Re: [Freesurfer] Converting thickness maps to vtk

[Derin Cobia]

Navid,

Are you needing to convert the thickness.mgh file or a surface (e.g., ?h.pial, 
?h.white, etc) file to .vtk?  We've used mris_convert many times to create .vtk 
files from FS surfaces.  The command is fairly straightforward.  

mris_convert /?h. /?h..vtk

I'm not sure you can convert the thickness.mgh files into .vtks, don't they 
only contain coordinate information?  Hope that helps.

-Derin


  
On Dec 12, 2011, at 9:13 AM, Navid Shiee wrote:

> Hello,
> 
> I was wondering if there is a command like mris_convert to create a thickness 
> map in vtk format (either on the white or pial surface) ?
> 
> Thanks,
> 
> -- 
> Navid Shiee
> Ph.D. Candidate
> Laboratory of MEDical Image Computing (MEDIC)
> Image Analysis and Communication Laboratory (IACL)
> Johns Hopkins University
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Re: [Freesurfer] longitudinal processing

[Derin Cobia]

So if I understand correctly, you would not recommend getting a jump start on 
cross-sectional processing and editing under 5.0, rerunning everything under 
5.1 once it comes out, then run (for the first time) longitudinal under 5.1?  
Are there going to be some incompatibilities with 5.1, where it cannot be run 
on top of 5.0 data?  Thanks.

-Derin


On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:

> I'll leave that for Martin
> 
> Bruce
> On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
> 
>> Hi Bruce,
>> 
>> What's the ETA for 5.1?
>> 
>> thanks
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Diretor de Operações
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://www.netfilter.com.br/mobile
>> 
>> 
>> 
>> 
>> On Mon, Oct 18, 2010 at 10:39, Bruce Fischl 
>> wrote:
>> 
>>> Hi Marie,
>>> 
>>> wait for 5.1. Martin has made some significant improvements.
>>> 
>>> cheers
>>> Bruce
>>> On Mon, 18 Oct
>>> 2010, Marie Schaer wrote:
>>> 
 Hi,
 
 I am planing to process a longitudinal dataset with 3 timepoints. Is
 it worthy to begin already the cross-sectional processing with version
 5.0 and then wait version 5.1 to continue from the template part. Or
 would you advice me to wait the release of version 5.1 for the entire
 processing?
 
 Thank you for your help,
 
 Marie
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[Freesurfer] FS 5.1

[Derin Cobia]

All,

Just curious about the current estimated timeline for version 5.1, trying to 
schedule some projects around it.  Thanks!

-Derin



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Re: [Freesurfer] single subject versus a group map in qdec

[Derin Cobia]

I'm curious about the use of this method as well (thanks for the paper PPJ).  
Bruce/Doug, how exactly does QDEC treat this design?  Can a single-subject 
comparison properly be done?  Thanks.  

-Derin


On Mar 23, 2011, at 4:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:

> We have dono something like this in Cortical thickness reduction of normal 
> appearing cortex in patients with polymicrogyria
> 
> cheers,
> 
> PPJ
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://www.netfilter.com.br/mobile
> 
> 
> 
> 
> On Wed, Mar 23, 2011 at 14:21, Emily Rogalski  wrote:
> Using q dec we have run a single patient versus a group of healthy control 
> subjects (n=20ish) and found significant differences even after FDR 
> correction.
> 
> Could you describe the process qdec uses to compute these differences? 
> Is it legitimate to report these single subject maps?
> Practically this is very useful for case reports but Im concerned about 
> violating statistical rules. 
> 
> Thanks!
> -- 
> Emily J Rogalski, PhD
> Assistant Research Professor
> Northwestern University
> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
> 320 E Superior Street
> Searle Building 11th Floor
> Chicago, IL 60611
> 312-503-1155 phone
> 312-908-8789 fax
> erogal...@gmail.com
> 
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Re: [Freesurfer] Power Analysis

[Derin Cobia]

Hi Doug,

To follow up on this question, we were able to calculate effect sizes for every 
vertex on the surface using the gamma(var).mgh files, as well as an average 
effect size across each hemisphere surface using the equation below.  In 
determining alpha, would the most appropriate method be to use the 
FDR-corrected alpha level that results from our pilot analysis?  For example, 
for a two-group comparison we FDR at 0.05, which results in a corrected p 
(alpha) of 0.001, and we use that for the power analysis calculation (#3 
below), thanks.

-Derin


On Mar 22, 2011, at 4:55 PM, Douglas N Greve wrote:

> For the power analysis, you need four things:
> 1. Effect Size
> 2. Number of Subjects
> 3. Target False Positive Rate (alpha)
> 4. Target False Negative Rate (beta)
> 
> Given any 3, you can compute the 4th. You can get the Effect Size from 
> the output of the QDEC analysis. Each analysis creates a GLM directory, 
> and there is a directory for each contrast in the GLM dir. In the 
> contrast dir, you will find several files, but the important ones for 
> this are the gamma.mgh and the gammavar.mgh. The gammavar is the square 
> of the error bar (ie, t=gamma/sqrt(gammavar)). The gamma will not change 
> as you add subjects (at least in expectation). The gammavar will drop 
> linearly with the number of subjects (again in expectation). The effect 
> size will then be gamma/sqrt(gammavar*Npilot), where Npilot is the 
> number subjects in the pilot study. In a new study with Nnew subjects, 
> the expected t will be tnew = gamma/sqrt(gammavar*Npilot/Nnew)
> 
> doug
> 
> 
> 
> Emily Rogalski wrote:
>> How would you complete a power analysis for a whole brain group 
>> comparison qdec analysis?
>> 
>> Thanks,
>> Emily
>> 
>> 
>> 
>> -- 
>> Emily J Rogalski, PhD
>> Assistant Research Professor
>> Northwestern University
>> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
>> 320 E Superior Street
>> Searle Building 11th Floor
>> Chicago, IL 60611
>> 312-503-1155 phone
>> 312-908-8789 fax
>> erogal...@gmail.com 
>> 
>> 
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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
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] long_mris_slopes error

