[Freesurfer] N3 for improving cerebellum segmentation

[Tetiana Dadakova]

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 for the options: -distance and -iterations?

Cerebellum is very important for our study, therefore I am looking for
ways of how to make the segmentation as good as possible.

Thank you for your time and help,
Tanja.
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Re: [Freesurfer] recommende pc and cuda

[Knut J Bjuland]

Will a Tesla C2050 or another good CPU be able to reduce the running time from 
20-24 hr to less time like for instance 8hr or below that time.

Knut J

> From: rg...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 4 Apr 2011 09:23:07 -0400
> Subject: Re: [Freesurfer] recommende pc and cuda
> 
> 
> On Mon, 2011-04-04 at 13:13 +0200, Knut J Bjuland wrote:
> 
> > I am in the process of acquiring a new computer to run freesurfer on.
> > I am currently think about buying a PC with a geforce 4X0 and a Tesla
> > card along with a two screen setup running either Ubuntu or Redhat
> > Linux enterprise 6.0. I think the PC should be a core i7 with 6 core
> > and above 12 gigs byte of ram. What kind of tesla card is recommend
> > for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0.
> 
> If your budget can withstand a Tesla C2050, by all means go for it. I've
> not checked in detail how much GPU RAM FreeSurfer requires, so it might
> be possible to run on a 'lesser' GeForce card. There's not enough double
> precision stuff to be significant in the GeForce vs Tesla choice. And I
> don't do overlapping transfers, which would be another factor. The main
> thing to do is make sure you have a 'Fermi' GPU - that's a Tesla 20
> series, or GeForce GTX 400 or 500 series. Large speed ups depend on the
> Fermi card.
> 
> As for the CPU... just make sure it's Nehalem class. FreeSurfer on both
> the CPU and GPU likes fast RAM access.
> 
> As for CUDA 4.0 support that will depend on NVIDIA not breaking
> backwards compatibility (not an absolute given - they are not IBM). I
> don't expect any trouble, but until we upgrade to CUDA 4.0 here (and 3.2
> just broke binary compatibility), I wouldn't want to promise anything.
> 
> HTH,
> 
> Richard
> 
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[Freesurfer] edit volume remotely

[Sara Lozano-Zahonero]

Dear all,

We are trying to edit a new wm volume  remotely. We want to substitute
   the mouse click with an external command. Since we are not familiar with
tcl/tk we don't know where this action (mouse click to
edit volume) happens within the script tkmedit.tcl. Could you please
help us: How could we edit (or delete) voxel programmatically? The
resulted wm volume should be saved for regenerating the surfaces with
?recon-all?.
Thanks in advance for your help
Sara


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Re: [Freesurfer] recommende pc and cuda

[Richard G. Edgar]

On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote:
> Will a Tesla C2050 or another good CPU be able to reduce the running
> time from 20-24 hr to less time like for instance 8hr or below that
> time.

On the standard test case we use here, a full recon-all run takes 8
hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using
the Tesla C2050.

Richard

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Re: [Freesurfer] different vertexes and faces on pial and inflated surface of the same hemisphere

[Sita Kakunoori]

Hi Forrest,

You can probably try running

recon-all -make all -s 

and see if that fixes the problem.

Sita.



On Sun, 3 Apr 2011, Forrest Sheng Bao wrote:

> hi all,
>
> I encountered a strange problem today. I used
>
> recon-all -all
>
> to get surfaces of a subject. I have no problem with his/her left
> hemisphere. But for the right hemisphere, the numbers of vertexes and faces
> of pial surface are different from those of the inflated surface. I checked
> the headers of curavture and convexity maps also. They all tell the same
> information as the pial surface's header. But not the same as the header of
> inflated surface. I also checked the file content. The file did not seem
> like corrupted.
>
> I have never had the problem with other data i have. Only on this hemisphere
> of the subject.
>
> Has anyone out there experienced the same problem before?
>
> Cheers, Forrest
>
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Re: [Freesurfer] preproc-sess

[Douglas N Greve]

Make sure that your subjectname file has the name of the FreeSurfer 
subject folder as found in $SUBJECTS_DIR (it looks like it is empty). 
You don't need the retinotopy data in the $SUBJECTS_DIR.
doug

Michelle Umali wrote:
> Dear Freesurfers,
> I am still struggling with the retinotopy analysis.  Whenever I try to 
> run preproc-sess, I get this message:
>
> Session: /home/fsl/structural/LD08 
> Tue Apr  5 07:22:28 BST 2011
>  is not in SUBJECTS_DIR
>   SUBJECTS_DIR is /home/fsl/structural
>
> I put the retinotopic and structural data into the structural 
> directory.  In addition, I have the subjectname file that contains 
> LD08 in this case.
>
> Any help would be most appreciated.  I am attaching the output, in 
> case it is helpful.
>
> Thanks.
> Michelle
>
>
>>>
>>> ing Douglas N Greve :
>>>
 I don't have a formal manual yet (working on it). Below are a list of
 steps that you need to run. The version 5 retinotopy stream is now
 integrated with the rest of FSFAST, which is documented here:
 http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt

 doug

 1. Create retinotopy paradigm file in each run directory, eg,
 session/bold/001/rtopy.par
 session/bold/002/rtopy.par etc

  This text file identifies the data in the directory in terms of the
  stimulus type (polar or eccen) and the direction (pos or neg).  Its
  contents should look somethign like:

   stimtype polar
   direction pos

 2. Run preprocessing

  preproc-sess -surface self lhrh -fwhm 5

 3. Create analysis (30 sec period, 'rtopy.par' is the name of the
  paradigm file from above):

 mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \
   -retinotopy 30 -paradigm rtopy.par
 mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \
   -retinotopy 30 -paradigm rtopy.par

 4. Run analysis

 selxavg3-sess -a rtopy.self.lh -sf ...
 selxavg3-sess -a rtopy.self.rh -sf ...
 fieldsign-sess -a rtopy.self.lh -occip -sf ...
 fieldsign-sess -a rtopy.self.rh -occip -sf ...

 5. View results
 a. Significance maps:
 tksurfer-sess -a rtopy.self.lh -s sessid
 b. Display raw angle
 tksurfer-sess -a rtopy.self.lh -s sessid -map angle
 c. Display angle masked by by sig
 tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked
 d. Display field sign
 tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] Convert annotations longitudinally

[Andrew Dumas]

Hi FreeSurfer experts,

Is there a way to move annotations from the same subject at one
timepoint to another? I've tried doing this using a discrete-valued
surface and using seg2annot, but, when I convert surfaces there are
vertices between regions whose values are averages of bordering
vertices. This ruins the continuity of each individual label with little
islands of various values. Is there a mri_annot2annot or equivalent?
Thanks!

Andrew Dumas

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Re: [Freesurfer] recommende pc and cuda

[Ian Malone]

Richard G. Edgar wrote:

On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote:
  

Will a Tesla C2050 or another good CPU be able to reduce the running
time from 20-24 hr to less time like for instance 8hr or below that
time.



On the standard test case we use here, a full recon-all run takes 8
hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using
the Tesla C2050.

  


Would I be right in concluding that a 4-core Nehalem (e.g. i7) has more 
throughput than the C2050 then?


