hi Glen, no cluster will show up if the p-value for all clusters is
above .05. You can change this with --cwpvalthresh to something like
.99. That should give you all the clusters. Also, you don't have to run
the full simulation again; you can use the --no-sim option and it will
use the simul
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial
recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under
5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
recon-all -s s_ALS51
Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
wrote:
> You will need more like 1 iterations instead of 100.
> doug
>
> On 06/03/2013 04:49 PM, Glen Lee wrote:
> > Hello Fr
Do you have read permission to it?
doug
On 06/03/2013 06:26 PM, Manish Dalwani wrote:
> I need help with this error...I do see the a LICENSE file in the
> freesurfer directory.
>
> --
> ERROR: FreeSurfer license file /Applica
It looks like you don't have permissions to that file. Try changing the
permission with chmod (need to change them for all your dicom files)
doug
On 06/03/2013 06:17 PM, Manish Dalwani wrote:
> Dear Freesurfer's
>
> I have been using (a slightly older version) Freesurfer on linux and
> it works f
I need help with this error...I do see the a LICENSE file in the freesurfer
directory.
--
ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found.
If you are outside the NMR-Martinos Center,
go to ht
Dear Freesurfer's
I have been using (a slightly older version) Freesurfer on linux and it works
fine. I just recently installed freesurfer on the mac workstation OS X 10.8.1.
I get the following error:
server:subjects manishdalwani$ cd anat_5214
server:anat_5214 manishdalwani$ recon-all -i MR1
If you have 5.3 installed, you can just run
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.v53.stats --pv
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-u
Hi Siddharth
yes, the brain.finalsurfs.mgz will be a skull stripped image (as will
brianmask.mgz)
cheers
Bruce
On Mon, 3 Jun 2013, Ray, Siddharth wrote:
Hi,
I am new to freesurfer and just want to know can I just have skull-stripped
image (with cerebellum) anywhere between stages in Fre
Hi,
I am new to freesurfer and just want to know can I just have skull-stripped
image (with cerebellum) anywhere between stages in Freesurfer 5.3??
Please let me know.
Thanks,
Siddharth
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Freesurfer mailing list
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https:
You will need more like 1 iterations instead of 100.
doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result (which was
> already done using mri_glmfit), but I was not able to get any result
> out of it.
>
> E
if you are working with the aseg, then you could
aseg = MRIread('aseg.mgz');
overlay = aseg;
overlay.vol = zeros(size(overlay.vol));
ind = find(aseg.vol == 17); % Find left hippocampal voxels
overlay.vol(ind) = value from you table corresponding to left hippo
you would then replicate with each R
Hi Chris,
this is a good question for the list (cc'ed), others may or will have
the same problem.
The problem is with your table file, specifically the new line
character. DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.
The problem is that the
Hi Adam
you don't need to rerun mris_make_surfaces I don't think, but you will
want to rerun mris_thickness to recompute the thickness after saving the
new (repositioned) surfaces
cheers
Bruce
On Mon, 3 Jun 2013, Adam Martersteck wrote:
Hi Freesurfer experts,
I noticed that Freeview has go
Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was
already done using mri_glmfit), but I was not able to get any result out of
it.
Even with a quite liberal threshold (2), no vertices came out (below is
what I typed in for the random permutation).
Hi Freesurfer experts,
I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the
reposition tool now has a GUI and it works!
Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012
that the pipeline for the reposition surface tool was not yet implemented
and you sti
Hi all,
Sorry to post a question not related to the brain surface analysis.
I wonder why there are not many studies looking into the correlation between
perfusion and resting state fmri. Perfusion should play an important role in
modulating resting bold signal. Does any one have some experien
Thank you Doug. Any pointers you can provide on how to try out this process
in Matlab would be great.
Best wishes,
Sal
On Mon, Jun 3, 2013 at 11:19 AM, Douglas N Greve
wrote:
> we don't have a way to do this. With a little programming you could do
> this in matlab. let me know if you need poin
I only have one input. The last posting's orig.jpg was 001.mgz, and
motioncor.jpg is orig.mgz. We usually run motioncor because it produces the
orig.mgz which has been conformed.