[Derin Cobia]

I received the follow error while running a set of subjects under 
'long_mris_slopes,' and wasn't able to decipher the problem.  It appears that 
mris_calc is not able to do the division for these files (dividing by 0 
perhaps?).  Any help appreciated, here's the command and tail end of 
output/error, thanks.

-Derin


> long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas thickness --hemi 
> lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
> scan_interval --qcache fsaverage
> 
> 
> ===
> SUBJECT CH1840 fwhm 0  computing SPC
> 
> mris_calc -o 
> /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh
>  ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div 
> ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh
> 
> ERROR 1 : mris_calc compute sym. pct. change (spc) problem?
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[Freesurfer] libvtkpng.so.5.2 missing?

[Derin Cobia]

We're running subjects under the new 4.3.0 version (CentOS 4  
platform), and are experiencing the following error during the  
cortical ribbon mask stage:



#...@# Cortical ribbon mask Wed Apr  8 07:12:20 CDT 2009
/disk/NIACAL/human/freesurfer/conte_mprage_v4.3/020319_2263/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 -- 
label_right_white 41 --label_right_ribbon 42 --save_ribbon -- 
save_distance 020319_2263


mris_volmask.bin: error while loading shared libraries: libvtkpng.so. 
5.2: cannot open shared object file: No such file or directory
Linux heinz 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64  
x86_64 x86_64 GNU/Linux


recon-all exited with ERRORS at Wed Apr  8 07:12:21 CDT 2009


It appears that libvtkpng.so.5.2 does indeed not exist (in fact, no  
libvtkpng* files were found) in ~/freesurfer/lib/vtk/lib/vtk-5.2 for  
the current 4.3.0 CentOS 4 (32-bit) distribution we have, but found  
them present in our 4.1.0 (32-bit) and 4.3.0 (64-bit) distros .  This  
may just be a case of "the missing libraries," but are they supposed  
to be gone?  If not, are we safe to just copy them into the 4.3.0 vtk  
dir as a short term fix?  Thanks.


-Derin

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[Freesurfer] FS compatibility w/OS X 10.6 Snow Leopard

[Derin Cobia]

I'm assuming FreeSurfer should work with the new OS given the relative  
minor adjustments to it, but wasn't sure.  You may not have a copy of  
it yet, but was wondering if you knew of any foreseeable problems.  
Thanks.

-Derin
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Re: [Freesurfer] FDR correction

[Derin Cobia]

I would be interested in this as well.

-Derin


On Oct 16, 2009, at 11:40 AM, Doug Greve wrote:

>
> Good point (meaning that I don't know the answer). I'll see if I can
> find out.
>
> doug
>
>
>
> On Fri, 16 Oct 2009, Donna Dierker wrote:
>
>> Regardless:  FDR's sensitivity appears resolution-dependent to me.
>>
>> On 10/16/2009 10:39 AM, Michael Harms wrote:
>>> Interesting post Donna, but my understanding of FDR is that it  
>>> sets the
>>> p-value threshold based on the LARGEST p-value that satisfies the  
>>> FDR
>>> relationship.
>>>
>>> That is, steps 3 and 4 in Genovese et al. (2002) are:
>>> 3) Let r be the largest i for which p <= i/V*q  (assuming c=1)
>>> 4) Threshold the image at the p-value p(r).
>>>
>>> So, it isn't the case that you require the most significant p- 
>>> value to
>>> satisfy p <= 0.05/V "just to get past i=1" as you put it in your  
>>> post.
>>>
>>> Rather, you pick the largest p-value that satisfies the  
>>> relationship,
>>> meaning that lower (more-significant) p-values may not have  
>>> necessarily
>>> satisfied p <= i/V*q for their particular position in the sorted  
>>> list of
>>> p-values.
>>>
>>> cheers,
>>> Mike H.
>>>
>>>
>>> On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote:
>>>
 I never heard anything on my post here, but it might just be high
 surface resolution:

 http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html

 On 10/16/2009 09:58 AM, Michael Harms wrote:

> Your FDR analysis sounds correct.  You probably have a rather  
> small
> number of "marginally" significant vertices, which is why none  
> survive
> FDR.  You could try increasing the "q" value from say 0.05 to  
> 0.1, in
> which case 10% of the surviving vertices would be expected to be  
> false
> positives.
>
> cheers,
> Mike H.
>
> On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote:
>
>
>> Dear Freesurfer team,
>>
>> We are currently doing a cortical thickness studies between a  
>> group of
>> psychiatric patients (n=60) and controls (n=30). We tested  
>> several
>> smoothing levels (15mm, 20mm, 25mm)
>>
>> When setting an uncorrected threshold (such as p<0.005), we  
>> obtained
>> several regions of decreased thickness, which are consistent  
>> with the
>> pathology.
>>
>> However, when trying to correct for multiple comparisons using  
>> FDR
>> ("Set Using FDR" button in qdec), the computed threshold is  
>> very high
>> (e.g. 4.3 for 20mm smoothing) and, obviously, no significant  
>> regions
>> are left.
>>
>> Did we do anything wrong in the analysis ?
>>
>> Thank you very much for your help,
>> Yulia
>>
>>
>>
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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
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Computer specifications for FreeSurfer

