Re: [Freesurfer] Results Vary

[Derin J Cobia]

Hi Nick,

Could you clarify this? So if we re-run a subject in 5.1 (say after doing some 
edits), we would then need to run it again a third time in order to maintain 
consistency? Thanks.

-Derin


On Jan 22, 2013, at 2:17 PM, Nick Schmansky  wrote:

> also there is an issue in v5.1 where the second run of recon-all on a
> given platform will produce different results from the first (but
> subsequent runs should produce identical results).  this issue has been
> fixed in the upcoming v5.2 release.
> 
> nick
> 
> 
> On Tue, 2013-01-22 at 10:18 -0500, Douglas N Greve wrote:
>> Hi Chikku, while we try to resolve these differences, you are not 
>> guaranteed to get identical results when you use different platforms. 
>> This is an issue with using different computes and applies to all 
>> software, not just FS.It is caused by the use of different math 
>> libraries and different binary operations. The difference you show is 
>> only 0.3% which should not be enough to cause false results.
>> doug
>> 
>> 
>> 
>> On 01/22/2013 08:13 AM, Varghese Chikku wrote:
>>> 
>>> Dear FS team,
>>> I processed two set of MRI  data for a  single  patient,Thats BL scan 
>>> and TP1.I ran both scans on a Mcbook Pro and  a PC with Virtual 
>>> machine installed.
>>> Though I was expecting the  same segstats,the  results vary from 
>>> Macpro to VM.For eg , for BL in Mac  SubCortGrayVol is 178038 but  for 
>>> the  same  images in VM  the  results are 177432.Does it happened to 
>>> any one beforeWhats the  reson its  happening and how  can  I  
>>> remedy,validate the  results.
>>> Much appreciate  your  advice,...
>>> In Thanks
>>> Chikku.
>>> 
>>> 
>>> 
>>> 
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> 
> 
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[Freesurfer] Reposition Surface

[Derin J Cobia]

Just a question about the Tools --> Reposition Surface... feature in Freeview. 
Is that up and running? Is there any accompanying documentation? Thanks.

-Derin



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Re: [Freesurfer] WM editing and longitudinal processing v5.3.0

[Derin J Cobia]

Could you clarify this a little more Bruce? I was under the same impression as 
Ed that 110s could be used in editing the wm volume (but cannot recall why/how 
I know that). We've edited using 110s and 255s with some limited success for 
both (rerunning occasionally deletes these manual edits or surface does not 
follow them) - maybe it is related to the mixing of intensities? In a sense 
does using 110s trigger the stream to think a control point was placed there 
(absent the Voronoi diagram, etc)? 

So, if manual 255s are always used, how are they differentiated from ventricle 
or internal capsule ones? Does this even matter? Broadly, does using a variety 
of intensity values affect other volumes (e.g. aseg, brainfinalsurfs, etc)? 

Thanks,
Derin


On Feb 4, 2014, at 11:25 AM, Bruce Fischl  wrote:

> Hi Ed
> 
> it was never the case that an edited on wm.mgz voxel had the value of 110. It 
> was always 255. 110 is the value that locations have when they are either an 
> automatically or manually added control point
> 
> cheers
> Bruce
> On Tue, 4 Feb 2014, Ed Gronenschild wrote:
> 
>> Hi Martin,
>> One thing I want to be sure of:
>> should the edited wm voxels really have a value of either 1 or 255.
>> In previous versions an added wm voxel had a value of about 110,
>> this is not anymore the case?
>> I'm asking this because I want to edit wm by using results from another
>> application that segments wm, so not by means of manually editing
>> with freeview.
>> Cheers,
>> Ed
>> On 4 Feb 2014, at 17:00, Martin Reuter wrote:
>> 
>>  Hi Ed,
>> take a look at this wiki page about edits in the long stream:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
>> everything should work. for long, you'd edit the base. If that is not
>> sufficient, you can edit the cross or the long. Edits from the cross
>> should be transferred to the long, except if the long already contain
>> manual edits.
>> Best, Martin
>> On Feb 4, 2014, at 9:06 AM, Ed Gronenschild
>>  wrote:
>> 
>>  Hi Bruce,
>> 
>>  When I have a look in the recon-all script I see that it
>>  is tested if  
>>  there
>>  are voxels present in wm.mgz with value 1 or 255. Both
>>  indicate
>>  wm editing. The comment in recon-all says that 1 means
>>  remove
>>  and 255 means add.
>>  And concerning my second question: are these edited voxels
>>  correcly processed with the option autorecon2-wm and
>>  subsequently
>>  with longitudinal processing?
>> 
>>  Cheers,
>>  ed
>> 
>>  On 4 Feb 2014, at 14:27, Bruce Fischl wrote:
>> 
>>Hi Ed,
>> 
>>yes, although we reserve the values under 5 I
>>think for editing  
>>changes,
>>I believe we only use 1 at the moment.
>> 
>>cheers
>>Bruce
>>On Tue, 4 Feb 2014, Ed Gronenschild
>>wrote:
>> 
>>  Hi,
>> 
>>  From what I can read in the wiki
>>  about wm editing, I understand
>>  that edited wm voxels have values
>>  of either 255 (added) or
>>  1 (removed) and no other values.
>>  These are stored in the file
>>  wm.mgz. Is that correct?
>>  Before processing a lot of data I
>>  want to be sure that running
>>  recon-all with the option
>>  autorecon2-wm will recognize these
>>  voxels, also during longitudinal
>>  processing. Can you confirm
>>  this.
>> 
>>  FreeSurfer v5.3.0 Mac OSX10.6
>> 
>>  Kind regards,
>>  Ed
>> 
>>  ___
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>>The information in this e-mail is intended
>>only for the person to  
>>whom it is
>>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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>> -
>> Dr. Martin Reuter
>> Assistant in Neuroscience - Massachusetts General Hospital
>> Instructor in Neurology   - Harvar