On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl wrote:
> what does the 001.mgz look like? Do you have more than one inpu
Hi Adam, if the subject folder exists and you pass recon-all a -i flag,
then it will exit with error saying that the data exist (otherwise it
would overwrite what is there). However, just because the subject folder
exists does not mean that there is any data sitting in subject/mri/orig.
Then it
what does the 001.mgz look like? Do you have more than one input
(otherwise you wouldn't need motion correction)? If so, you'll need to do
this for each one
On Mon, 3 Jun 2013, Erin Browning wrote:
The orig.mgz is hyerintense (there's a screenshot of it in another post
now). The AFNI file is i
try what I suggested and see if that helps
On Mon, 3 Jun 2013, Erin Browning
wrote:
Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.
Hello users,
I am trying to get Freesurfer (5.2) working properly off-site and am
encountering errors I did not have while working at the Martinos center. We
use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data
is similar to work with.
I have been using dcmunpack since unpa
Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.
On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl wrote:
> Hi Erin
>
> that can happen i
Great, thanks for your help Doug!
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 03, 2013 2:55 PM
To: freesurfer@nmr.mgh.harvard.edu
S
what is the problemexactly? how do the surfaces look?
doug
On 06/03/2013 02:54 PM, Erin Browning wrote:
>
> It seems like it getting darker messes up the normalization later on;
> could this be the case? Here's what it looks like in AFNI
> (1029-afni.jpg), and here's what it looks like after we
Hi Erin
that can happen if you lose too much dynamic range when "conforming". What
does the orig.mgz look like? What voxel format is the afni file in (uchar?
float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no
scale"). If the brik was in float you could use something like (
yes, I think so. Maybe others can comment.
On 06/03/2013 02:49 PM, Fotiadis, Panagiotis wrote:
> Ok, great, it seems in this case that even though the overlays in both cases
> are very similar, the kurtosis in the second analysis (Diseased vs Controls
> no gender taken under consideration) is s
Ok, great, it seems in this case that even though the overlays in both cases
are very similar, the kurtosis in the second analysis (Diseased vs Controls no
gender taken under consideration) is slightly better. Therefore would it be
correct to assume that the second analysis is more trustworthy?
yes
On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
> I see. Would it be correct to say that better kurtosis would be illustrated
> as less significant clusters in the kurtosis.mgh overlay?
>
> Panos
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [
that will not change the intensities at all. It is probably just a
display issue. Try changing the brightness/contrast. The artifact might
cause problems later on, but this is not an issue I think
doug
On 06/03/2013 02:20 PM, Erin Browning wrote:
> We use:
>
> mri_convert N1029-anat+orig.BRIK
Ok.
Thanks a lot!
Cheers
Claudia
Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
> yes, you should be running
>
> recon-all -autorecon2-cp
>
> cheers
> Bruce
>
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
> Is this the problem? Is there an incorrect command?
>> Thanks.Cheers
>>
I see. Would it be correct to say that better kurtosis would be illustrated as
less significant clusters in the kurtosis.mgh overlay?
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
We use:
mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz
where freesurfer is our freesurfer subject folder.
On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
wrote:
> what is your mri_convert command line?
>
> On 06/03/2013 02:11 PM, Erin Browning wrote:
> > Hi everyone--
> >
> > We
we don't have a way to do this. With a little programming you could do
this in matlab. let me know if you need pointers
doug
On 06/01/2013 04:43 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your response. I am not sure I understand what I would
> be overlaying.
>
> I would like to displ
what is your mri_convert command line?
On 06/03/2013 02:11 PM, Erin Browning wrote:
> Hi everyone--
>
> We have a series of scans with an hyperintense artifact cutting
> through the temporal and frontal lobe. When we run mri_convert to
> convert from AFNI .BRIK files to .mgz fles, the results lo
On 06/03/2013 02:03 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> I looked that the morphometryStats table that you sent and looks like I need
> the following measure.
