Re: [Freesurfer] bbregister: PET and MRI

[Douglas N Greve]

why are you using the --t1 option? Looks like gray matter is brighter 
than white matter, so --t2 (same as --bold) is more appropriate.


Rafa x wrote:

Dear FS Team,

I have a problem with the bbregister command. I used it for coregister
a MRI with a PET.
My first step is set the same origin and orientation for both images
(approximately) (I use SPM or tkregister2).
After, I write in the terminal "bbregister --mov s24PET.img --t1 --s
sr24 --init-fsl --reg register.dat"(s24 is the name of my patient)
The result of the process is a bad corregister (see the included file).

 I would like to improve this result.
 Maybe the number of iterations is too less (I'm not sure of that)
 I probed with the flags  SPM, FSL and HEADER but they don't provide
good result.


 Thank you all in advance.
  






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[Freesurfer] Qdec question

[Devdutta W]

Hi,
I am using qdec for analysis and noticed that in addition to thickness
measures I can select others such as area and volume.  I have been trying to
figure out what exactly the area measure refers to (surface area, etc.).  I
did not find it on the website.  Can someone clarify that for me?  If this
is a repeat question, I apologize and ask that you point me to the archived
post.

Thank you,
Dev
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Re: [Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

[Avram Holmes]

All,

Nevermind. It looks like the error was being caused by a space issue.

Sorry for eating up your time,
Avram

On 2/16/2009 1:34 PM, Avram Holmes wrote:

All,

I'm encountering an error when I run selxavg3-sess and I am not sure 
how to get around the problem, or what it means.


I am running the following command, which has worked with the data for 
the other participants in my study.


selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

Several minutes in I am getting the following error...

GLS Beta Pass
 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

 run 2t= 5.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/007/flanker_nResp.par 
as a par3 file.

 run 3t=11.3
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/008/flanker_nResp.par 
as a par3 file.

 run 4t=17.1
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/009/flanker_nResp.par 
as a par3 file.

 run 5t=22.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/010/flanker_nResp.par 
as a par3 file.

GLS Residual Pass
/users/aholmes/.bashrc: line 229: SetUpFreeSurfer.sh: No such file or 
directory

 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

??? Error using ==> fclose
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in ==> save_nifti at 162
fclose(fp);

Error in ==> MRIwrite at 145
 err = save_nifti(hdr,fspec);

Error in ==> fast_selxavg3 at 634
 MRIwrite(rrunmri,fname);

>> --
ERROR: fast_selxavg3() failed\n


Does anyone know what might be going on and/or how I can correct the 
problem?


Thanks,
Avram



--

Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall  Phone:(617) 495-0790
33 Kirkland Street   Fax:(617) 495-3728
Cambridge, MA 02138, USA Email: hol...@fas.harvard.edu


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RE: [Freesurfer] still exiting with errors

[Bruce Fischl]

the current versions should have aseg.auto_noCCseg.mgz. When you rerun 
recon-all doesn't it create them?



On Sun, 15 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:

The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz.  The 
scans that are working seem to have aseg.auto_noCCseg.mgz instead of 
CCseg.mgz.



-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Fri 2/13/2009 8:44 PM
To: Dankner, Nathan (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] still exiting with errors

what files are in [subject path]/mri/*aseg*.mgz?

On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:


Sorry to post this again, but I am still having issues with surfaces exiting 
with errors.  These are the two outputs that I have gotten:

MRI_fill: could not read segmentation from aseg.auto_noCC.mgz
reading segmented volume aseg.auto_noCCseg.mgz...
ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz
No such file or directory

and

ERROR: cannot find [subject path]/mri/aseg.mgz

Mr. Schmansky indicated that this may be due to 2 different versions being 
used.  I have been running recon-all on version 4.1.0 on a 64 bit linux 
machine, and editing on the same version but on a mac.  Also, I attempted to 
use the -clean-aseg command as directed, but this doesn't seem to have fixed 
the problem.  I'm currently in the process of updating both machines to version 
4.2.0, so I don't know how this will affect things.  Any suggestions?  Thanks 
in advance,

