Re: [Freesurfer] Are the average subjects generated by different version of Freesurfer differ greatly?

[Bruce Fischl]

the average subject is mostly for visualization, so I wouldn't think it 
would matter that much.


cheers,
Bruce

On Fri, 12 Sep 2008, Zhangyuanchao wrote:


Are the average subjects generated by different version of Freesurfer differ 
greatly?
 I obtained the cortical thickness,lGI using Freesurfer 4.0.3,
 However, average subject can not be generated using Freesurfer 4.0.3 because 
of error.Can I use the average subject generated using Freesurfer of another 
version?
 Thanks!


-
ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] freesurfer

[Hwee Ling Lee]

Hi All,

I was looking for methods to create a superior temporal sulcus
mask (upper and lower boundary).
>From my understanding, Freesurfer does a pretty good job in labeling the
sulcus, hence I was wondering if there are possible ways to write the
particular ROI as a mask image for each individual subject, and preferably
to be in the MNI space or if not, at least in the native space.

Thank you.

Best wishes,
HweeLing



---
Hwee Ling, Lee
Max-Planck Institute for Biological Cybernetics
Cognitive Neuroimaging
Spemannstrasse 41
72076 Tuebingen
Germany
Tel: +49-70701-601-1785
Fax: +49-7071-601-616
[EMAIL PROTECTED]
[EMAIL PROTECTED]
http://www.kyb.mpg.de/~hweeling
---





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

[Keith Duncan]

I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I 
think made in tkmedit) shows canonical slices with small green crosses - 
is there a way to do a similar thing (preferably not by placing the 
crosses manually) on the inflated brain?


Thanks again,

Keith
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

[Bruce Fischl]

Hi Keith,

I guess you could write your cross locations into an annotation file then 
they would be displayed as small colored patches. I'm not sure which 
figure you are referring to, or exactly what you're trying to do though.


Bruce
On 
Fri, 12 Sep 2008, Keith Duncan wrote:


I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I think 
made in tkmedit) shows canonical slices with small green crosses - is there a 
way to do a similar thing (preferably not by placing the crosses manually) on 
the inflated brain?


Thanks again,

Keith
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to display a large set of peaks on inflated brain?

[Bruce Fischl]

Hi Keith,

this is inevitable when sampling from the volume onto the surface, 
particularly if the volume maps are blurry. Then a single volume blob will 
intersect e.g. two banks of a sulcus and show up as two distinct blobs.


cheers,
Bruce


On Thu, 
11 Sep 2008, Keith Duncan wrote:



Hi FS experts,

I am trying to display a large set of peaks on an inflated brain to
illustrate the spread of the peaks over a gyrus & sulcus, similar to
what might be done in a meta-analysis. Is there an easy way to do this?

I tried generating a binary mask in 3D (in MNI space) and then
converting that to a .w file using mri_vol2surf but some of the peaks
seem to be lost and the peaks that do appear, are splodges rather than a
neat circle/ellipse/whatever, which makes it look like an activation map.

Thanks in advance!

Keith

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer

[Bruce Fischl]

Hi HweeLing,

I think the aparc.a2005s has the STS labeled in it, so you should already 
have what you need in individual space. You could use mri_annot2label, 
mri_label2vol and mri_vol2vol to transform this into MNI if you need to.


cheers,
Bruce



 On Fri, 12 Sep 2008, Hwee Ling Lee wrote:



Hi All,

I was looking for methods to create a superior temporal sulcus
mask (upper and lower boundary).

From my understanding, Freesurfer does a pretty good job in labeling the

sulcus, hence I was wondering if there are possible ways to write the
particular ROI as a mask image for each individual subject, and preferably
to be in the MNI space or if not, at least in the native space.

Thank you.