>
> BrainSegNotVent - this I believe doesnt include cerebellum etc and no
> ventricles.
It does include cerebellum. It does exclude
Hi everyone--
We have a series of scans with an hyperintense artifact cutting through the
temporal and frontal lobe. When we run mri_convert to convert from AFNI
.BRIK files to .mgz fles, the results look like the attached image.
How can I correct for this? We tried skullstripping in AFNI first t
Hi Doug,
I looked that the morphometryStats table that you sent and looks like I need
the following measure.
BrainSegNotVent - this I believe doesnt include cerebellum etc and no
ventricles.
But all my data are run through 5.1. How do I get this measure ? If I run the
5.2 version of mri_segst
yes, you should be running
recon-all -autorecon2-cp
cheers
Bruce
On Mon, 3 Jun 2013, Claudia Dacquino wrote:
Is this the problem? Is there an incorrect command?
Thanks.Cheers
Claudia
Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
Hi Claudia
there is no autorecon3-
no, it does not include cerebellum
On 06/03/2013 01:42 PM, Ritobrato Datta wrote:
> In the website below,
> lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume
> inside the white surface minus anything that is not WM. CorticalWhiteMatter
> includes hypointensities. This uses
Not necessarily. It could have been in the FS analysis. You can run
mri_glmfit with --kurtosis (a hidden option). This will create a
kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
the residuals (larger being less gaussian). The pkurtosis the the sig
(-log10(p)) of the
In the website below,
lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume inside
the white surface minus anything that is not WM. CorticalWhiteMatter includes
hypointensities. This uses the surface-based volume computation for part of the
calculation and counts voxels to su
Is this the problem? Is there an incorrect command?
Thanks.
Cheers
Claudia
Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
> Hi Claudia
>
> there is no autorecon3-cp, just autorecon2-cp
>
> cheers
> Bruce
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
> Hi Freesurfers,
>> I did autorec
See if this answers your question
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
this is for v5.2 and beyond
On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
> ic thats rightI was getting confused. So the total gm vol includes
> cerebellar gm vol but the cortical wm vol only include
I see. Yes from the one hand the results that I got make a lot more sense in
the second type of analysis, compared to the first one, however, there are some
somewhat important difference between the two analyses. If there is an issue
with the data, do you believe that it would be in the acquisit
ic thats rightI was getting confused. So the total gm vol includes
cerebellar gm vol but the cortical wm vol only includes the wm vol under the
cortical ribbon and around the subcortical gm structures? Or does that
include wm under the cerebellar cortex as well ?
Is there a table somew
On 06/03/2013 12:37 PM, Robert Schulz wrote:
> Dear Douglas,
>
> thank you for your reply.
>
>> Hi,
>> I have two questions:
>> 1.
>> I have created specific surfaces in fsaverage rh for each of my 20
>> subjects. (xy.mgh)
>> I'd like to run statistical analysis within the common surface area
>> w
Hi Rito, I don't think we report a total wm volume, do we?
doug
On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> Just following up on your reply sometime back -
> Does total white volume include cerebellar wm vol also ?
>
> Please let me know.
>
> Thanks
>
> Rito
>
> - Origina
Hi Chris, this problem was created because of a change in the way
tcshell works. When fname2stem fails, it should not go on to set fsvol =
tmp because status should be set to 1. This is the way tcshell used to
work. With newer version of CentOS, it sets status=0 because the set tmp
was success
Dear Douglas,
thank you for your reply.
> Hi,
> I have two questions:
> 1.
> I have created specific surfaces in fsaverage rh for each of my 20
> subjects. (xy.mgh)
> I'd like to run statistical analysis within the common surface area
> which is included in all subjects.
> Therefore I wonder how
Hi Robert,
On 06/03/2013 12:12 PM, Robert Schulz wrote:
> Hi,
> I have two questions:
> 1.