Nathan

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Re: [Freesurfer] manual segmentation of subcortical structures

[Bruce Fischl]

Hi Jose,

not sure I understand. Do you mean to edit the aseg.mgz to improve 
hippocampus and thalamus? We don't have any protocols for this, although 
you could certainly do it in tkmedit or freeview. Changing these shouldn't 
have much affect on cortical thickness.


cheers,
Bruce




On Mon, 16 Feb 2009, Jose Luis Cantero Lorente wrote:


Hi there,

we have a bunch of MRI scans already segmented by using the typical FS 
recons protocol. Now we would like to improve the hippocampus and thalamus 
delimitation by manual segmentation, but several basic questions arose:


1. Are there radiological protocols (commonly used) to segment these 
subcortical structures from FS? Any help with this issue will be very welcome.

2. Is there any tutorial to manually segment subcortical structures from FS? We 
just performed cortical segmentation and are not familiar at all with manual 
subcortical segmentation menus and steps to follow.

3. Will these subcortical changes affect to our cortical thickness values and 
cortical parcellation?

Thanks for your help.

Best regards,
Jose

---
Jose Luis Cantero, Ph.D.
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] Wrong Red Line and Yellow Line

[Nick Schmansky]

Haobo,

Adding a control point might help.  See this tutorial:

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

which describes the problem you are seeing and how to fix it.

Don't put the control point at the very end of the gyrus, as this voxel
might be partial-volumed and marking it as white matter with a control
point will mess-up the segmentation.  It should be placed at the base
(just inside your circle in your drawing).

Nick


On Sat, 2009-02-14 at 17:39 +1100, Haobo Zhang wrote:
> Hi all,
> 
> After running with Freesurfer, I found the red line cutting through
> the superior temporal gyrus in the coronal view slice. And the yellow
> line excluded part of the white matter in this area. Please check the
> attachment. Does anyone have experience in fixing this type of
> problems? Thank you for your help!
> 
> Cheers,
> Haobo Zhang
> 
> School of Psychiatry,
> University of New South Wales
> 
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Re: [Freesurfer] Version re-run

[Nick Schmansky]

Martin,

There is no need to rerun the -autorecon1 step as long as you are happy
with the brainmask.mgz (ie, miminal or no skull, and cerebellum
retained), and the talairach.xfm is good (which would be the case if
your prior runs completed successfully).

We'll probably release another version in mid to late March.  

Nick


On Mon, 2009-02-16 at 16:49 +0100, Martin Ystad wrote:
> Hi all,
> I have 100-something scans already run on a FreeSurfer version from 2005 
> that I'd like to re-run with the newest version of FreeSurfer. The 
> subjects contain manual edits to the brainmask.mgz and wm.mgz, as well 
> as control points. As far as I have understood, when running autorecon2 
> my manual edits will be saved by default. However, is there any need to 
> re-run the autorecon1-steps for my subjects?
> Also: when do you plan to release the next version of FreeSurfer?
> 
> Many thanks,
> Martin Ystad
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Re: [Freesurfer] In common stereotactic space?

[Nick Schmansky]

Jurgen,

To create thickness difference maps, follow the instructions on this
page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility

In your case, you would skip step 1, since the recon-all -long will
create the .lta transform (from tp1 to tp2) already (look for it in the
tp2subj/mri/transform dir).  You can use this .lta file to transform the
T1.mgz image in tkmedit, so that they are in the same stereotactic
space, for viewing.

If you are not doing a group analysis, then you only need to run step 2,
mri_thickness_diff, which creates the overlay file.  Note that smoothing
is not done (as was the case in the thickness repeatability study from
which these steps originate).

You would do mri_surf2surf if doing a group analysis, per the
instructions.