Best wishes,
HweeLing



---
Hwee Ling, Lee
Max-Planck Institute for Biological Cybernetics
Cognitive Neuroimaging
Spemannstrasse 41
72076 Tuebingen
Germany
Tel: +49-70701-601-1785
Fax: +49-7071-601-616
[EMAIL PROTECTED]
[EMAIL PROTECTED]
http://www.kyb.mpg.de/~hweeling
---





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

[Keith Duncan]

Hi Bruce,

Basically I have data from 45 subjects, and I would like to show the 
variability in the location of the individuals peak activation. They are 
all on the ventral surface, and are in occipitotemporal sulcus and 
fusiform gyrus - so ideally I'd like to use the inflated brain as it 
would nicely illustrate the variability The peaks could be represented 
by crosses or dots, but they'd have to be small enough, too big and the 
45 peaks would end up looking like an activation map. Would this be 
possible using the annotation file?  If so, how do I go about writing 
one? (Sorry if this is a basic question - I've just started using 
Freesurfer)


Thanks again,

Keith


Bruce Fischl wrote:

Hi Keith,

I guess you could write your cross locations into an annotation file 
then they would be displayed as small colored patches. I'm not sure 
which figure you are referring to, or exactly what you're trying to do 
though.


Bruce
On Fri, 12 Sep 2008, Keith Duncan wrote:

I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I 
think made in tkmedit) shows canonical slices with small green 
crosses - is there a way to do a similar thing (preferably not by 
placing the crosses manually) on the inflated brain?


Thanks again,

Keith
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

[Bruce Fischl]

No problem. What I would do is create a surface-based label file with the 
peak in each subject, then use mris_spherical_average to generate an 
average label (this will be in spherical coords). A typical command line 
would be:


set average_subject=fsaverage
mris_spherical_average -osurf sphere -sdir $SUBJECTS_DIR -n -o
 ${average_subject} label ${hemi}.$label $hemi sphere.reg $SUBJECTS  \
 $SUBJECTS_DIR/${average_subject}/label/${hemi}.$label.label


note that the -n means "normalize" so that it will divide by the total 
number of subjects. Taking this out will make the output in [0 nsubjects] 
instead of [0 1]. You can then load the the  average label in tksurfer on 
the fsaverage subjects, use tools->label->copy label statistics to overlay, 
and directly visualize the probability of each point on the surface being 
in the label.


cheers,
Bruce



 On Fri, 12 Sep 2008, Keith 
Duncan wrote:



Hi Bruce,

Basically I have data from 45 subjects, and I would like to show the 
variability in the location of the individuals peak activation. They are all 
on the ventral surface, and are in occipitotemporal sulcus and fusiform gyrus 
- so ideally I'd like to use the inflated brain as it would nicely illustrate 
the variability The peaks could be represented by crosses or dots, but they'd 
have to be small enough, too big and the 45 peaks would end up looking like 
an activation map. Would this be possible using the annotation file?  If so, 
how do I go about writing one? (Sorry if this is a basic question - I've just 
started using Freesurfer)


Thanks again,

Keith


Bruce Fischl wrote:

Hi Keith,

I guess you could write your cross locations into an annotation file then 
they would be displayed as small colored patches. I'm not sure which figure 
you are referring to, or exactly what you're trying to do though.


Bruce
On Fri, 12 Sep 2008, Keith Duncan wrote:

I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I think 
made in tkmedit) shows canonical slices with small green crosses - is 
there a way to do a similar thing (preferably not by placing the crosses 
manually) on the inflated brain?


Thanks again,

Keith
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] MNI152

[Cherif Sahyoun]

Hi,

I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152
volume. Any ideas on how to do it?
Usually I'd mri_label2label and then mri_label2vol, but I don't think there
is a surface version of MNI152, is there?

Thanks!
Cherif
--
Cherif P. Sahyoun HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[EMAIL PROTECTED]

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
---
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Methodology Papers.

[Matt Clarkson]

Dear everyone,

Hopefully someone can help me.  If I do "recon-all --help" i can see a 
list of 31 steps for the main cortical thickness pipeline.  Does anyone 
have a list that links each of the 31 steps to the most current 
methodology paper?


I've been reading most of the methodology papers referenced in the wiki, 
but the software has clearly evolved over the years, and even though you 
can read the wiki, and trawl through log files, I want to be absolutely 
sure that for each step, I know exactly what algorithm is applied.  Has 
anyone gone through this before?


Thanks in advance,

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MNI152

[Doug Greve]

You can use mri_label2vol and spec 
$FREESURFER_HOME/average/mni152.register.dat as the registration file.