> I have created specific surfaces in fsaverage rh for each of my 20
> subjects. (xy.mgh)
> I'd like to run statistical analysis within the common surface area
> which is included in all subjects.
> Therefo
Hi Claudia
there is no autorecon3-cp, just autorecon2-cp
cheers
Bruce
On Mon, 3 Jun 2013, Claudia
Dacquino wrote:
> Hi Freesurfers,
> I did autorecon3-cp and exited with errors.
> Ould anyone help me to understand what's the roblem?
> You can find the recon-all.log attached.
> Thanks in advance
sure
On Mon, 3 Jun 2013, sle...@nmr.mgh.harvard.edu wrote:
> Hi Bruce,
>
> I see that somebody copied talairach_mixed_with_skull.gca to
>
> /usr/local/freesurfer/stable5/average/
>
> thank you, but FreeSurfer seems to be looking for it here:
>
> /usr/local/freesurfer/stable5_3_0/average/talairach_
Hi Bruce,
I see that somebody copied talairach_mixed_with_skull.gca to
/usr/local/freesurfer/stable5/average/
thank you, but FreeSurfer seems to be looking for it here:
/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca
Could you please have someone copy it there too?
He
Hi,
I have two questions:
1.
I have created specific surfaces in fsaverage rh for each of my 20 subjects.
(xy.mgh)
I'd like to run statistical analysis within the common surface area which is
included in all subjects.
Therefore I wonder how to combine those surfaces.
My idea would be to add
I would not expect them to be identical but similar. If they change a
lot there may be an issue with your data.
doug
On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> I have run a group analysis on my data with two different ways. (The input is
> cortical thickness.) In the fir
brainstem is not part of cortex. Use mri_cor2label with the aseg. get
the id from $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
On 6/3/13 6:17 AM, LAOUCHEDI MAKHLOUF wrote:
Hi
i used mri_annotation2label to extract the cortical labels. for
this command we must specify which hemisphere
Hi Joshua, when you add --fwhm 15 to the command line you are
instructing mri_glmfit to smooth by 15mm. Is this what you want? Or is
the data already smoothed?
doug
On 6/3/13 12:26 AM, Joshua deSouza wrote:
Hi Doug,
The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C
t1.
Hey Doug,
I have run a group analysis on my data with two different ways. (The input is
cortical thickness.) In the first analysis, I specified 4 groups
(Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in
the second, just two groups (Diseased, Healthy). One of the comp
if they are named orig/00[012345].mgz then I think they will be averaged
but without motion correction, which is almost certainly not what you want
On Sun, 2 Jun 2013,
obre...@nmr.mgh.harvard.edu wrote:
> Hi Bruce,
>
> Thanks for responding! For the sake of clarification, let's say I have
> mul
Hi Shani
you'll need to send us some images and the recon-all.log for us to diagnose
the problem
Bruce
On Mon, 3 Jun 2013,
Shani Ben Amitay wrote:
> Hello all
> I have created white matter surface of a non primate brain and I'm trying to
> use mris_make_surfaces to position the pial surface.
>
Thank you Chris for pointing this potential bug and the possible culprit
in the source code. We will take a closer look it and determine the best
way to proceed.
-Zeke
On 06/02/2013 10:16 PM, Chris Adamson wrote:
> During the reg-feat2anat script fslregister produces errors. I tracked
> it to
Hello all
I have created white matter surface of a non primate brain and I'm trying
to use mris_make_surfaces to position the pial surface.
The problem is that the resulted pial surface is miss-positioned-the
'growing' stops very close to the white surface (no gradient visible where
it stops)
Any
Hi Graham,
I think the distance error is in the creation of the ?h.qsphere.nofix and
can be ignored as can the others. It shouldn't be reported and I'll try to
find the time to take it out as there is no metric perservation in the
qsphere - it's only concerned with topology.
cheers
Bruce
Hi,
While you're on the subject, there's a version 1.12 available from
http://packages.bic.mni.mcgill.ca/tgz/ (dated January 2011, Freesurfer
wraps and uses 1.10). I'm running tests with this version, and it also
produces the errors mentioned.