Nick


On Mon, 2009-02-16 at 18:42 +0100, J=?ISO-8859-1?B?/A==?=rgen H=?
ISO-8859-1?B?5A==?=nggi wrote:
> Dear FS experts
> 
> I had run recon-all -long on two time points and would like to subtract the
> cortical thickness maps of the two time points.
> 
> Do the two ?h.thickness maps of the different time points are already in the
> same space so that they can be directly subtracted in MATLAB?
> 
> Or 
> 
> Do I have to use mri_surf2surf to register them before I can subtract them?
> 
> Do you recommend smoothing the thickness maps?
> 
> When looking at T1.mgz with the overlaying aseg the images of the two time
> points are not in the same stereotactic space: hence, I would like to known
> whether this is also the case for the thickness maps.
> 
> Sorry for reposting this question
> 
> Thanks
> Regards
> Jürgen
> 
> 
> Juergen Haenggi
> Ph.D. (Dr. des.)
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
> 
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
> 
> 
> 
> 
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[Freesurfer] manual segmentation of subcortical structures

[Jose Luis Cantero Lorente]

Hi there,

we have a bunch of MRI scans already segmented by using the typical FS recons 
protocol. Now we would like to improve the hippocampus and thalamus 
delimitation by manual segmentation, but several basic questions arose:

1. Are there radiological protocols (commonly used) to segment these 
subcortical structures from FS? Any help with this issue will be very welcome.

2. Is there any tutorial to manually segment subcortical structures from FS? We 
just performed cortical segmentation and are not familiar at all with manual 
subcortical segmentation menus and steps to follow.

3. Will these subcortical changes affect to our cortical thickness values and 
cortical parcellation?

Thanks for your help.

Best regards,
Jose

---
Jose Luis Cantero, Ph.D.
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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[Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

[Avram Holmes]

All,

I'm encountering an error when I run selxavg3-sess and I am not sure how 
to get around the problem, or what it means.


I am running the following command, which has worked with the data for 
the other participants in my study.


selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

Several minutes in I am getting the following error...

GLS Beta Pass
 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

 run 2t= 5.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/007/flanker_nResp.par 
as a par3 file.

 run 3t=11.3
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/008/flanker_nResp.par 
as a par3 file.

 run 4t=17.1
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/009/flanker_nResp.par 
as a par3 file.

 run 5t=22.7
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/010/flanker_nResp.par 
as a par3 file.

GLS Residual Pass
/users/aholmes/.bashrc: line 229: SetUpFreeSurfer.sh: No such file or 
directory

 run 1t= 0.0
Loaded 
/ncf/anl/anl08/CONCON/fMRI/functional/c43/Flanker/006/flanker_nResp.par 
as a par3 file.

??? Error using ==> fclose
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in ==> save_nifti at 162
fclose(fp);

Error in ==> MRIwrite at 145
 err = save_nifti(hdr,fspec);

Error in ==> fast_selxavg3 at 634
 MRIwrite(rrunmri,fname);

>> --
ERROR: fast_selxavg3() failed\n


Does anyone know what might be going on and/or how I can correct the 
problem?


Thanks,
Avram

--

Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall  Phone:(617) 495-0790
33 Kirkland Street   Fax:(617) 495-3728
Cambridge, MA 02138, USA Email: hol...@fas.harvard.edu


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[Freesurfer] In common stereotactic space?

[Jürgen Hänggi]

Dear FS experts

I had run recon-all -long on two time points and would like to subtract the
cortical thickness maps of the two time points.

Do the two ?h.thickness maps of the different time points are already in the
same space so that they can be directly subtracted in MATLAB?

Or 

Do I have to use mri_surf2surf to register them before I can subtract them?

Do you recommend smoothing the thickness maps?

When looking at T1.mgz with the overlaying aseg the images of the two time
points are not in the same stereotactic space: hence, I would like to known
whether this is also the case for the thickness maps.

Sorry for reposting this question

Thanks
Regards
Jürgen


Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
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e-mail. Any unauthorised copying, disclosure or distribution of the
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[Freesurfer] FreeSurfer Tutorial and Workshop in Sao Paulo, Brazil

[Pedro Paulo de Magalhães Oliveira Junior]

The FreeSurfer 
Development
Team is hosting a two-day course for beginner and experienced users of
FreeSurfer . Day 1 will
be an introduction
toFreeSurfer (or
a refresher for those more experienced). Day 2 will cover everything you
need to know for analyzing your data. Topics are listed below. There are
only *30 available spots* for this course. The course will not cover FS-FAST
neither fMRI analysis.

Computers will be provided to all pairs of registrants, which will have
FreeSurfer  and data
already installed. Attendees will work in pairs (sharing a computer).

The course will be held at Sao Paulo health care complex of HCFMUSP. The
lecturers will be: Nick Schmansky, Allison Stevens and Lilla Zollei

For more information:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule

For requesting a place in the course please write to my e-mail.

I think it's a great opportunity for people from Latin America and South
Africa.

Best Regards,

Pedro Paulo Oliveira Jr
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
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[Freesurfer] bbregister: PET and MRI

[Rafa x]

Dear FS Team,

I have a problem with the bbregister command. I used it for coregister
a MRI with a PET.
My first step is set the same origin and orientation for both images
(approximately) (I use SPM or tkregister2).
After, I write in the terminal "bbregister --mov s24PET.img --t1 --s
sr24 --init-fsl --reg register.dat"(s24 is the name of my patient)
The result of the process is a bad corregister (see the included file).

 I would like to improve this result.
 Maybe the number of iterations is too less (I'm not sure of that)
 I probed with the flags  SPM, FSL and HEADER but they don't provide
good result.


 Thank you all in advance.
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[Freesurfer] Version re-run

[Martin Ystad]

Hi all,
I have 100-something scans already run on a FreeSurfer version from 2005 
that I'd like to re-run with the newest version of FreeSurfer. The 
subjects contain manual edits to the brainmask.mgz and wm.mgz, as well 
as control points. As far as I have understood, when running autorecon2 
my manual edits will be saved by default. However, is there any need to 
re-run the autorecon1-steps for my subjects?

Also: when do you plan to release the next version of FreeSurfer?

Many thanks,
Martin Ystad
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Re: [Freesurfer] cortical thickness in temporal pole

[rahul]

Hi Lucia,

Just to re-iterate what Bruce already mentioned, you should really inspect
the temporal pole areas thoroughly (i.e. make sure the white and pial
surfaces are not including neighboring 'artifacts' such as temporal bone,
etc.). We usually find the signal intensity is generally decreased in this
area due to the complex anatomy (temporal bone, CN V nucleus, and carotid
vessels all are in the temporal pole neighborhood) and generally requires
more manual work.

Just curious, how old are your controls? For our older controls (age
65-80), using a standard MPRAGE sequence, we get mean thickness of 3.11
for left and 3.10 for right temporal pole.

Hope this is helpful.

Best,

rahul

> Many thanks for your e-mail, Bruce.
>
> Yes, I've inspected all data, and one of the things that makes me more
> worried is that I had to edit many subjects in this area because there was
> WM/GM that was cut. So, just in case you have previous results of mean
> cortical thickness for this area, would it be possible to let me know? I
> couldn't find that in any paper.
>
> Many thanks,
>
> Lucia
>
>> Hi Lucia,
>>
>> temporal pole is among the thickest cortical regions, but you should
>> visually inspect your data to check that it is accurate.
>>
>> cheers,
>> Bruce
>>
>>
>> On Mon, 16 Feb 2009, Lucia Garrido wrote:
>>
>>> Dear all,
>>>
>>> I'm comparing average cortical thickness values between groups using
>>> regions defined in the aparc files. I find significant differences in
>>> the
>>> right temporal pole. I was expecting difference here, but I'm concerned
>>> about the mean values of thickness. For controls, that value is 4.01,
>>> whereas in the left temporal pole is 3.80. Could anyone let me know if
>>> these values look too high?
>>>
>>> Thank you very much.
>>>
>>> best wishes,
>>>
>>> lucia
>>>
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>>>
>>>
>>
>
>
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>
>

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Re: [Freesurfer] cortical thickness in temporal pole

[Bruce Fischl]

Hi Lucia,

we published maps of mean thickness in our original Cerebral Cortex paper 
I think, and temporal pole was always among the thickest regions.


cheers,
Bruce
On Mon, 16 
Feb 2009, Lucia Garrido wrote:



Many thanks for your e-mail, Bruce.

Yes, I've inspected all data, and one of the things that makes me more
worried is that I had to edit many subjects in this area because there was
WM/GM that was cut. So, just in case you have previous results of mean
cortical thickness for this area, would it be possible to let me know? I
couldn't find that in any paper.

Many thanks,

Lucia


Hi Lucia,

temporal pole is among the thickest cortical regions, but you should
visually inspect your data to check that it is accurate.

cheers,
Bruce


On Mon, 16 Feb 2009, Lucia Garrido wrote:


Dear all,

I'm comparing average cortical thickness values between groups using
regions defined in the aparc files. I find significant differences in
the
right temporal pole. I was expecting difference here, but I'm concerned
about the mean values of thickness. For controls, that value is 4.01,
whereas in the left temporal pole is 3.80. Could anyone let me know if
these values look too high?

Thank you very much.

best wishes,

lucia

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Re: [Freesurfer] cortical thickness in temporal pole

[Lucia Garrido]

Many thanks for your e-mail, Bruce.

Yes, I've inspected all data, and one of the things that makes me more
worried is that I had to edit many subjects in this area because there was
WM/GM that was cut. So, just in case you have previous results of mean
cortical thickness for this area, would it be possible to let me know? I
couldn't find that in any paper.

Many thanks,

Lucia

> Hi Lucia,
>
> temporal pole is among the thickest cortical regions, but you should
> visually inspect your data to check that it is accurate.
>
> cheers,
> Bruce
>
>
> On Mon, 16 Feb 2009, Lucia Garrido wrote:
>
>> Dear all,
>>
>> I'm comparing average cortical thickness values between groups using
>> regions defined in the aparc files. I find significant differences in
>> the
>> right temporal pole. I was expecting difference here, but I'm concerned
>> about the mean values of thickness. For controls, that value is 4.01,
>> whereas in the left temporal pole is 3.80. Could anyone let me know if
>> these values look too high?
>>
>> Thank you very much.
>>
>> best wishes,
>>
>> lucia
>>
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>>
>>
>


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Re: [Freesurfer] cortical thickness in temporal pole

[Bruce Fischl]

Hi Lucia,

temporal pole is among the thickest cortical regions, but you should 
visually inspect your data to check that it is accurate.


cheers,
Bruce


On Mon, 16 Feb 2009, Lucia Garrido wrote:


Dear all,

I'm comparing average cortical thickness values between groups using
regions defined in the aparc files. I find significant differences in the
right temporal pole. I was expecting difference here, but I'm concerned
about the mean values of thickness. For controls, that value is 4.01,
whereas in the left temporal pole is 3.80. Could anyone let me know if
these values look too high?

Thank you very much.

best wishes,

lucia

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[Freesurfer] cortical thickness in temporal pole

[Lucia Garrido]

Dear all,

I'm comparing average cortical thickness values between groups using
regions defined in the aparc files. I find significant differences in the
right temporal pole. I was expecting difference here, but I'm concerned
about the mean values of thickness. For controls, that value is 4.01,
whereas in the left temporal pole is 3.80. Could anyone let me know if
these values look too high?

Thank you very much.

best wishes,

lucia

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