Cherif Sahyoun wrote:


Hi,

I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152 
volume. Any ideas on how to do it?
Usually I'd mri_label2label and then mri_label2vol, but I don't think 
there is a surface version of MNI152, is there?


Thanks!
Cherif
--
Cherif P. Sahyoun HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[EMAIL PROTECTED] 

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
---



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Methodology Papers.

[Bruce Fischl]

Hi Matt,

the methodologies are described in those papers. Sorry, I don't think 
there's any one or two paper summary - it's just too much stuff over the 
years (topology correction, segmentation, surface analysis, morphing, 
etc).


Bruce

On Fri, 12 Sep 2008, Matt Clarkson wrote:


Dear everyone,

Hopefully someone can help me.  If I do "recon-all --help" i can see a list 
of 31 steps for the main cortical thickness pipeline.  Does anyone have a 
list that links each of the 31 steps to the most current methodology paper?


I've been reading most of the methodology papers referenced in the wiki, but 
the software has clearly evolved over the years, and even though you can read 
the wiki, and trawl through log files, I want to be absolutely sure that for 
each step, I know exactly what algorithm is applied.  Has anyone gone through 
this before?


Thanks in advance,

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer

[Doug Greve]

You can also skip the 1st two steps and just convert aparc+aseg.mgz to 
MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then 
look for voxels with values 1030 (left STG) or 2030 (right STG).


doug

Bruce Fischl wrote:


Hi HweeLing,

I think the aparc.a2005s has the STS labeled in it, so you should 
already have what you need in individual space. You could use 
mri_annot2label, mri_label2vol and mri_vol2vol to transform this into 
MNI if you need to.


cheers,
Bruce



 On Fri, 12 Sep 2008, Hwee Ling Lee wrote:



Hi All,

I was looking for methods to create a superior temporal sulcus
mask (upper and lower boundary).

From my understanding, Freesurfer does a pretty good job in labeling 
the


sulcus, hence I was wondering if there are possible ways to write the
particular ROI as a mask image for each individual subject, and 
preferably

to be in the MNI space or if not, at least in the native space.

Thank you.

Best wishes,
HweeLing



---
Hwee Ling, Lee
Max-Planck Institute for Biological Cybernetics
Cognitive Neuroimaging
Spemannstrasse 41
72076 Tuebingen
Germany
Tel: +49-70701-601-1785
Fax: +49-7071-601-616
[EMAIL PROTECTED]
[EMAIL PROTECTED]
http://www.kyb.mpg.de/~hweeling
---





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ces and percent signal change

[Doug Greve]

It corresponds to the signal change, which is more-or-less A-fixation, 
but not exactly. The percent signal change is in cespct.


doug

Reza Rajimehr wrote:


Hi,

For a stimulus condition 'A' and a fixation condition, does the ces file
for the contrast 'A - fix' correspond to the % signal change for the
condition A?

Thanks,
Reza


Reza Rajimehr, MD
Postdoctoral Research Fellow

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th Street
Charlestown, MA 02129

Phone: 617-669-0930
Email: [EMAIL PROTECTED]

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] segmentation fault (core dumped)

[Zhangyuanchao]

Dear Mr or Ms,
  My computer was installed with Freesurfer v4.0.3,centos4,
  To make an average surface,I launch "make_average_subject" command,
  I come across an error : 
Processing subject 25/52 sh45 ...
  Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
  Segmentation fault (core dumped).
  Could you help me? How can I solve the problem? 
  Thanks!
   yczhang
  

   
-
 雅虎邮箱，您的终生邮箱！___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Methodology Papers.

[Matt Clarkson]

Hi Bruce,

for sure, I didnt expect it to all be in one place!

For example, what I believe are the original papers (Neuroimage 9 1999, 
and the 1993 Cognitive Neuroscience paper), describe the first method, 
then we have all the other subsequent papers. So for example, does the 
current methodology use the brain stripping from Neuroimage 22 (2004), 
(i believe it does, but I'm a newbie.), and is the volume segmentation 
best described in the 2002 Neurotechnique paper "Whole brain 
segmentation"?  Or has it been superceded by the methodology in 
Neuroimage 23 (2004) "Sequence-independent segmentation of magnetic 
resonance imaging".