[Derin Cobia]

FYI-

We've been experiencing much faster run times on the new Core i7  
architecture (for both Mac and Linux machines), on the order of 16-18  
hours for the entire recon-all ("-all') pipeline.  Although your  
mileage may vary (depending on scan quality, amount of RAM, etc).  The  
Radeon 4850 chip is more than enough to power visualization of  
tksurfer/tkmedit.


-Derin


On Oct 27, 2009, at 7:52 AM, Pedro Paulo de Magalhães Oliveira Junior  
wrote:



Hi,

This IMac is good for running up to 4 simultaneous recon-all

You can expect 30 hours for 4 simultaneous cases in this machine you  
described.


PPJ
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.2 www.Netfilter.com.br
--- Novo Netfilter Small Business



2009/10/27 
Hello,

I was wondering if the following specs on an IMac would meet the  
system requirements for FreeSurfer?



2.8GHz Quad-Core Intel Core i7
8GB 1066MHz DDR3 SDRAM - 2x4GB

1TB Serial ATA Drive
ATI Radeon HD 4850 512MB
8x double-layer SuperDrive

We are an outpatient facility and perform a good bit of Brain  
imaging on an older population and my Radiologists are interested in  
performing Brain volume for MCI and Alzhiemer Dementia patients.   
From the preliminary information that I read on the FreesurferWiki,  
the software application is very intensive and tends to run the  
computer system pretty rough.



One of the biggest concerns would be the Graphics card?  Is there a  
minimum memory spec (512mb or should it be higher)?



Any help would be greatly appreciated.


Regards,


Bill






William Smithtro RT(R)(MR)
Chief MRI Technologist
Laurel Highlands Advanced Imaging
Johnstown PA
www.LHAI.org


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[Freesurfer] Job announcement

[Derin Cobia]

Posted on behalf of a colleague:

FACULTY POSITION, MEG-fMRI NEUROIMAGING





Saint Louis University, is a Jesuit, Catholic university dedicated to  
teaching, research, health care and community service and is seeking a  
scientist at an open rank level for a non-tenure track, grant-funded  
faculty position in the Division of Neurosurgery, Department of  
Surgery at St. Louis University School of Medicine.


The successful candidate will head the Division’s imaging research  
using the  installed 275 channel magnetoencephalography (MEG) system  
and 3 Tesla MRI and manage a multimillion dollar research grant funded  
by the Department of Defense. This project will span 4 years and study  
traumatic brain injury in combat veterans using MEG, positron emission  
tomography (PET/CT) and functional MRI with diffusion tensor imaging  
(fMRI with DTI). ).  A team of research staff members has been  
assembled to perform the study assisted by graduate and post-graduate  
students assigned to the project. The ideal candidate would hold a  
Ph.D. in any of the following areas: biomedical engineering,  
physiology, experimental/cognitive psychology, neuroscience, MEG, or  
other applicable disciplines. Candidates should be familiar with  
standard computational software packages for neuro-imaging such as  
Curry, Unix, MatLab, Slicer, and C/C++, and have at least five (5)  
years of clinical research experience, preferably in the  
neurosciences. Previous experience in neurological functional imaging  
is expected. Preferred candidates will have proficiency in  
epidemiology, biostatistics, registration techniques using deformable  
templates to create standardized atlases, and training/certification  
in clinical research. Salary will be commensurate with academic  
credentials and experience. Candidates will be expected to apply and  
obtain funding from external agencies to continue the work of the  
Division within the area of neuroimaging using the installed base of  
equipment.




Interested candidates should submit a cover letter, application,  
relevant reprints, and current curriculum vitae to  http:// 
jobs.slu.edu.  An initial letter of interest describing current  
research interests and future research goals should be sent along with  
a curriculum vitae to:




Richard Bucholz, MD, FACS

Director and Professor, Division of Neurosurgery

Department of Surgery

Saint Louis University

3635 Vista Ave.

St. Louis, MO  63110-0250

Phone: 314-577-8795

Email: rich...@bucholz.org



Saint Louis University is an affirmative action, equal opportunity  
employer, and encourages nominations and applications of women and  
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Re: [Freesurfer] Qdec table

[Derin Cobia]

Nathan,

Here are the steps I use to create QDEC dat files on a Mac:

-Export/save your data in SPSS/Excel as a .csv file
-Open the .csv file in TextWrangler (a free text editor for Mac)
-Do a Find & Replace of the "," for " " to make it a space  
separated file
-Down at the bottom of the TextWrangler window is a drop down box to  
specify the type of hard returns ('Classic Mac' or 'Unix'); make sure  
the last line ends in a return

-Save as a ~.qdec.table.dat file

Hope that helps.

-Derin


On Nov 17, 2009, at 5:00 PM, Krish Subramaniam wrote:


Some programs notoriously add Ctrl-M at the end of every line ( or
every cell )

If you have the vi editor you can follow this method 
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/
 to remove all the instances of Ctrl-M and again try in qdec.
Unfortunately I am not able to reproduce the error here because i
don't have excel.