Re: [Freesurfer] Stylus Input for Cortical Edits

[Derin J Cobia]

Wil,

We've been using the Cintiq models 
with great success for the past several years, it really speeds up manually 
editing. Only Windows and OS X are 'officially' supported by Wacom, but there 
is a thriving 
community
 that builds and continually develops drivers for these devices on various 
Linux platforms. We've been using ours on CentOS 4 and 5 builds without 
problems; it takes a little tinkering with the xorg.conf and other files, but 
you should be fine.

-Derin


On Apr 11, 2012, at 12:01 PM, Alan Francis wrote:

Hi Wil:

The model we use for manual morphometry is the Wacom BAMBOO (pen) : Model 
CTL-460.

best,

Alan

On Mon, Apr 9, 2012 at 12:22 PM, Irwin, William 
mailto:wir...@memory.ucsf.edu>> wrote:
Hi-

I have been considering this option, and these comments pretty much make it a 
given.

Could you provide a bit more details: Which models? Are you using tablets with 
Linux (RH or Ubuntu) and/or MAC OS?

Thanks,
Wil

William Irwin | Imaging Core Supervisor
UCSF | Memory and Aging Center
350 Parnassus Avenue, Suite 905
San Francisco  CA  94143-1207
wir...@memory.ucsf.edu | 
memory.ucsf.edu
p: 415.476.1680 | f: 415.476.1816



From: Alan Francis 
[mailto:alandarkene...@gmail.com]
Sent: Thursday, April 05, 2012 6:53 AM
To: Jeff Stout
Cc: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] Stylus Input for Cortical Edits


Hi Jeff:

We too have found Wacom tablets are great for editing and also these are easy 
on the back and eyes.

best,

Alan
On Wed, Apr 4, 2012 at 6:46 PM, Emily Rogalski 
mailto:erogal...@gmail.com>> wrote:

We have found Wacom tablets are excellent for editing.
On Apr 4, 2012 4:40 PM, "Jeff Stout" 
mailto:jstout...@yahoo.com>> wrote:
Hi All,

We have a large number of subjects that need minor edits (orbital frontal 
cortex/eye issues subcortical parcellation etc.).  To speed up the process I 
was wondering if a stylus input would help with the editing.

Do the graphics tablets (stylus input) work with freesurfer editing?  Do they 
end up being useful or is it not worth investing in?  And if so, could someone 
recommend a brand (wacom?) that would work with Ubuntu 10.04 (or just linux in 
general).


Thank you,
Jeff Stout



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[Freesurfer] long_qdec_table error

[Derin J Cobia]

Martin,

I'm getting the following error when running long_qdec_table:

=
[derin@otis ccnm_mprage_v4.5_long]$ long_qdec_table --qdec 
qdec/ccnm_prog_30_long_Th.qdec.table.dat --cross --out 
qdec/ccnm_prog_30_long_Th.cross.qdec.table.dat 
Parsing the qdec table: qdec/ccnm_prog_30_long_Th.qdec.table.dat
Traceback (most recent call last):
  File "/pkg/brainmap/freesurfer-v5.1.0/bin/long_qdec_table", line 142, in ?
longqdec = LongQdecTable(options.qdec)
  File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 30, in 
__init__
self.parse(stpmap)
  File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 58, in parse
if strlst[0].upper() == 'SUBJECTS_DIR':
IndexError: list index out of range
=

I haven't had much luck troubleshooting it, maybe I have too many numerical 
variables in the table? I guess I could always reconstruct it by hand, but 
wondering if you had any thoughts, thanks.