I suppose, another way of phrasing the question is simply, which 
methodology papers are in the current software version, which ones have 
been superseded, and which ones are totally cutting edge research, and 
not part of the software package?
I just wondered if anyone had a view on this, or compiled a handy list 
that they would be willing to share?


Many thanks in advance.

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066



Bruce Fischl wrote:

Hi Matt,

the methodologies are described in those papers. Sorry, I don't think 
there's any one or two paper summary - it's just too much stuff over 
the years (topology correction, segmentation, surface analysis, 
morphing, etc).


Bruce

On Fri, 12 Sep 2008, Matt Clarkson wrote:


Dear everyone,

Hopefully someone can help me.  If I do "recon-all --help" i can see 
a list of 31 steps for the main cortical thickness pipeline.  Does 
anyone have a list that links each of the 31 steps to the most 
current methodology paper?


I've been reading most of the methodology papers referenced in the 
wiki, but the software has clearly evolved over the years, and even 
though you can read the wiki, and trawl through log files, I want to 
be absolutely sure that for each step, I know exactly what algorithm 
is applied.  Has anyone gone through this before?


Thanks in advance,

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Methodology Papers.

[Bruce Fischl]

Hi Matt,

the Segonne paper is the current skull stripping (the hybrid one), although 
it's evolved somewhat since then (unpublished). The segmentation is both 
those papers (the first one is the segmentation methodology, the 2nd is the 
addition of a nonlinear warp), plus the more recent one with Han as the 1st 
author describing how we reestimate the atlas to account for sequence 
differences.  The surface stuff is similar in that the 93 paper is still 
relevant as are the two 99 papers, then the parcellation, spherical 
morphing, topology correction and more recent (Desikan) parcellation.


cheers,
Bruce


On Fri, 12 Sep 2008, Matt 
Clarkson wrote:



Hi Bruce,

for sure, I didnt expect it to all be in one place!

For example, what I believe are the original papers (Neuroimage 9 1999, and 
the 1993 Cognitive Neuroscience paper), describe the first method, then we 
have all the other subsequent papers. So for example, does the current 
methodology use the brain stripping from Neuroimage 22 (2004), (i believe it 
does, but I'm a newbie.), and is the volume segmentation best described in 
the 2002 Neurotechnique paper "Whole brain segmentation"?  Or has it been 
superceded by the methodology in Neuroimage 23 (2004) "Sequence-independent 
segmentation of magnetic resonance imaging".


I suppose, another way of phrasing the question is simply, which methodology 
papers are in the current software version, which ones have been superseded, 
and which ones are totally cutting edge research, and not part of the 
software package?
I just wondered if anyone had a view on this, or compiled a handy list that 
they would be willing to share?


Many thanks in advance.

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066



Bruce Fischl wrote:

Hi Matt,

the methodologies are described in those papers. Sorry, I don't think 
there's any one or two paper summary - it's just too much stuff over the 
years (topology correction, segmentation, surface analysis, morphing, 
etc).


Bruce

On Fri, 12 Sep 2008, Matt Clarkson wrote:


Dear everyone,

Hopefully someone can help me.  If I do "recon-all --help" i can see a 
list of 31 steps for the main cortical thickness pipeline.  Does anyone 
have a list that links each of the 31 steps to the most current 
methodology paper?


I've been reading most of the methodology papers referenced in the wiki, 
but the software has clearly evolved over the years, and even though you 
can read the wiki, and trawl through log files, I want to be absolutely 
sure that for each step, I know exactly what algorithm is applied.  Has 
anyone gone through this before?


Thanks in advance,

Matt

Matt Clarkson
Senior Research Associate
Dementia Research Centre
UCL
Institute Of Neurology
Queen Square
London WC1N 3BG

[EMAIL PROTECTED]
Tel: 08451 555 000 ext. 723653
Fax: 020 7676 2066


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer










___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] segmentation fault (core dumped), when making average subject

[Zhangyuanchao]

Dear Mr or Ms,
  My computer was installed with Freesurfer v4.0.3,centos4,
  To make an average surface,I launch "make_average_subject" command,
  I come across an error : 
Processing subject 25/52 sh45 ...
  Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
  Segmentation fault (core dumped).
  Could you help me? How can I solve the problem? 
  Thanks!
   yczhang

   
-
 雅虎邮箱，您的终生邮箱！___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mris_volmask error

[Dahlia Sharon]

Hi,

 

I ran recon-all, and it exited with an error at this command:

 

mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance subj10

 

The error message reads: 

 

mris_volmask.bin: error while loading shared libraries: libvtkpng.so.5.2:
cannot open shared object file: No such file or directory

 

On the off-chance that it's missing an input file, I made sure that I have
orig.mgz in the mri folder and ?h.white and pial in the surf folder.