--
imalone
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Re: [Freesurfer] Convert annotations longitudinally

[Douglas Greve]

Try using mri_surf2surf with the --sval-annot flag.

doug

On 4/5/11 11:20 AM, Andrew Dumas wrote:
> Hi FreeSurfer experts,
>
> Is there a way to move annotations from the same subject at one
> timepoint to another? I've tried doing this using a discrete-valued
> surface and using seg2annot, but, when I convert surfaces there are
> vertices between regions whose values are averages of bordering
> vertices. This ruins the continuity of each individual label with little
> islands of various values. Is there a mri_annot2annot or equivalent?
> Thanks!
>
> Andrew Dumas
>
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>
>
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Re: [Freesurfer] recommende pc and cuda

[Richard G. Edgar]

On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote:
> Richard G. Edgar wrote: 
> > On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote:
> >   
> > > Will a Tesla C2050 or another good CPU be able to reduce the running
> > > time from 20-24 hr to less time like for instance 8hr or below that
> > > time.
> > > 
> > 
> > On the standard test case we use here, a full recon-all run takes 8
> > hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using
> > the Tesla C2050.
> > 
> >   
> 
> Would I be right in concluding that a 4-core Nehalem (e.g. i7) has
> more throughput than the C2050 then?

Yes, but less than having 3 CPU jobs, and one GPU one. I did test once,
and there isn't much penalty to running one recon-all job per core on a
Nehalem system.

Right now, the CPU still does most of the work in the recon-all stream -
it's something of a game of Amdahl's Law Wac-A-Mole. You could always
try starting 4 GPU jobs at once I've not done the testing, but a
C2050 would probably have enough RAM, and in any given recon-all run,
the GPU does spend a lot of time idle. Hence, it would end up being
divvied up between the four jobs.

Richard

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Re: [Freesurfer] Convert annotations longitudinally

[Martin Reuter]

Hi Andrew,

not sure if I understand. 

The surfaces in the longitudinal directories across time (within
subject) are in registration, so you should be able to use the same
annotation for all time points.

Martin

On Tue, 2011-04-05 at 11:20 -0400, Andrew Dumas wrote:
> Hi FreeSurfer experts,
> 
> Is there a way to move annotations from the same subject at one
> timepoint to another? I've tried doing this using a discrete-valued
> surface and using seg2annot, but, when I convert surfaces there are
> vertices between regions whose values are averages of bordering
> vertices. This ruins the continuity of each individual label with little
> islands of various values. Is there a mri_annot2annot or equivalent?
> Thanks!
> 
> Andrew Dumas
> 
> ___
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> 
> 

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[Freesurfer] preproc-sess path structure

[Michelle Umali]

Hi Doug,
Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program  
is?  I had done this:

setenv SUBJECTS_DIR /home/fsl/structural
So this SUBJECTS_DIR is not located where FreeSurfer is.

Is the following the exact correct path:
FreeSurfer/$SUBJECTS_DIR/LD08/subjectname
where LD08 is the file subjectname says LD08 and freesurfer must be  
capitalized as FreeSurfer?

and all the retinotopy data can be in:
/home/fsl/structural/bold

and recon-all subfolders and data in
/home/fsl/structural

Sorry for such a basic question.

Thanks.
Michelle


Quoting Douglas N Greve :

> Make sure that your subjectname file has the name of the FreeSurfer
> subject folder as found in $SUBJECTS_DIR (it looks like it is empty).
> You don't need the retinotopy data in the $SUBJECTS_DIR.
> doug
>
> Michelle Umali wrote:
>> Dear Freesurfers,
>> I am still struggling with the retinotopy analysis.  Whenever I try  
>>  to run preproc-sess, I get this message:
>>
>> Session: /home/fsl/structural/LD08 
>> Tue Apr  5 07:22:28 BST 2011
>> is not in SUBJECTS_DIR
>>  SUBJECTS_DIR is /home/fsl/structural
>>
>> I put the retinotopic and structural data into the structural   
>> directory.  In addition, I have the subjectname file that contains   
>> LD08 in this case.
>>
>> Any help would be most appreciated.  I am attaching the output, in   
>> case it is helpful.
>>
>> Thanks.
>> Michelle
>>


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Re: [Freesurfer] Convert annotations longitudinally

[Andrew Dumas]

Thanks, Doug-- that's what I was looking for!

Andrew

On Tue, 2011-04-05 at 11:51 -0400, Douglas Greve wrote:
> Try using mri_surf2surf with the --sval-annot flag.
> 
> doug
> 
> On 4/5/11 11:20 AM, Andrew Dumas wrote:
> > Hi FreeSurfer experts,
> >
> > Is there a way to move annotations from the same subject at one
> > timepoint to another? I've tried doing this using a discrete-valued
> > surface and using seg2annot, but, when I convert surfaces there are
> > vertices between regions whose values are averages of bordering
> > vertices. This ruins the continuity of each individual label with little
> > islands of various values. Is there a mri_annot2annot or equivalent?
> > Thanks!
> >
> > Andrew Dumas
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> ___
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> 
> 

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Re: [Freesurfer] preproc-sess path structure

[Douglas Greve]

Hi Michelle,

  the SUBJECTS_DIR is an environment variable that you have to set prior 
to running the anatomical analysis (disregarding the functional analysis 
for a moment). Before running the functional analysis, you must run 
recon-all on the anatomical data, eg

recon-all -all -subject LD08-anat -i anatomical.dicom

this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have 
not done this, you should do this first. Look at the wiki for how to run 
the anatomical analysis.

Once this is done, you should unpack your functional data (looks like 
you might have done this already). In the session directory, create a 
text file called "subjectname". Put the subject name (ie, LD08-anat) 
into the subjectname file.

doug





On 4/5/11 2:15 PM, Michelle Umali wrote:
> Hi Doug,
> Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program
> is?  I had done this:
>
> setenv SUBJECTS_DIR /home/fsl/structural
> So this SUBJECTS_DIR is not located where FreeSurfer is.
>
> Is the following the exact correct path:
> FreeSurfer/$SUBJECTS_DIR/LD08/subjectname
> where LD08 is the file subjectname says LD08 and freesurfer must be
> capitalized as FreeSurfer?
>
> and all the retinotopy data can be in:
> /home/fsl/structural/bold
>
> and recon-all subfolders and data in
> /home/fsl/structural
>
> Sorry for such a basic question.
>
> Thanks.
> Michelle
>
>
> Quoting Douglas N Greve:
>
>> Make sure that your subjectname file has the name of the FreeSurfer
>> subject folder as found in $SUBJECTS_DIR (it looks like it is empty).
>> You don't need the retinotopy data in the $SUBJECTS_DIR.
>> doug
>>
>> Michelle Umali wrote:
>>> Dear Freesurfers,
>>> I am still struggling with the retinotopy analysis.  Whenever I try
>>>   to run preproc-sess, I get this message:
>>>
>>> Session: /home/fsl/structural/LD08 
>>> Tue Apr  5 07:22:28 BST 2011
>>> is not in SUBJECTS_DIR
>>>   SUBJECTS_DIR is /home/fsl/structural
>>>
>>> I put the retinotopic and structural data into the structural
>>> directory.  In addition, I have the subjectname file that contains
>>> LD08 in this case.
>>>
>>> Any help would be most appreciated.  I am attaching the output, in
>>> case it is helpful.
>>>
>>> Thanks.
>>> Michelle
>>>
>
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>
>
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[Freesurfer] Mapping segmentations to SPM Functional Space

[Palzes, Vanessa]

I am wondering if there is a similar function as aseg2feat (which maps
the automatic segmentations from Freesurfer to FSL FEAT functional
space) for the use in SPM functional analysis. This tool poses to be
very useful in creating ROI masks, however, we are using SPM for
functional analysis rather than FSL FEAT.

Thanks,

Vanessa Palzes
Research Assistant
Brain Imaging & EEG Lab
San Francisco VA Medical Center
4150 Clement Street
San Francisco, CA 94121
Tel: 415-221-4810 ext. 6155


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Re: [Freesurfer] Mapping segmentations to SPM Functional Space

[Douglas Greve]

There's nothing explicit, but it's not hard to do. You need to analyze 
your SPM data in the native functional space. Then register the 
functional to the anatomical using bbregister. Then map the 
segmentations into the functional space with mri_label2vol.

doug

On 4/5/11 3:04 PM, Palzes, Vanessa wrote:
> I am wondering if there is a similar function as aseg2feat (which maps
> the automatic segmentations from Freesurfer to FSL FEAT functional
> space) for the use in SPM functional analysis. This tool poses to be
> very useful in creating ROI masks, however, we are using SPM for
> functional analysis rather than FSL FEAT.
>
> Thanks,
>
> Vanessa Palzes
> Research Assistant
> Brain Imaging&  EEG Lab
> San Francisco VA Medical Center
> 4150 Clement Street
> San Francisco, CA 94121
> Tel: 415-221-4810 ext. 6155
>
>
> ___
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>
>
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Re: [Freesurfer] Interpreting results from Qdec

[Gallen, Courtney (NIH/NIDA) [F]]

Hi Doug

Thanks for helping me with this!

First time around I did everything as is outlined in 'Define a Region of 
Interest' here: 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. 

I'll try your suggestion now. The input data would be something like 
?h.volume.fwhm10.fsaverage.mgh, correct?

Thanks again
Courtney

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Sent: Thursday, March 31, 2011 5:44 PM
To: Gallen, Courtney (NIH/NIDA) [F]
Cc: Nick Schmansky; Freesurfer Mailing List
Subject: Re: [Freesurfer] Interpreting results from Qdec

Hi Courtney, did you transfer the label to each individual subject using 
mri_label2label? A better way to replicate your qdec results is to run 
mri_segstats on the input data to qdec (y.mgh usually). Specify the 
label with "--slabel subject hemi yourlabel". Also specify "--avgwf 
subjectdata.txt". This will create this text file with a list of the 
input data for each subject averaged over your label.

doug

Gallen, Courtney (NIH/NIDA) [F] wrote:
> Hi Nick
>
> I'm revisiting this issue and have a few more questions. First, I have a 
> significant interaction between two variables on cortical volume. I drew a 
> label on this ROI and ran mris_anatomical_stats on the label (thank you for 
> that suggestion).
>
> For stats in the output table file, is the column 'GrayVol' the same thing as 
> the cortical volume I looked at in Qdec? I'm asking because when I export 
> GrayVol values into SPSS, there is no longer a significant interaction 
> between my variables (and if this ROI is significant after multiple 
> comparisons across the brain, I'd expect the mean volume from the ROI to be 
> very significant in SPSS).
>
> Please let me know if my questions aren't clear. Thanks in advance
> Courtney 
>
>
> Courtney Gallen
> Post-baccalaureate IRTA
> Neuroimaging Research Branch
> National Institute on Drug Abuse (IRP)
> 251 Bayview Blvd
> Suite 200
> Baltimore, MD 21224
> Tel: (443) 740-2631
>
>
> -Original Message-
> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
> Sent: Thursday, January 13, 2011 3:08 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> Courtney,
>
> if i understand your question, i think one way to do that is to use qdec
> to draw a label on the blob of interest, and the run 'map label to
> subjects', which creates a label file in each subjects label dir, then
> you can run stats on that with mris_anatomical_stats. 
>
> (btw, i'm putting this answer on the list, as others may have better
> ideas.)
>
> n.
>
>
>
> On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F]
> wrote:
>   
>> Hi Nick
>>
>> Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is 
>> my first time using Freesurfer.
>>
>> A follow up question to your answer for question 1. I see that the group 
>> data will be plotted in Qdec for significant blobs, but say there is a 
>> significant interaction between two variables and it's not entirely apparent 
>> what is driving this interaction.
>> Is there a way to extract the mean of this blob for each individual (i.e., 
>> treat it as an ROI or something similar) to determine what's driving the 
>> significance?
>>
>> Thanks in advance!
>> Courtney
>>
>> -Original Message-
>> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
>> Sent: Thursday, December 30, 2010 2:44 PM
>> To: Gallen, Courtney (NIH/NIDA) [F]
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>
>> ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a
>> plot of the data at that surface vertex will appear.  the group will be
>> apparent from that (say, demented group is thinner than non-demented
>> group).  this data is significance data (log p, so '2' is 0.01), so mean
>> and stdev wouldnt apply in that case.  the file 'y.mgh' is the raw data
>> of all subjects in the analysis, so you could extract mean and stdev
>> from that.
>>
>> ans. 2. - slide the 'annotation' opacity slider to show the annotation
>> data (cortical parcellation).  the ctrl left click will also put the
>> region info for that vertex on the lower left of the display.
>>
>> see also: 
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
>>
>> n.
>>
>> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F]
>> wrote:
>> 
>>> Hi,
>>>
>>>  
>>>
>>> I’m currently running analyses in Qdec and have identified areas that
>>> show significant effects in my contrasts. I have two questions related
>>> to interpreting these results.
>>>
>>>  
>>>
>>> 1. How can you interpret the effect in each “blob?” (i.e., which
>>> group has a greater cortical surface area, etc.). Right now, all I
>>> know is that there is an effect in certain areas. Can you export this
>>> data to get means and standard errors?
>>>
>>> 2. Is t

[Freesurfer] 2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy

[angelika lingnau]

*2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento,
Italy*



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http://www.unitn.it/en/cimec),
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Some recent publications as well as further descriptions of our ongoing
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Informal inquiries should be sent to Angelika Lingnau (
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Re: [Freesurfer] preproc-sess path structure

[Michelle Umali]

Hi Doug,

I've run recon-all -all.  I ended up inputing an .mgz file converted  
from a .nii file that was converted from a .dicom.  Was needed info  
lost somewhere along the way?

Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does  
one need -anat?)successfully, because it generated the following  
folders:
bem, label, mri, scripts, src, stats, surf, tmp, touch, trash.  And  
the bem, src, and trash folders are empty, but the others are full of  
files.

Eek.

-Michelle

> Hi Michelle,
>
>   the SUBJECTS_DIR is an environment variable that you have to set prior
> to running the anatomical analysis (disregarding the functional analysis
> for a moment). Before running the functional analysis, you must run
> recon-all on the anatomical data, eg
>
> recon-all -all -subject LD08-anat -i anatomical.dicom
>
> this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have
> not done this, you should do this first. Look at the wiki for how to run
> the anatomical analysis.
>
> Once this is done, you should unpack your functional data (looks like
> you might have done this already). In the session directory, create a
> text file called "subjectname". Put the subject name (ie, LD08-anat)
> into the subjectname file.
>
> doug
>
>
>
>
>
> On 4/5/11 2:15 PM, Michelle Umali wrote:
>> Hi Doug,
>> Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program
>> is?  I had done this:
>>
>> setenv SUBJECTS_DIR /home/fsl/structural
>> So this SUBJECTS_DIR is not located where FreeSurfer is.
>>
>> Is the following the exact correct path:
>> FreeSurfer/$SUBJECTS_DIR/LD08/subjectname
>> where LD08 is the file subjectname says LD08 and freesurfer must be
>> capitalized as FreeSurfer?
>>
>> and all the retinotopy data can be in:
>> /home/fsl/structural/bold
>>
>> and recon-all subfolders and data in
>> /home/fsl/structural
>>
>> Sorry for such a basic question.
>>
>> Thanks.
>> Michelle


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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Interpreting results from Qdec

[Douglas N Greve]

yes, something like ?h.volume.fwhm10.fsaverage.mgh
doug

Gallen, Courtney (NIH/NIDA) [F] wrote:
> Hi Doug
>
> Thanks for helping me with this!
>
> First time around I did everything as is outlined in 'Define a Region of 
> Interest' here: 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. 
>
> I'll try your suggestion now. The input data would be something like 
> ?h.volume.fwhm10.fsaverage.mgh, correct?
>
> Thanks again
> Courtney
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
> Sent: Thursday, March 31, 2011 5:44 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Cc: Nick Schmansky; Freesurfer Mailing List
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> Hi Courtney, did you transfer the label to each individual subject using 
> mri_label2label? A better way to replicate your qdec results is to run 
> mri_segstats on the input data to qdec (y.mgh usually). Specify the 
> label with "--slabel subject hemi yourlabel". Also specify "--avgwf 
> subjectdata.txt". This will create this text file with a list of the 
> input data for each subject averaged over your label.
>
> doug
>
> Gallen, Courtney (NIH/NIDA) [F] wrote:
>   
>> Hi Nick
>>
>> I'm revisiting this issue and have a few more questions. First, I have a 
>> significant interaction between two variables on cortical volume. I drew a 
>> label on this ROI and ran mris_anatomical_stats on the label (thank you for 
>> that suggestion).
>>
>> For stats in the output table file, is the column 'GrayVol' the same thing 
>> as the cortical volume I looked at in Qdec? I'm asking because when I export 
>> GrayVol values into SPSS, there is no longer a significant interaction 
>> between my variables (and if this ROI is significant after multiple 
>> comparisons across the brain, I'd expect the mean volume from the ROI to be 
>> very significant in SPSS).
>>
>> Please let me know if my questions aren't clear. Thanks in advance
>> Courtney 
>>
>>
>> Courtney Gallen
>> Post-baccalaureate IRTA
>> Neuroimaging Research Branch
>> National Institute on Drug Abuse (IRP)
>> 251 Bayview Blvd
>> Suite 200
>> Baltimore, MD 21224
>> Tel: (443) 740-2631
>>
>>
>> -Original Message-
>> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
>> Sent: Thursday, January 13, 2011 3:08 PM
>> To: Gallen, Courtney (NIH/NIDA) [F]
>> Cc: Freesurfer Mailing List
>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>
>> Courtney,
>>
>> if i understand your question, i think one way to do that is to use qdec
>> to draw a label on the blob of interest, and the run 'map label to
>> subjects', which creates a label file in each subjects label dir, then
>> you can run stats on that with mris_anatomical_stats. 
>>
>> (btw, i'm putting this answer on the list, as others may have better
>> ideas.)
>>
>> n.
>>
>>
>>
>> On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F]
>> wrote:
>>   
>> 
>>> Hi Nick
>>>
>>> Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this 
>>> is my first time using Freesurfer.
>>>
>>> A follow up question to your answer for question 1. I see that the group 
>>> data will be plotted in Qdec for significant blobs, but say there is a 
>>> significant interaction between two variables and it's not entirely 
>>> apparent what is driving this interaction.
>>> Is there a way to extract the mean of this blob for each individual (i.e., 
>>> treat it as an ROI or something similar) to determine what's driving the 
>>> significance?
>>>
>>> Thanks in advance!
>>> Courtney
>>>
>>> -Original Message-
>>> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
>>> Sent: Thursday, December 30, 2010 2:44 PM
>>> To: Gallen, Courtney (NIH/NIDA) [F]
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>>
>>> ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a
>>> plot of the data at that surface vertex will appear.  the group will be
>>> apparent from that (say, demented group is thinner than non-demented
>>> group).  this data is significance data (log p, so '2' is 0.01), so mean
>>> and stdev wouldnt apply in that case.  the file 'y.mgh' is the raw data
>>> of all subjects in the analysis, so you could extract mean and stdev
>>> from that.
>>>
>>> ans. 2. - slide the 'annotation' opacity slider to show the annotation
>>> data (cortical parcellation).  the ctrl left click will also put the
>>> region info for that vertex on the lower left of the display.
>>>
>>> see also: 
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
>>>
>>> n.
>>>
>>> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F]
>>> wrote:
>>> 
>>>   
 Hi,

  

 I’m currently running analyses in Qdec and have identified areas that
 show significant effects in my contrasts. I have two questions related
 to interpreting these results.

  

>

Re: [Freesurfer] preproc-sess path structure

[Douglas N Greve]

You should check that anatomical analysis and make sure that it is 
correct. Once that is done, make sure that the subjectname in the 
subjectname file is correct, then preproc-sess should run.

doug

Michelle Umali wrote:
> Hi Doug,
>
> I've run recon-all -all.  I ended up inputing an .mgz file converted 
> from a .nii file that was converted from a .dicom.  Was needed info 
> lost somewhere along the way?
>
> Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does 
> one need -anat?)successfully, because it generated the following folders:
> bem, label, mri, scripts, src, stats, surf, tmp, touch, trash.  And 
> the bem, src, and trash folders are empty, but the others are full of 
> files.
>
> Eek.
>
> -Michelle
>
>> Hi Michelle,
>>
>>   the SUBJECTS_DIR is an environment variable that you have to set prior
>> to running the anatomical analysis (disregarding the functional analysis
>> for a moment). Before running the functional analysis, you must run
>> recon-all on the anatomical data, eg
>>
>> recon-all -all -subject LD08-anat -i anatomical.dicom
>>
>> this will create a folder in $SUBJECTS_DIR called LD08-anat. If you have
>> not done this, you should do this first. Look at the wiki for how to run
>> the anatomical analysis.
>>
>> Once this is done, you should unpack your functional data (looks like
>> you might have done this already). In the session directory, create a
>> text file called "subjectname". Put the subject name (ie, LD08-anat)
>> into the subjectname file.
>>
>> doug
>>
>>
>>
>>
>>
>> On 4/5/11 2:15 PM, Michelle Umali wrote:
>>> Hi Doug,
>>> Does the $SUBJECTS_DIR folder have to be where the FreeSurfer program
>>> is?  I had done this:
>>>
>>> setenv SUBJECTS_DIR /home/fsl/structural
>>> So this SUBJECTS_DIR is not located where FreeSurfer is.
>>>
>>> Is the following the exact correct path:
>>> FreeSurfer/$SUBJECTS_DIR/LD08/subjectname
>>> where LD08 is the file subjectname says LD08 and freesurfer must be
>>> capitalized as FreeSurfer?
>>>
>>> and all the retinotopy data can be in:
>>> /home/fsl/structural/bold
>>>
>>> and recon-all subfolders and data in
>>> /home/fsl/structural
>>>
>>> Sorry for such a basic question.
>>>
>>> Thanks.
>>> Michelle
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] recommende pc and cuda

[Ian Malone]

On 05/04/11 16:55, Richard G. Edgar wrote:
>
> On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote:
>> Richard G. Edgar wrote:

>>> On the standard test case we use here, a full recon-all run takes 8
>>> hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using
>>> the Tesla C2050.
>>>
>>>
>>
>> Would I be right in concluding that a 4-core Nehalem (e.g. i7) has
>> more throughput than the C2050 then?
>
> Yes, but less than having 3 CPU jobs, and one GPU one. I did test once,
> and there isn't much penalty to running one recon-all job per core on a
> Nehalem system.
>
> Right now, the CPU still does most of the work in the recon-all stream -
> it's something of a game of Amdahl's Law Wac-A-Mole. You could always
> try starting 4 GPU jobs at once I've not done the testing, but a
> C2050 would probably have enough RAM, and in any given recon-all run,
> the GPU does spend a lot of time idle. Hence, it would end up being
> divvied up between the four jobs.
>

Thanks, that's interesting to know.

-- 
imalone
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