Here's another method : 
http://www.unix.com/shell-programming-scripting/25658-removing-control-ms-m.html

Best
Krish

On Nov 17, 2009, at 5:21 PM, Dankner, Nathan (NIH/NIMH) [F] wrote:


Unfortunately I'm not running windows.  Are you familiar with any
tricks I can use on a mac?


On 11/17/09 5:15 PM, "Douglas N Greve" 
wrote:

If you're creating the file in windows, try running dos2unix on the
file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:

Hi all,

I am attempting to create a qdec.table.dat file, and have been
unable to find a way to paste my data into it in a way that will
make it readable.  When I paste it in qdec always outputs an error
when trying to open it, even if visually the file appears to be
correct.  Is there an easy way to import data from excel into
something readable by qdec?  I'm hoping to avoid having to manually
enter everything because there is quite a lot of data, so any help
would be appreciated.  Thanks,

Nathan

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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] Creating a Mask or ROI

[Derin Cobia]

Doug,

I think what Emily wants to do is something like running mri_glmfit on an ROI 
(i.e., surface label drawn in QDEC).  Then be able to display the results in 
tksurfer, showing flame-scale map results for only the ROI/label (not just 
singular values for the entire ROI/label).  Would this be what the mri_glmfit 
'--label' flag is for?  

-Derin


On Jan 26, 2010, at 10:53 AM, Douglas N Greve wrote:

> 
> You can run something like the following:
> mri_segstats --slabel fsaverage lh 
> $SUBJECTS_DIR/fsaverage/label/lh.BA1.label --i y.mgh --sum junk --avgwf 
> avgwf.dat
> 
> y.mgh is created by qdec and should be in the qdec output. avgwf.dat 
> will be a text file with a value for each of your subjects. This is the 
> data you want (I think).
> 
> doug
> 
> 
> 
> Emily Rogalski wrote:
>> 
>> Hello Group,
>> 
>> We would like to create an ROI label in qdec and then run a 
>> correlation analysis with another factor to determine the relationship 
>> between thinning in the ROI and the measure of interest. Instead of 
>> looking at a single value from the ROI we want to look at the 
>> correlation across each vertex within the ROI. Basically we want to 
>> create a color map of the correlation within the ROI. Is this possible?
>> 
>> Thanks,
>> Emily
>> 
>> -- 
>> Emily J Rogalski, PhD
>> Assistant Research Professor
>> Northwestern University
>> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
>> 320 E Superior Street
>> Searle Building 11th Floor
>> Chicago, IL 60611
>> 312-503-1155 phone
>> 312-908-8789 fax
>> erogal...@gmail.com 
>> 
>> 
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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
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] Longitudinal processing clarification

[Derin Cobia]

(Questions for all, but maybe more directed towards Martin)

I have some questions about manual edits in regard to the longitudinal stream.  
Based on the current info on the wiki page, it appears that no edits are pushed 
forward from the cross-sectional (initial) runs of the subject data, as any 
information on the *.long.* runs come from the template.  However, I've noticed 
that WM edits and surfs from the template are used in for the *.long.* 
processing.  In essence, my question is when/where should manual edits (i.e., 
control points, WM, pial edits) occur when conducting longitudinal processing 
in 4.5?  It seems I remember that in 4.3 edits in the cross-sectional work 
would be pushed forward to the *.long.* images, but such is not the case 
anymore (?).  Are edits to occur in the template (i.e., 'base') now, or in the 
*.long.* runs?  Thanks.

-Derin


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[Freesurfer] Longitudinal processing clarification

[Derin Cobia]

Bumping this back up to the list.  Could someone please address?  

To be more concise, during longitudinal processing, where are wm/gm edits made? 
 On the cross-sectional runs, to the base, or on the .long. runs themselves?  
Thanks.

-Derin

Begin forwarded message:

> From: Derin Cobia 
> Date: February 1, 2010 3:54:46 PM CST
> To: "freesurfer@nmr.mgh.harvard.edu Help" 
> Subject: Longitudinal processing clarification
> 
> (Questions for all, but maybe more directed towards Martin)
> 
> I have some questions about manual edits in regard to the longitudinal 
> stream.  Based on the current info on the wiki page, it appears that no edits 
> are pushed forward from the cross-sectional (initial) runs of the subject 
> data, as any information on the *.long.* runs come from the template.  
> However, I've noticed that WM edits and surfs from the template are used for 
> the *.long.* processing.  In essence, my question is when/where should manual 
> edits (i.e., control points, WM, pial edits) occur when conducting 
> longitudinal processing in 4.5?  It seems I remember that in 4.3 edits in the 
> cross-sectional work would be pushed forward to the *.long.* images, but such 
> is not the case anymore (?).  Are edits to occur in the template (i.e., 
> 'base') now, or in the *.long.* runs?  Thanks.
> 
> -Derin
> 
> 

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Re: [Freesurfer] modification made to longitudinal results

[Derin Cobia]

Martin,

Not to add more to the confusion, but what if the final longitudinal scans are 
"not fine" and need some editing.  Can they be rerun in the standard way to 
incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something 
different be done?  Will rerunning these edited long scans in the standard 
fashion disrupt them in some way?  My hunch is that it won't, but I want to 
make sure.  Thanks.  