FS v5.1.0 CentOS 4

-Derin


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Re: [Freesurfer] Question about version upgrade

[Derin J Cobia]

FWIW, in our experience this isn't always the case. When re-running edited and 
"cleared" subjects in 4.5.0 up to 5.1.0, we have had to return and re-edit the 
vast majority of these individuals order to obtain accurate surfaces. To be 
specific, we are not finding control points or pial edits disappearing, but the 
loss of wm edits (and sometimes introduction of new ones) to the wm.mgz. Our 
population may be unique in that they are subjects with a significant 
neurodegenerative condition (PPA) with age-matched (older) healthy controls, so 
I'm sure your mileage may vary.

-Derin


On May 2, 2012, at 10:55 AM, Douglas N Greve wrote:

> It's worth pointing out that your edits will be preserved, so it should 
> just be computer time.
> 
> On 05/02/2012 09:08 AM, Bruce Fischl wrote:
>> Hi Efrat,
>> 
>> no, we don't recommend this, otherwise you run the risk of increasing
>> variance and introducing a bias.
>> 
>> sorry
>> Bruce
>> On Wed, 2 May 2012, Efrat Kliper wrote:
>> 
>>> Dear FreeSurfer expert,
>>> 
>>> 
>>> I am currently working on FreeSurfer Version 4.5.0 and already performed an 
>>> analysis for approximately 200 subjects. Is there a way
>>> to change the version that I am working on (4.5.0) to 5.0.1 without the 
>>> need to run recon-all again in the new version?
>>> 
>>> Thanks in advanced,
>>> 
>>> 
>>> efrat
>>> 
>>> 
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>> 
> 
> -- 
> 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
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Re: [Freesurfer] mri_vol2surf masking

[Derin J Cobia]

Bump.

I'm interested in the answer to this question as well. Doug/Bruce, do you know?

-Derin


On May 29, 2012, at 8:43 PM, Kathryn I. Alpert wrote:

Dear Freesufer experts,

I am wondering if it is possible to tell mri_vol2surf to ignore certain voxels 
in the src volume, for instance, by setting their intensity to -999.
I'm trying to project only gray matter voxels from a PET scan onto the 
fsaverage surface, but when I use an only-GM PET image as the src, the 
zeroed-out WM/CSF voxels are occasionally projected onto the surface (with 
--interp nearest).
Any suggestions?

Thanks!
Kate
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[Freesurfer] Postdoctoral position at Northwestern University

[Derin J Cobia]

(Posted on behalf of a colleague)



A postdoc position is available immediately in the Neuroimaging and Applied 
Computational Anatomy Lab, Department of Psychiatry and Behavioral Sciences at 
the Northwestern University Feinberg School of Medicine. Our laboratory aims to 
develop multidimensional and multimodal neuroimaging biomarkers using the tools 
of computational anatomy. Working with collaborators from engineering, 
mathematics, psychology and clinical specialties, our research is focused on 
the following major areas: automated pipelines for mapping of brain structures 
using MRI, development of complex neuroimaging biomarkers, clinical 
applications in dementia, psychosis, mood disorders and genetics, 
neuroinformatics, and neuroimaging of animal models.

This position is initially limited to two years with the possibility of 
extension.  It will be partially funded by a new 5-year NIH study (PI Greg 
Miller, PhD) of the relationship between socioeconomic status and maturation 
patterns in the corticolimbic and corticostriatal circuitries of school-age 
youths. The successful applicant will work primarily on T1, DTI and 
resting-state fMRI analysis in this and various other clinical populations with 
a particularly emphasis on multimodal approaches. The position will be 
integrated closely with the existing collaborative environment. Additionally, 
supervision of graduate and medical students will be required.

Candidates should hold a Ph.D. in neuroscience, psychology, engineering or 
related fields. A strong publication record and background on structural 
neuroimaging research should be demonstrated. Experience with fMRI analysis is 
highly desirable. Applicants should have strong analytical skills and 
experience with existing tools for large-scale analysis of neuroimaging data 
(i.e., FreeSurfer, 3D Slicer, SPM, FSL, AFNI, etc.). Proficiency in relevant 
programming languages (e.g. MATLAB, Python) and statistical analysis (R, SAS, 
SPSS) is required. Working experience in epidemiological research or 
large-scale clinical studies is highly desirable. The successful candidate must 
be capable of working independently and taking initiatives. The candidate is 
expected to be a team-player with excellent communication and writing skills.

Please send a letter of research interest, CV, and names of 3 references to Dr. 
Lei Wang (leiwa...@northwestern.edu).

Northwestern University is an Equal Opportunity, Affirmative Action Employer of 
all protected classes, including veterans and individuals with disabilities. 
Women and minorities are encouraged to apply. Hiring is contingent upon 
eligibility to work in the United States.


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