 

 

Does anyone have an idea what could be wrong here?

 

Thanks!

Dahlia.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] tksurfer woes

[Mark J. Pearrow]

Hi all,

FYI, this same problem has been bugging me for several months. Most  
ATI chipsets have a nice driver installer bundle that, once installed,  
will let you run tksurfer without a problem. However, this particular  
chipset, the ES1000, which is the chipset on Dell PowerEdge servers,  
is unsupported and seems to have been abandoned by ATI/AMD/whoever  
they are this week.


If you happen to be unlucky enough to have Dell PowerEdge servers with  
this chipset and the need to run tksurfer, you're out of luck, until  
you put a slightly "better" graphics card in. I just managed to  
install an nVidia 8400GS (the x1 PCI-e version - the poweredge PCI-e  
bus is x8, which means it won't work with any of the most recent  
cards, but will work with slightly older x1 cards) and tksurfer works  
fine now. I can provide the gory details if you're in this boat.


mjp




On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote:


Hi all,
I’m having trouble using freesurfer’s tksurfer program (I only get a  
sliver of the brain).  Here is the error info I get:


[ghidra: subjects]$ tksurfer 77059 lh pial
surfer: current subjects dir: /home/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/freesurfer/subjects
surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ 
T1.mgz

surfer: vertices=184362, faces=368720
Loading /home/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(77059)
surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...

The driver info (from /etc/X11/xorg.conf) is:
Section "Device"
  BoardName"ES1000 515E"
  BusID"14:13:0"
  Driver   "radeon"
  Identifier   "Device[0]"
  Option   "GARTSize" "32"
  Option   "usevnc" "yes"

Section "DRI"
Group  "video"
Mode   0660
EndSection


I’m have an onboard ATI ES1000 515E graphics chip.

Any ideas??
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine


IMPORTANT NOTICE: This e-mail is meant only for the use of the  
intended recipient. It may contain confidential information which is  
legally privileged
or otherwise protected by law. If you received this e-mail in error  
or from someone who was not authorized to send it to you, you are  
strictly prohibited
from reviewing, using, disseminating, distributing or copying the e- 
mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND  
DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mris_volmask error

[Nick Schmansky]

Dahlia,

Try again now, I just fixed it.

Nick


On Fri, 2008-09-12 at 12:21 -0700, Dahlia Sharon wrote:
> Hi,
> 
>  
> 
> I ran recon-all, and it exited with an error at this command:
> 
>  
> 
> mris_volmask --label_left_white 2 --label_left_ribbon 3 --
> label_right_white 41 --label_right_ribbon 42 --save_ribbon --
> save_distance subj10
> 
>  
> 
> The error message reads: 
> 
>  
> 
> mris_volmask.bin: error while loading shared libraries:
> libvtkpng.so.5.2: cannot open shared object file: No such file or
> directory
> 
>  
> 
> On the off-chance that it’s missing an input file, I made sure that I
> have orig.mgz in the mri folder and ?h.white and pial in the surf
> folder.
> 
>  
> 
>  
> 
> Does anyone have an idea what could be wrong here?
> 
>  
> 
> Thanks!
> 
> Dahlia.
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] (no subject)

[Wang, Xin]

Hello, Group,
 
I have a hard time to register the functional ROIs to the exact location 
(x,y,z) on thickness map. I can't find articles that register the fsl result 
onto freesurfer thickness map and then do the ROI analysis. Could someone 
kindly list some references for me? I appreciate if anyone is willing to share 
his/her experience on registration of functional and thickness maps (especially 
ROIs).  
Thanks in advance,
 
Xin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer