Dear FS experts,
I try to look at correlation between thickness and performance. I run
mri_glmfit (using performance as covariate) and mri_glmfit-sim. After
this I get some significant clusters.
I would like to ask if I could get a correlation coefficient for these
clusters, or/and a regression pl
pretty modest at 3T
> although they are visible. I think control points would be your best bet.
>
>
> cheers
> Bruce
>
>
> On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
>
>> Hello Bruce. Thank you for your reply.
>>
>> I am not sure why the wm is too dark. Our
, Bruce Fischl
wrote:
> Hi Tanja
>
> why is the wm too dark? Can you tell us something about your data
> (population, coil, scanner, etc...)?
>
> cheers
> Bruce
>
> On Wed, 28 Mar 2012, Tetiana Dadakova wrote:
>
>> Hi Louis,
>>
>> thank you very much for
bly one or two control points carefully placed along the wm finger
> on voxels with the highest intensity (in the middle it looks like). Not
> sure what the other coronal slices look like, but you may want to do
> something similar on other slices.
> -Louis
>
>
> On Tue, 27 Mar
autorecon2-cp -autorecon3, then please check if any of the
> control points were placed in GM or really close to GM.
>
> Sita.
>
>
>
> On Wed, 7 Mar 2012, Tetiana Dadakova wrote:
>
>> Dear FS list,
>>
>> We started using FS 5.1 and encountered a problem with con
Hi Fidel,
The bvecs/bvals files should have 3/1 columns respectively (as opposed
to 3/1 rows that yours have). Could you try if transposing the entries
in your files help?
Tanja.
On Fri, Feb 17, 2012 at 12:29 PM, Fidel wrote:
> Dear all,
>
> I have tried to execute trac-all and I have found thi
nja.
On Tue, Feb 14, 2012 at 7:31 PM, Tetiana Dadakova wrote:
> I see, thank you :)
>
>
> On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
> wrote:
>>
>> PS: The info on what you need to set it here:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
>
: Read from DICOM header
> #
> set nb0 = 10
>
>
>
> On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
>
>> Dear Priti, Anastasia,
>>
>> Thank you for your help, I created bvec and bval files and it went fine.
>> But now I have another error in preprocessi
gt;>>.
>>>> I also attach a picture of my file tree and a track-all.log file.
>>>>
>>>> Thank you for your time and help,
>>>> Tanja.
>>>>
>>>> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
>>>> wrot
gt;
>> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki
>> wrote:
>>>
>>> Hi Tanja - The file is supposed to be created under
>>> $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
>>> /dmri/bvecs,
>>> this means that somethi
Dear list,
I try to run TRACULA pre-processing step and I get the following
error: /dmri/bvecs: No such file or directory.
I have a folder with reconstructed T1 data and a folder with raw dicom
DTI data. When I start trac-all -prep, it creates directory /dmri/,
but it doesn't create the bvecs fil
Dear FreeSurfer list,
I ran recon-all -bert -hippo-subfields, which finished without error.
Now I try to open it with freeview using:
cd $SUBJECTS_DIR/bert/mri
freeview nu.mgz \
-p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
-p-labels posterior_right_* posterior_Right-Hippocampu
Hi Maria,
Yes, you are editing aseg.mgz. After saving the segmentation, you should run
.
If you also added some control points, then you should run
Best wishes,
Tanja.
On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski
wrote:
>
> Hi,
>
> I am a relatively new user of Freesurfer and hav
Dear FreeSurfer list,
I was trying to edit wm surface by adding control points. After saving
them and re-running recon-all -autorecon2-cp -autorecon3, the control
points are still there, but wm is not edited (although cp worked in
other places for the same brain). The intensity there is around 95-
gt; given triangle of the mesh is more reflective of the mesh tesselation
> than an intrinsic property of that subject's brain (see previous posts
> regarding that as well).
>
> cheers,
> -MH
>
>
> On Wed, 2011-11-02 at 14:39 +0100, Tetiana Dadakova wrote:
>
.
> PubMed PMID: 21684724.
>
>
> 5: Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R. Correction for
> intracranial
> volume in analysis of whole brain atrophy in multiple sclerosis: the
> proportion
> vs. residual method. Neuroimage. 2004 Aug;22(4):1732-43. PubMed PMID:
&g
Dear FreeSurfer experts,
I have a question regarding pial area analysis.
What is commonly used as a nuisance variable to correct for brain size
difference between groups (e.g men vs women)? Can you suggest any
article where this is discussed or has been done?
Thank you,
Tanja.
__
Dear Doug,
Just wanted to ask you when approximately the fix will be ready? I
really looking forward to it, to be able to explain some results.
Thank you for your time and constant help,
Tanja.
On Fri, Aug 19, 2011 at 4:07 PM, Douglas N Greve
wrote:
>
> Hi Y'all, I recently found a bug in the
Dear Doug,
I am looking forward to laterality processing stream as well. Could
you please tell approximate release date for that?
Thank you,
Tanja.
On Tue, Sep 27, 2011 at 6:07 PM, Lena Palaniyappan
wrote:
> HI Doug
>
> Do we now have the means for computing point to point asymmetry difference
Dear list,
I would like to calculate mean and stdev of thickness group-wise.
Could you please give me a hint how to do it?
Thank you,
Tanja.
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Thank you Michael. I have more questions on this:
1. Is there a method to calculate if I have global difference in
thickness between groups?
2. How can I control for global thickness difference vertex-wise using
freesurfer?
Best wishes,
Tanja.
On Mon, Sep 5, 2011 at 7:42 PM, Michael Harms wrot
Dear list,
I have two question:
1. Is it possible to do the asymmetry analysis in FS, I mean to
compare left and right hemispheres within one group?
2. Is it necessary to somehow control for global abnormality of
thickness while looking at regional abnormality, e.g. if one group has
thinner brai
Thank you Doug,
One more question: what does the column Max mean in the table with
clusters' info?
Tanja.
On Fri, Sep 2, 2011 at 6:28 PM, Douglas N Greve
wrote:
> I'm not sure about #1, maybe BF can chime in.
>
> Tetiana Dadakova wrote:
>>
>> Dear FS list,
>
Dear FS list,
1. What does a label Thalamus Proper include? Is it the same as thalamus?
2. After correcting for multiple comparisons, I get a table of
clusters. I have several questions regarding this table: What do the
columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs
column: is it
Dear FS experts,
I have two questions:
1. In qdec.table.dat file I am specifying several continuous factors,
e.g factor1 and factor2. For some subjects factor2 is missing,
therefore I leave empty space in those cells. When I load a
qdec.table.dat into qdec, the whole line of the subject with miss
sk for the DODS vs DOSS choice.
Thank you, I appreciate you time and help,
Tanja.
On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova wrote:
> Thank you, Douglas.
>
> On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve
> wrote:
>>
>> Hi Tanja, you should use DODS and test for
Hi Julia,
After the skull strip was corrected, you should run:
recon-all -autorecon2 -autorecon3 -s Subject_name
this will create new surfaces based on new skull strip.
Tanja.
On Mon, Aug 22, 2011 at 6:47 AM, Julia Hill wrote:
> Hi Bruce
>
> I am new to freesurfer and im having a few issues
Dear list,
In qdec in "Measure" option I can choose either area or area.pial.
What is the difference between them?
Thank you,
Tanja.
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file in each
folder. Can it cause the problem?
Thank you,
Tanja.
On Wed, Jul 20, 2011 at 1:30 PM, Tetiana Dadakova wrote:
> Hi Nick,
>
> Unfortunately doesn't help. When I remove the folder
> qdec_project_archive from /tmp, and then try to Load Project File, a
> new qde
Dear all,
I have two groups of subjects, and I want to see a difference in
thickness between them controlling for age.
I couldn't find any information in the literature on how the subject's
brains in my groups develop with age. Therefore I can't tell whether
thickness as a function of age for both
Dear list,
Could you please recommend the literature about multiple comparisons
correction, especially about Monte-Carlo simulation.
Thank you,
Tanja.
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>
> n.
>
>
> On Tue, 2011-07-12 at 19:10 +0200, Tetiana Dadakova wrote:
>> When the Load Project is run, nothing is created in
>> /tmp/qdec_project_archive, and then the error appears in terminal
>> window.
>> The only files/folders I have in /tmp/qdec_pro
Hi Wang,
You can try
foreach s (subj1 subj2 etc)
mri_convert $s.nii $s.nii.gz
end
Hope it works,
Tanja.
2011/7/15 汪贵宏 :
> Hi Bruce,
>
> In our research,if there are 100 subjects,how can I process these data
> easily.For example，when I want to compare their thickness's difference，at
> f
at directory.
>
> n.
>
> On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote:
>> Hi Nick,
>>
>> I have Mac OS X 10.6.7.
>> Now I found the tmp folder, and can explain in more details what happens:
>> As I save the Project File, the qdec_project_archive/qd
before? Do you know what the
problem can be?
Thank you,
Tanja.
On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky
wrote:
> what is your operating system? linux and mac typically have a /tmp dir,
> unless you're running on a cluster?
>
> n.
>
> On Wed, 2011-07-06 at 15:46
Dear experts,
When I try to load a saved Project File, I get an error:
Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.
I do not have any /tmp subdirectory. Should it appear when I save t
Dear list,
I would like to install both 5.0 and 5.1 versions on my computer. But
I am not sure how exactly I should proceed after downloading the 5.1
(5.0 is already installed).
For example, how should I set FREESURFER_HOME, can it be the same for
both versions? Also, can I have my 5.0 in /Applica
Hi Sophy,
According to Qdec wiki page, you should also run
recon-all -s -qcache
This will create the pre-smoothed surfaces in surf/ directory.
Best wishes,
Tanja.
On Wed, Jun 29, 2011 at 3:16 AM, Sophy Zhu wrote:
>
> Hi Freesurfers,
>
> There existed an error "Error in Analyze: Couldn't open
Ok, now everything works. I just opened the file in terminal using
pico and saved it.
On Mon, May 23, 2011 at 9:43 AM, Tetiana Dadakova wrote:
> Thank you Nick,
>
> Now I have another error:
>
> Loading data table
> /Applications/freesurfer/subjects/group_analysis/qdec/qdec.tab
bottom of the file.
>
> n.
>
>
>
> On Sat, 2011-05-21 at 14:34 +0200, Tetiana Dadakova wrote:
>> Dear list,
>>
>> I am trying to load qdec.table.dat file using qdec, and get the following
>> error:
>>
>> Loading data table
>>
Dear list,
I am trying to load qdec.table.dat file using qdec, and get the following error:
Loading data table
/Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat...
QdecDataTable::Load: will attempt to open as Mac text file...
Number of columns: 3
fsid column:1
Number o
, Bruce Fischl wrote:
> Hi Tanja
>
> yes, there is really no visible extreme capsule white matter, I guess
> because it is so thin. If you are trying to fix the surfaces you will want
> to edit the wm.mgz though, not the aseg.mgz.
>
> cheers
> Bruce
>
> On Thu, 5 Ma
dit, in that same area, do you see an
>> error? Looking at your snapshot, it looks like it could be normal.
>>
>> On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova wrote:
>>
>>> Dear FreeSurfer list,
>>>
>>> When I look at inflated surface of my
Dear list,
Could you please recommend me the literature on non-linear volumetric
registration used in FS?
Also, is there a possibility to view talairach.m3z file?
Thank you,
Tanja.
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uding
> the structure name). Eg:
>
> cuneus 1722 1127 2145 1.835 0.411
> 0.160 0.072 45 5.1
>
> this one has:
> NumVert 1722 SurfArea 1127 GrayVol 2145
> ThickAvg 1.835
>
> doug
>
>
>
>
>
> Tetiana Dada
Dear list,
I was trying to find the values of volumes for different cortical
regions. What I found is the 4th column (called GrayVol) in
?h.aparc.stats file.
Although, the values don't really seem to be what I look for, as
values are too small (e.g. 0.5 mm^3 for cuneus).
Could you please guide me
Dear list,
I have a question regarding intensity non-uniformity correction using
N3 (as in Boyes et al, 2008).
Does anyone have experience of using it for improving cerebellum
segmentation, specifically distinguishing between white and grey
matter in cerebellum?
If yes, what are the best values fo
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using
Edit Segmentation Tool.
And my question is: how should I proceed after saving aseg.mgz? Should
I re-run autorecon2 with some options?
Thank you,
Tanja.
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Dear FreeSurfer list,
I try to open RB_all_2008-03-26.gca by typing
mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz
and get an error:
mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from RB_all_2008-03-26.gca...
readi
23, 2011 at 4:59 PM, Bruce Fischl
wrote:
> hmm, that is large, but the tiny one-voxel border you showed in your image
> wouldn't come close to explaining that. Do you want to upload the subject
> and we'll take a look?
> Bruce
>
>
> On Wed, 23 Feb 2011, Tetiana
#x27;re seeing are just the consequences of a voxel-based
> segmentation. The borders have to be voxelated. Note that much of this will
> be corrected in the volume calculation that performs a partial-volume
> correction.
>
> cheers
> Bruce
>
> On Wed, 23 Feb 2011, Tetiana Dad
Dear Freesurfer users,
For some of my subjects Freesurfer strongly overestimates hippocampus'
volume. Is there any way to fix the segmentation of hippocampus by
e.g. adding some control points (like for white matter here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)?
Thank yo
ou are interested, compute it's tal coords and if the x is negative
> assign it to one pool and if it is positive assign it to the other
>
> cheers
> Bruce
>
>
> On Wed, 16 Feb 2011, Tetiana Dadakova wrote:
>
>> Thank you, Bruce.
>>
>> Could you recomm
could use the Talairach x
> coordinate to try to differentiate.
>
> cheers
> Bruce
> On Wed, 16 Feb 2011, Tetiana Dadakova wrote:
>
>> Dear list,
>>
>> I would like to calculate CSF volume separately for left and right
>> hemispheres. In aseg.stats file I ha
Dear list,
I would like to calculate CSF volume separately for left and right
hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th
ventricles as a whole.
Is there any possibility to get volume values for right/left parts of
3rd, 4th and 5th ventricles?
Thank you,
Tanja.
___
Dear FreeSurfer community,
You were very helpful for my last question, thank you.
Now I have three basic questions.
1. I would like to check the segmentation by loading T1.mgz and
aseg.mgz as an -aux volume, so that I can switch between them. How can
I do this? ( gives some king of
black and whi
mess with the watershed/gcut.
>
> cheers
> Bruce
>
>
> On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
>
>> Dear FreeSurfer users,
>>
>> I run a for one of my subjects. When I check the
>> segmentation, it looks incorrect (see attached picture).
>
Dear Freesurfer users,
I installed Freesurfer and now I am trying to test the installation.
When I type , I get an error
But actually I do have write permission to this folder. Do you have
any idea what can be wrong? Or what else should I check regarding
installation to understand where this pr
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