to a line in the thickness ascii
(each line
   > is a vertex).
   >
   >
   > doug
   >
   > Feng-Xian Yan wrote:
   >
   >
   > Hi,
   >
   > I try it again with you recommend me, but the produced asc
   > file (lh.white.tal.asc) only contain x, y, z
coordinates. (The
   > following shows that.)
   >
   >
   > #!ascii version of lh.white.tal
   >
   > 155006 310008
   >
   > -13.424789 -125.068245 12.671550 0
   >
   > -13.939213 -125.063232 12.714314 0
   >
   > -14.861158 -125.268639 12.404987 0
   >
   >
   >
   > But, I want to have cortical thickness value with Tal
   > coordinates. This file doesn?t satisfy our demand.
   >
   >
   > Our demand should contain two points.
   >
   > 1) Each vertex across the mantle was represented with an
   > estimated value of cortical thickness and these estimated
   > values of cortical thickness should have their coordinates.
   >
   > 2) We want to analysis the cortical thickness difference of
   > three groups, so we want to the cortical thickness value of
   > each vertex across each subjects should be matched. That
is to
   > say, the cortical thickness should superimposed on a
template
   > surface like fsaverage.
   >
   > Therefore, how do we do to obtain the asc file matching our
   > demands?
   >
   >
   > Thank you in advance.
   >
   >
   > Feng-Xian
   >
   >
   >
>>

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