Dear FS experts,
I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis.
After recon-all with hippo-subfield, only 45 brain volumes were genreated in
aseg.stats file.
Freesurfer v.5.1 analysis were able to generate cortical structure's volumes
also.
Where v.5.2 mainly gen
Dear freesurfers,
Is there a way to visualize glm for volume segments in qdec, i.e., instead
of analyzing and visualizing vertices on the surface we analyze and
visualize voxels on the volume?
For example, I would like to ask whether or not regions of
posterior/anterior cingulate shrink/expand wi
Dear Doug,
Thank you very much!
Sincerely,
Ye
On Tue, Sep 3, 2013 at 5:29 PM, Douglas N Greve
wrote:
> Yes, that is correct for DODS. For DOSS, it is y = e + bi*xi + ci*zi
> doug
>
>
> On 09/03/2013 01:03 PM, ye tian wrote:
>
>> Dear Doug,
>>
>> Would you please let me know what the general fo
Dear FS Experts,
My model has two categorical variable: Diagnosis and Sex. I am interested in
the effect of Diagnosis but I want to control the Sex effect. Toward this goal,
I want to model two main effects and want to avoid modeling their interaction
term. Is this something feasible in FreeSur
Hi David
I would do what I suggested:
1. Create a template froma ?h.sphere.
2. Register a bunch of subjects to the template to create a bunch of
shpere.reg files.
3. Rebuild the template from the sphere.reg files.
4. Register to this one
5. Rebuild the template
cheers
Bruce
On Tue, 3 Sep 2
Suppose the subjects were from a species of primate that has never been
scanned before, and that native spheres have been found for each subject --
how would you create a sphere.reg for a bunch of subjects in that case?
>From the webpage I mentioned, it seems that it suggests repeated
applications
I see. Usually we start with a sphere, and create a sphere.reg for a
bunch of subjects, then remake the template with those
Bruce
On Tue, 3 Sep 2013,
David Romano wrote:
Hi Bruce,
The workflow that I mentioned from the wiki is for creating a new template
in the absence of any ?.sphere.reg fi
Hi David
usually you need a ?h.sphere.reg as the ?h.sphere files are in (arbitrary)
spherical coordinates, while the ?h.sphere.reg ones are in registered ones
cheers
Bruce
On Tue, 3 Sep 2013, David
Romano wrote:
Hi everyone,
If I only have lh.sphere and lh.sulc files for each of collecti
Hi everyone,
If I only have lh.sphere and lh.sulc files for each of collection of
subjects, would this be enough information to generate a template for
registering further subjects?
I was thinking of trying to follow the workflow described on the page:
https://surfer.nmr.mgh.harvard.edu/fs
Hi Bruce,
The workflow that I mentioned from the wiki is for creating a new template
in the absence of any ?.sphere.reg files; here's relevant language from
the webpage:
"Creating a registration template from scratch (GW)
(This section reports on what I (GW) have learned of the
Yes, that is correct for DODS. For DOSS, it is y = e + bi*xi + ci*zi
doug
On 09/03/2013 01:03 PM, ye tian wrote:
> Dear Doug,
>
> Would you please let me know what the general formula for the model is
> for discrete variables x1, x2, , xN, covarying with continuous
> variables z1, z2, ...,
Use "--sval-area white" not "--sval-area area" if you want the area of
the white surface
doug
On 09/03/2013 12:26 PM, fatma zribi wrote:
>
>
> -- Forwarded message --
> From: *fatma zribi* mailto:zribi.fa...@gmail.com>>
> Date: 2013/9/3
> Subject: How to smoothing area with mri_s
Not necessarily.
On 09/03/2013 12:31 PM, ye tian wrote:
> Dear freesurfers,
>
> When I look at the statistical map for the average thickness, there
> are regions where thickness is "statistically zero" (null hypothesis
> kept). Does this indicate error in manual editing?
>
> Thank you very muc
Hi Alan,
lGI is different from the folding index. lGI is not yet extracted automatically
in the different regions, because it's more meant to be use at the vertexwise
level. But you can easily obtain the lGI values averaged over the Desikan's ROI
using the following command:
mris_anatomical_s
Hi Marie et al,
I have run recon all on the data and calculated LGI for all the brains in
my dataset. How does one go about extracting LGI values for each region (eg
left Pars Triangularis). Is the Folding index given in the aparc stats
sheet the same as LGI?
thanks so much,
Alan
___
Hi Katica
after you move the dicoms you have to run recon-all. Something like:
recon-all \
-sd /usr/local/freesurfer/subjects2 \
-s \
-i \
-all
this will create the directory
/usr/local/freesurfer/subjects2/
and populate it with the analysis results averag
Hi Doug:
I solved the problem. The aparcstats2table script works. But I have
another. It appears that the script does not recognize "foldind" or
FoldInd, so how do I get LGI values of the Brodmann areas?
thank you,
Alan
On Tue, Sep 3, 2013 at 1:30 PM, Alan Francis wrote:
> Hi Doug:
>
> Maybe
Dear All,
We are pleased to announce the 0.4 release of PySurfer, a Python-based
package for visualizing Freesurfer data. This release includes bugfixes and
multiple enhancements, including:
- Displaying data from both hemispheres simultaneously
- Displaying multiple views simultaneously
- Toggli
Hi Bruce!