Best Regards,
Christian
On 06/03/2013 02:56 PM, Bruc
Hi Peter
I would try this:
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
Bruce
On Mon, 3 Jun 2013,
Peter Wendorff wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi Brucel
> yes, sure - sorry.
> I followed your advice (your response to my first mail here), and found
> h
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Brucel
yes, sure - sorry.
I followed your advice (your response to my first mail here), and found
http://www.bic.mni.mcgill.ca/Research/Homepage which - if I'm not
mistaken - is the MNI institute you pointed me to.
As there's no John Sled listed on
Hi Daniel,
All the information wrt memory and file naming conventions is described
in:
mri_cvs_register --help
The final output file should be named final*norm.mgz
Lilla
On Mon, 3 Jun 2013, Barron, Daniel S wrote:
> Hi All,
>
> Was able to register 3 subjects to a common space with really gr
that usually means that the surfaces are inconsistent. Try running
recon-all -make all
instead. That should figure out what needs rebuilding and do so
cheers
Bruce
On Mon, 3 Jun 2013, LAOUCHEDI
MAKHLOUF wrote:
Hi
i run recon-all -autorecon3 on a normal subject and after a while, it
ex
Hi Elisa
usually we acquire sagitally as that is the shortest direction, but it
shouldn't matter as long as your voxels are close to 1mm isotropic (just
longer scans).
cheers
Bruce
On Mon,
3 Jun 2013, elisa veronese wrote:
> Hi,
> I am a beginner in the use of Freesurfer. I was wondering if t
Hi Peter,
did you mean MNI when you said MRI? I think that they are still
maintaining it - I would be surprised otherwise
Bruce
On Mon, 3 Jun 2013, Peter
Wendorff wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi again.
>
> So: is the MRI stuff dead code?
> I wrote an email to Jen
Hi Lucy
if you have a dicom series, you would run:
recon-all -s -i \
-sd -all
then wait 15 hours or so.
cheers
Bruce
On
Mon, 3 Jun 2013, ?? wrote:
> Hi expert,
> If I want to get the cortical thickness,what will I do in the freesurfer?
>
>
>
>
> All suggestions welcome.
> Thanks
Hi All,
Was able to register 3 subjects to a common space with really great accuracy
(both of the overall volumes and of the aseg files).
Note: cvs_register takes up quite a bit of RAM (how much exactly?) which caused
my desktop to slow and, essentially, crash. Ended up running them on the
se
Hi
i run recon-all -autorecon3 on a normal subject and after a while, it exited
with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and
recon-all.error and recon-all.log i found the following messages :
error.log :
mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match
Hi
i used mri_annotation2label to extract the cortical labels. for this command
we must specify which hemisphere (--hemi ?h) and i want to extract the
brainstem which is not a lateralized structure, is there any command like
mri_annotation2label to extract the brainstem ?
thanks
Hi everyone,
I´m trying to do cvs registration using freesurfer 5.3 and I get this
message:
"The following files are missing:
/Applications/freesurfer/bin/mri_cvs_register.settings.txt
You need to find these files or run reconall on the data in order to run
mri_cvs_register"
Any idea wo
Hi,
I am a beginner in the use of Freesurfer. I was wondering if the T1w volume
used as input for the recon-all has to be acquired in axial direction or
not. In other words, is there a recommended acquisition direction?
Thank you,
Elisa
--
Elisa Veronese - PhD
http://www.dei.unipd.it/~verones1/
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi again.
So: is the MRI stuff dead code?
I wrote an email to Jennifer Chew asking for the right contact for
bugs/issues regarding that code.
That mail has been sent on May 22nd and I didn't get any response, yet.
Is that code ever updated by the fre
Hi expert,
If I want to get the cortical thickness,what will I do in the freesurfer?
All suggestions welcome.
Thanks in advance,
Lucy___
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