So, before my subject folder was in a shared folder with the VM and my PC
(mnt/hgfs/Linux_Share/subjects)
After the recon with errors (see first emails) I was advised to set the
subject folder (which I understand is where the dicoms are stored, but I might
be mistaken) locally to the
Hi Katicia
can you be more detailed about what you did? What command did you issue
after you moved the dicoms? Where did you move them to? In general you
shouldn't need to move the dicoms.
Bruce
On Tue, 3 Sep 2013, Boric, Katica A.
wrote:
> Hi Bruce!
> So I created a new subject folder in the
Hi Catherine,
running them with the normal recon-all command is the first step of the
longitudinal pipeline, then create the 'base' (subject template) for
each subject and finally run all individual time points again through
the -long command.
see
https://surfer.nmr.mgh.harvard.edu/fswiki/Lo
Hi Brenna
that's a bit strange. Yes, you will want to correct the aseg in either
tkmedit or freeview as the presence of the putamen causes the surfaces to
be clamped.
cheers
Bruce
On Tue, 3 Sep 2013, Brenna Day wrote:
> Hi,
>
> I have a file where the pial surface is excluding some of the gr
Hi Bruce!
So I created a new subject folder in the same local system of freesurfer. Since
there already was a folder named subjects in usr/local/freesurfer I named it
subjects 2: /usr/local/freesufer/subjects2
I moved the dicoms into this new folder. Then I did setenv SUBJECTS_DIR
/usr/local/f
no, there are midline non-cortical regions where the gray/white and pial
surfaces are clamped that will have exactly 0 thickness
cheers
Bruce
On Tue, 3 Sep 2013, ye
tian wrote:
> Dear freesurfers,
> When I look at the statistical map for the average thickness, there are
> regions where thickn
Hi Doug:
Maybe I did not communicate this effectively. Since the lh.BA.stats files
are smaller in kb than the aparc files, I keep getting an error message
when I run the aparcstats2table command which is as follows:
Parsing the .stats files
ERROR: The stats file /HM0403/stats/lh.BA.stats is not f
Dear Doug,
Would you please let me know what the general formula for the model is for
discrete variables x1, x2, , xN, covarying with continuous variables
z1, z2, ..., zM?
Is it
y = error + bi*xi + cij*xi*zj ?
Otherwise, how does freesurfer decide what model to use?
Thank you very much!
S
Thanks Doug. So I change the command line syntax to the following:
csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM0603 /HM0703
/HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003
/HM2103 /HM2203 /HM230
-- Forwarded message --
From: fatma zribi
Date: 2013/9/3
Subject: How to smoothing area with mri_surf2surf?
To: Bruce Fischl
Dear Bruce,
Would you mind help me. I would like to smooth area surface with the
command mri_surf2surf.
I have done this instruction:
mri_surf2surf --h
oh, then
setenv SUBJECTS_DIR new_path
On Tue, 3 Sep 2013, Boric, Katica A. wrote:
> Thanks Bruce!
> So, I just move the SUBJECT_DIR folder and then setenv? I do want to set the
> subject directory to a new path
> Thanks again,
> Katica
>
> From: freesur
setenv FREESURFER_HOME /usr/local/freesurfer
On Tue, 3 Sep 2013, Boric,
Katica A. wrote:
>
>
> Hi everyone!
> I wrote you last Friday regarding an error at the last moment of the MRI
> processing (see e-mails below)
> Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the same
Thank you. One more question, is there any way to check if this affect the
surfaces after running recon-all -all?Or I need to complete the whole analysis
before looking into this?Cheers,Pablo
> Date: Tue, 3 Sep 2013 11:07:36 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvar
Thanks Bruce!
So, I just move the SUBJECT_DIR folder and then setenv? I do want to set the
subject directory to a new path
Thanks again,
Katica
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
Hi everyone!
I wrote you last Friday regarding an error at the last moment of the MRI
processing (see e-mails below)
Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the same
folder system as $FREESURFER_HOME.
Could someone please show me how to set the directory with a tcs
Hi Doug:
Here is the message it gives. It's not so much an error message as an
advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903
/HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103
/HM2203 /HM2303 /HM2403 /HM2503 /HM
Your comamnd line is incorrect. Use --subjects instead of -s. Or just
use only the --subjectsfile.
doug
On 09/03/2013 11:55 AM, Alan Francis wrote:
> Hi Doug:
>
> Here is the message it gives. It's not so much an error message as an
> advisory on usage.
>
> thanks so much,
>
> Alan
>
> aparcs
Hi FreeSurfer folks:
I am trying to extract LGI values from Brodmann Areas 44 and 45. I am using
the following script. Unfortunately it gives me an error message. Could you
please help me.
aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003
/HM1103 /HM1203 /HM1303 /HM1403 /
Yes, that is just some eyeball that has not been stripped. It is ok as
long as it does not affect the surfaces.
doug
On 09/03/2013 10:54 AM, pablo najt wrote:
> Hi Doug,
> Thank you very much for your output about my output files. Yes, I
> understand that these images are skull stripped. But s
Hi Alan, it would be a lot easier to help if you told us what the error
msg is:). Please supply the full terminal output including error msg.
thanks
doug
On 09/03/2013 10:52 AM, Alan Francis wrote:
> Hi FreeSurfer folks:
>
> I am trying to extract LGI values from Brodmann Areas 44 and 45. I am
Thanks, Doug; I'd only gone through the information I could find online and
didn't see there was a --help flag available. I'll try that now. And out
of curiosity in case something similar happens with other freesurfer
commands, is the --help flag standard in freesurfer?
Thanks again,
David
On
It is fairly standard, at least in the programs I write. It sometimes
appears with a single dash (-help)
doug
On 09/03/2013 10:59 AM, David Romano wrote:
>
> Thanks, Doug; I'd only gone through the information I could find
> online and didn't see there was a --help flag available. I'll try th
look inthe ?h.aparc.stats files
doug
On 08/31/2013 06:33 AM, Anupa AV wrote:
> Dear FS experts,
>
> I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my
> analysis.
> After recon-all with hippo-subfield, only 45 brain volumes were
> genreated in aseg.stats file.
> Freesurfer v.5.
Hi David, did you check the help within mri_surf2surf? Run mri_surf2surf
--help. I think it has an example of what you want to do.
doug
On 08/30/2013 06:57 PM, David Romano wrote:
> Hi everyone,
>
> In an earlier post, I had asked how to transform the white surface of
> one subject to the white
Hi everyone!
I wrote you last Friday regarding an error at the last moment of the MRI
processing (see e-mails below)
Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the same
folder system as $FREESURFER_HOME.
Could someone please show me how to set the directory with a tcsh
Hi Luzia, do you have permission to see that file? Can you send the
recon-all.log file?
doug
On 09/03/2013 07:32 AM, Troebinger, Luzia wrote:
> Hi all,
>
> I posted a message regarding this problem a while ago, but still not
> resolved. Basically, freesurfer exits with errors in the final
> (a
Hi Pablo, this is a skull stripped image. In the human brain there is no
brain tissue ventral to the orbital frontal areaso any tissue there has
been stripped away.
doug
On 09/02/2013 12:49 AM, pablo najt wrote:
>
> Dear FS experts,
> I have a doubt about a potential registration problem after
Dear Freesurfers,
I transferred the white matter binary mask (derived from aseg, volume) to FSL
and performed probabilistic tractography in it.
Now I'd like to project the 'outer' white matter results (vol) onto the white
surface.
To test for the acuracy of this approach, I tried to project
you can sample under the wm surface by using negative proj fracts or
proj dists
doug
On 09/03/2013 09:32 AM, Robert Schulz wrote:
> Dear Freesurfers,
> I transferred the white matter binary mask (derived from aseg, volume)
> to FSL and performed probabilistic tractography in it.
> Now I'd like
Dear Freesurfers,
I transferred the white matter binary mask (derived from aseg, volume) to FSL
and performed probabilistic tractography in it.
Now I'd like to project the 'outer' white matter results (vol) onto the white
surface.
To test for the acuracy of this approach, I tried to project
Hi all,
I posted a message regarding this problem a while ago, but still not resolved.
Basically, freesurfer exits with errors in the final (autorecon-3) stages,
because of what must be a problem with the symbolic link lh.EC_average. The
link is created as should be, but I get an error message
Hi Doug,
I found a workaround. I used matlab code from from gradient_nonlin_unwarp to
remove the c_ras offset from the vertex coordinates and set c_ras to 0. Then I
mris_convert the new surface to .gii. This gives me perfectly aligned surfaces.
Thanks for your help,
Franz
> [surf_struct, tags,
Thank you!
Still somehow I haven't manage to make it work when I ran the suggested
command I get an error saying :
ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error
occurred while parsing element line number: 1 column number: 1.
Any advise?
Thanks again
Shani
On Mon, Sep 2
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