-Derin

On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote:

> OK I get it. There was a confusion about adding control points and
> adding new time points. My answer concerns adding new time points, so
> you can ignore it. Do not add any edited results as new time points.
> 
> Concerning your question see the discussion on this list from Feb 12
> that treats exactly this topic.
> 
> In short:
> - edit the cross sectionals (you have done that)
> - run the base and edit the base 
> - then the longitudinals should be fine
> 
> 
> Martin
> 
> On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
>> Hello,  Martin,
>> 
>> Thanks a lot for your reply, but I am still not very clear about few
>> issues.
>> I think that is because of my unclear description.
>> 
>> What happen is:
>> I have two scans which I want to do longitudinal analysis, however,
>> when I finish the 
>> cross-sectional analysis, I found the results are not so good because
>> of the low contrast 
>> between white matter and gray matter. I added control points to these
>> two scans, rerun them. 
>> The results looks much better now, then I go to the longitudinal
>> stream. However, when I load the 
>> longitudinal results, I found the kind of problem happens again (lots
>> of no-label region in superior frontal). 
>> So I added control points to the longitudinal results directly, and I
>> want rerun them. 
>> 
>> Based on your reply, I need consider those longitudinal results which
>> I added control points to as new timepoints, 
>> rerun them cross-sectionally again, is it correct?
>> 
>> Thanks!
>> Guang
>> 
>> 
>> Here, I just want to add some control points to the FreeSurfer
>> longitudinal results, 
>> not new time points. 
>> 
>>> Subject: Re: [Freesurfer] modification made to longitudinal results
>>> From: mreu...@nmr.mgh.harvard.edu
>>> To: freesurfer...@hotmail.com
>>> CC: freesurfer@nmr.mgh.harvard.edu
>>> Date: Thu, 25 Feb 2010 10:33:36 -0500
>>> 
>>> Hi Guang,
>>> 
>>> Depending on what you do you can choose different routes. Note, for
>> both
>>> of these you first need to run the new timepoint cross sectionally
>> (step
>>> 1 in the description
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ):
>>> recon-all -all -s newtpid -i path/to/dicom
>>> 
>>> Here are the two options once the cross sectional results are there:
>>> 
>>> 1. you have only very few timepoints in the base/template so far (2
>> or
>>> 3). In those cases I would recommend to rerun the base and rerun all
>> the
>>> longitudinals with the new and more accurate base. The commands are
>> on
>>> the Wiki and are the same as usual.
>>> 
>>> 2. you have many time points in your base, the additional time point
>> is
>>> not likely to change the base much. In that case you can simply
>> 'patch'
>>> the base without reprocessing and only run a single longitudinal
>> run. 
>>> 
>>> Let me know if you want to go route 2 because I am writing a script
>> to
>>> patch the base (there are a few files that need to be added so that
>> the
>>> longitudinal run will go through). If there is demand, I will put
>>> priority on this and make it available.
>>> 
>>> Best, Martin
>>> 
>>> On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
 Hi, there,
 
 I need add some control points to the longitudinal results.
 After adding control points, I need rerun it. which command should
>> I
 use?
 
 recon-all -s subj.long.baseid 
 or
 recon-all -long subj baseid 
 
 
 Thanks!
 Guang
 
 
 
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Re: [Freesurfer] Creating a distance scale bar for a pial surface-render viewed in tksurfer

[Derin Cobia]

Along these same lines, is it possible to overlay/display a Cartesian grid on 
the surface, a la the Neuroimage '99 II paper (Fig 7)?  And is it possible to 
specify what the 'north pole' of this coordinate system is?  For example, if I 
wanted it to be at the posterior end of the STS.  I'm looking to do this on a 
flat patch. Thanks.

-Derin

On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:

> Hi Eric,
> 
> in tksurfer click view->scale bar to see the 1cm bar.
> 
> cheers,
> Bruce
> On Thu, 25 Mar 2010, 
> Eric Moulton wrote:
> 
>> I was wondering if freesurfer has a way of generating a scale for
>> distance, similar to what one would see in the legend of a roadmap.
>> I'm thinking of using such a scale for a 3-d pial surface-render of an
>> averaged brain (as generated using make_average_surface).  Since it's
>> a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale,
>> with scale bars for the x, y, and z directions.  Does freesurfer have
>> some visual representation of a distance scale like I've described, or
>> perhaps some alternative?
>> 
>> Eric Moulton PhD
>> Assistant Neuroscientist
>> P.A.I.N. Group
>> Brain Imaging Center
>> McLean Hospital
>> 115 Mill Street
>> Belmont, MA 02478
>> Phone: 617-855-2604
>> Fax: 617-855-3772
>> 
>> 
>> 
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>> 
>> 
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Re: [Freesurfer] Creating a distance scale bar for a pial surface-render viewed in tksurfer

[Derin Cobia]

Don't have the source, but I could download it.  What am I looking for?  Do you 
think it would it be possible to do this in Matlab or something, and import in 
(as an overlay maybe)?  New territory for me, I'm sorry too... :(

-Derin

On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:

> Hi Derin,
> 
> you could try this in tksurfer, but it isn't terribly well documented or 
> supported (or remembered by me). I hacked some stuff together in tksurfer 
> to get those images, but haven't used it in more than 10 years. Do you have 
> the source? You're welcome to poke through it, but I'm not sure it works 
> anymore.
> 
> sorry for the unhelpful answer :<
> Bruce
> 
> 
> On Thu, 25 Mar 2010, Derin Cobia wrote:
> 
>> Along these same lines, is it possible to overlay/display a Cartesian grid 
>> on the surface, a la the Neuroimage '99 II paper (Fig 7)?  And is it 
>> possible to specify what the 'north pole' of this coordinate system is?  For 
>> example, if I wanted it to be at the posterior end of the STS.  I'm looking 
>> to do this on a flat patch. Thanks.
>> 
>> -Derin
>> 
>> On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
>> 
>>> Hi Eric,
>>> 
>>> in tksurfer click view->scale bar to see the 1cm bar.
>>> 
>>> cheers,
>>> Bruce
>>> On Thu, 25 Mar 2010,
>>> Eric Moulton wrote:
>>> 
>>>> I was wondering if freesurfer has a way of generating a scale for
>>>> distance, similar to what one would see in the legend of a roadmap.
>>>> I'm thinking of using such a scale for a 3-d pial surface-render of an
>>>> averaged brain (as generated using make_average_surface).  Since it's
>>>> a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale,
>>>> with scale bars for the x, y, and z directions.  Does freesurfer have
>>>> some visual representation of a distance scale like I've described, or
>>>> perhaps some alternative?
>>>> 
>>>> Eric Moulton PhD
>>>> Assistant Neuroscientist
>>>> P.A.I.N. Group
>>>> Brain Imaging Center
>>>> McLean Hospital
>>>> 115 Mill Street
>>>> Belmont, MA 02478
>>>> Phone: 617-855-2604
>>>> Fax: 617-855-3772
>>>> 
>>>> 
>>>> 
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>> 
>> 
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Re: [Freesurfer] Longitudinal pial editing

[Derin Cobia]

Hi Martin,

Thanks for the input.  You are correct that the slices from the tp's to base 
are slightly off, this is because of the poor correspondence in slice numbering 
between them.  And yes, there was still skull/dura several slices forward and 
back.  

Are you sure that the -long runs don't need to be edited in this case?  Even 
with clearly bad pial surfaces?  I believe that the brainmask.mgz in the base 
is correct, however, my concern is that it is being poorly mapped to the 
longitudinals.  There are multiple instances in this same subject where the 
brainmask.mgz differs between the -long and base; particularly, excess 
skull/dura in the -long runs, where it has been edited out in the base.  What 
would cause this?  

I like the idea of copying over the cross-sectional brainmask.mgz to initialize 
the longitudinal pipeline (as opposed to masking T1.mgz with 
norm_template.mgz).  Is there a reason why this is not the default?  This would 
make sense to me given the time/effort put into edits at tp1 - tpn, then they 
can just be pushed forward to the longitudinal runs.  Maybe Nick or Doug could 
comment on it?  I'll test it out and see.  Thanks.

-Derin


On Sep 3, 2010, at 4:37 PM, Martin Reuter wrote:

> Hi Derin,
> 
> as far as I can see your description is correct.
> Note: in your screenshots the base is shown in a different slice (but I
> believe that you probably scrolled through the image to make sure no
> skull is included in a different slice).
> 
> Actually in this situation, the long runs should not need editing, if
> the brainmask.mgz in the base is accurate. It is mapped to the
> longitudinals and used as a brainmask there.
> 
> Have you tried editing the brainmask in the longitudinal directory (or
> if done in the cross sectional you can simply copy it over as it is in
> the same space). Then pass -long  and -autorecon2-pial -autorecon3?
> Not sure what this does or if it works, but it's worth a try. If it does
> not work, I guess we need to look at this data, to see what is going
> on. 
> 
> Currently I am working on testing out the 5.0 fix and some other
> possible improvements...
> 
> Best, Martin
> 
> On Fri, 2010-09-03 at 13:54 -0500, Derin Cobia wrote:
>> Based on our understanding of the longitudinal pipeline for 4.5, image edits 
>> for the -long runs come mostly from the template/base subj (with an optional 
>> flag for CPs to be copied from the template; 
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13256.html, 
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html).  
>> In addition, our assumption is that pial edits will come via the template, 
>> as the -long brainmask, is a result of masking the -long T1.mgz by the 
>> template brainmask.mgz (which itself is the norm_template.mgz, a combination 
>> of every time point's norm.mgz [which is pre-edit stage]).  
>> 
>> We've run into an issue where our -long runs are still in need of pial 
>> editing, despite edits having been done to both the cross sectional and 
>> template runs (see attached).  However, it's also our understanding that we 
>> should not edit the -long runs and try to re-run (using -autorecon2-pial 
>> -autorecon3), as this will pollute the correction for intrasubject variation 
>> (per communication from Martin).  How would you recommend to proceed?  
>> Thanks.
>> 
>> -Derin
>> 
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Re: [Freesurfer] Fwd: Mapping labels to the RH on Macs

[Derin Cobia]

I'm experiencing this as well on my Mac OS X distribution of FS v5.0.0.  Here 
is terminal output when running the "Map Label to Subjects" command on the rh, 
with a rh label in QDEC (below).  Looks like there is a small bug in the code 
where it points to the left hemi for registration instead of the right ("--hemi 
lh").  

-Derin

===
mri_label2label --srclabel rh_ifg_test --srcsubject fsaverage --trgsubject C1a 
--trglabel rh_ifg_test --regmethod surface --hemi lh

srclabel = rh_ifg_test
srcsubject = fsaverage
trgsubject = C1a
trglabel = rh_ifg_test
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Volumes/project/freesurfer/PPA
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 7351 points in source label.
Starting surface-based mapping
Reading source registration 
 /Volumes/project/freesurfer/PPA/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /Volumes/project/freesurfer/PPA/C1a/surf/lh.white
Reading target registration 
 /Volumes/project/freesurfer/PPA/C1a/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7351 nlabel points
Performing mapping from target back to the source label
===


On Oct 11, 2010, at 9:51 AM, Tessa Harrison wrote:

> Hi FreeSurfers, 
> 
> I posted this question to the listserv a little over a week ago-- does anyone 
> have any insight as to what is going on with our RH labels?
> 
> -Tessa
> 
> 
> 
> -- Forwarded message --
> From: Tessa Harrison 
> Date: Thu, Sep 30, 2010 at 9:36 AM
> Subject: Mapping labels to the RH on Macs
> To: freesurfer@nmr.mgh.harvard.edu
> 
> 
> Dear FreeSurfers,
> 
> I am running FS 4.5 or FS 5.0 on Mac OS X 10.6.4 -Intel (see attached 
> screenshot).
> 
> I am not able to map RH labels created in fsaverage to the RH of any of my 
> subjects. LH labels map to the LH from qdec "Map Label to All Subjects" 
> option and from the command line with no problem. However, when I try to map 
> RH labels (that map correctly to the RH in fsaverage) to individual subjects, 
> the command appears to work (no error messages), but something goes wrong. It 
> appears that the label is actually mapped to the LH because when I pull it up 
> on the RH in an individual subject it looks like scattered dots (see attached 
> image). 
> 
> The same thing happens on another Mac in our lab. I have tried both FS 4.5 
> and 5.0 and the problem occurs in both versions. Could this be a bug in the 
> Mac FS release? I did not find any mention of this problem in the archives. 
> 
> Thank you for you help!
> 
> -Tessa
> 
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Re: [Freesurfer] Cortical gray matter volume

[Derin Cobia]

Bruce,

Sorry, I think I was confusing.  Basically I was wondering how the numbers
in mris_anatomical_stats are calculated, and if I can independently verify
them.  Does a paper/article address this?  Thanks again for your help.

-Derin

> Hi Derin,
>
> no, they aren't quantized - they are computed from the surfaces, which
> live in a continuum.
>
> Bruce
>
> On Wed, 12 Jul 2006 [EMAIL PROTECTED] wrote:
>
>> Are not the mris_anatomical_stats voxel-based as well?  I thought that
>> was
>> what I was measuring in *total gray matter volume*.  If the aseg &
>> ribbon
>> files are quantized to 1mm^3, what is the surface?  Plus, is there any
>> way
>> to verify the stats I'm getting in mris_anatomical_stats?  Thanks.
>>
>> -Derin
>>
>>> the aseg will be different, since it's voxel-based (and typically not
>>> as
>>> accurate as the surfaces)
>>> On Mon, 10 Jul 2006 [EMAIL PROTECTED] wrote:
>>>
 Is this true of the aseg files as well?  I tried *double-checking* the
 mris_anatomical_stats by using the aseg file in MatLab (assigning
 values
 to the voxel-intensities, counting them up, etc, etc) and the numbers
 came
 up different.  Is that why?  Probably not the best method now that I
 think
 about it...  Thanks Doug & Bruce.

 -Derin

> It is only cortical. And you don't want to use ?h.ribbon.mgz as this
> is
> quantized to 1mm^3 and will be less accurate than mris_anatomical
> stats.
>
> doug
>
>
>
>
>
> [EMAIL PROTECTED] wrote:
>
>> Hi,
>>
>> I am attempting to assess (& compare) total cortical gray matter
>> volume
>> in
>> a series of subjects (schiz vs. control), and was wondering if the
>> tabular
>> mris_anatomical_stats gm output consisted of only cortical gm, or
>> included
>> subcortical and other nuclei as well.  I've searched the wiki,
>> articles,
>> and listserve archive with not much success; I get the sense that it
>> is,
>> but want to make sure.  Additionally, what is shown in the
>> ?h.ribbon.mgz
>> files appears to be exactly what I am looking for.  Is there any way
>> to
>> run the mris_anatomical_stats command on these files (use
>> mris_convert
>> maybe)?  Thanks in advance.
>>
>> -Derin
>>
>>
>>
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>>
>
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> [EMAIL PROTECTED]
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> Fax: 617-726-7422
>
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>>>
>>
>>
>>
>>
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[Freesurfer] Gray matter volumes

[Derin Cobia]

Hi again,

Two questions:

1).  You said earlier that GM volumes from mris_anatomical_stats are more
accurate than from the aseg files.  Would you recommend using the
surface-based GM volumes instead of the ones from the aseg.stats files?  I
ask because we have ~200 subjects processed for volume, but not surface,
meaning no mris_anatomical_stats.  If we could avoid the added processing
time on these it would be helpful, but don't want to do it at the expense
of accuracy.

2).  What structures are calculated into "total white matter volume" under
mris_anatomical_stats?  Does it include corpus callosum and others? 
Thanks.

-Derin



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[Freesurfer] FLASH atlas

[Derin Cobia]

Hello,

I read in the archive that you were planning on releasing two new atlases
(for MP-RAGE and FLASH) last year.  Were those (or even newer ones)
distributed?  I have some FLASH sequences I want to run.  Thanks!

-Derin



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[Freesurfer] Skull Stripping

[Derin Cobia]

Hello,

After having run -autorecon1 on all of my subjects I've noticed
skullstripping has edited out the cerebellum/brainstem on some, but not on
others.  Because I'm not interested in these structures, can I just leave
the files as is (i.e.-not bother adjusting the wsthreshold level,
re-running, etc)?  Or will I run into problems with the -autorecon2 & 3
processing streams down the line?  Thanks again!

-Derin



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[Freesurfer] tkmedit crashes/freezes

[Derin Cobia]

I've been experiencing some crashes/freezing using tkmedit lately, and
have been able to reproduce it pretty reliably.  It occurs when I scroll
through the slices of the subject either using the arrows keys or clicking
through on the toolbar.  It happens when viewing a variety of volumes
(brainmask, T1, etc), and from a variety of perspectives (coronal,
sagittal, etc); it  also happens on different subjects as well.  This
occurs no matter what workstation I use in the lab (networked
environment).  My X freezes up as well as the keyboard, but the mouse
doesn't.  I used to be able to restart my X remotely, but now tkmedit
locks up so bad I have to reboot.  Any ideas?

Dell Precision 670 Workstations
CentOS 4.1 (32-bit)

 freesurfer-Linux-centos4-stable-pub-v3.0.3 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /pkg/brainmap/freesurfer
FSFAST_HOME /pkg/brainmap/freesurfer/fsfast
SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/
FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions
MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin
MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib
PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0
GSL_DIR /pkg/brainmap/freesurfer/lib/gsl
QTDIR   /usr/lib/qt-3.3
TCLLIBPATH  /pkg/brainmap/freesurfer/lib/tcltktixblt/lib
FSL_DIR /pkg/brainmap/freesurfer/fsl

[EMAIL PROTECTED] ~]$ which tkmedit
/pkg/brainmap/freesurfer/bin//tkmedit

cd /disk/k2/freesurfer/neuromorph_v1_flash/

Thanks in advance.

-Derin

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Re: [Freesurfer] tkmedit crashes/freezes

[Derin Cobia]

Kevin-
Yeah, either way.  In my "infinite" wisdom I thought that scrolling slower
would help, but not so.

Nick-
I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or
subjects directory.  Would it be somewhere else?  It looks like we're
using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site
shows a 1.0-8762 as the latest.  I'll see if we can update it today, maybe
that will help.

On the side...  why are my intensity values "infinite" for the following
subject?  I've briefly checked brainmask.mgz, and differing intensities
appear.  Any ideas?  Thanks.

-Derin

#
[EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006

 mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM: nan +- nan [10.0 --> -10.0]
GM: nan +- nan [10.0 --> -10.0]
mri_segment: class statistics not finite - check input volume!
Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686
i386 GNU/Linux

recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006


> Hm, I can't reproduce this.
>
> So, you load up a volume, and repeatedly press an arrow key to scroll
> through the slices? Or hold the button down?
>
> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote:
>> I've been experiencing some crashes/freezing using tkmedit lately, and
>> have been able to reproduce it pretty reliably.  It occurs when I scroll
>> through the slices of the subject either using the arrows keys or
>> clicking
>> through on the toolbar.  It happens when viewing a variety of volumes
>> (brainmask, T1, etc), and from a variety of perspectives (coronal,
>> sagittal, etc); it  also happens on different subjects as well.  This
>> occurs no matter what workstation I use in the lab (networked
>> environment).  My X freezes up as well as the keyboard, but the mouse
>> doesn't.  I used to be able to restart my X remotely, but now tkmedit
>> locks up so bad I have to reboot.  Any ideas?
>>
>> Dell Precision 670 Workstations
>> CentOS 4.1 (32-bit)
>>
>>  freesurfer-Linux-centos4-stable-pub-v3.0.3 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME /pkg/brainmap/freesurfer
>> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast
>> SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/
>> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions
>> MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin
>> MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib
>> PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0
>> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl
>> QTDIR   /usr/lib/qt-3.3
>> TCLLIBPATH  /pkg/brainmap/freesurfer/lib/tcltktixblt/lib
>> FSL_DIR /pkg/brainmap/freesurfer/fsl
>>
>> [EMAIL PROTECTED] ~]$ which tkmedit
>> /pkg/brainmap/freesurfer/bin//tkmedit
>>
>> cd /disk/k2/freesurfer/neuromorph_v1_flash/
>>
>> Thanks in advance.
>
>
> --
> Kevin Teich
>

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Re: [Freesurfer] tkmedit crashes/freezes

[Derin Cobia]

Bruce,

No, I processed all of them the same way (converted files, -autorecon1,
etc).  The scan quality differs among them, but I tossed the really bad
ones.  Here is the xdebug file.  Also, is what I'm seeing in this slice
(see attached jpg) something to worry about?  If I scroll through other
slices, then come back to it, the artifacts are gone.  This happens
randomly on various slices on some of the subjects, but it never stays.

I have updated the drivers for the video card, and haven't had any issues
(yet).  I'll keep my eye on it.  Thanks for your help.

-Derin

> were these processed any differently? The .xdebug_tkmedit should be in pwd
> wherever you ran it from.
>
> Bruce
>
>
> On Tue, 29 Aug 2006, Derin Cobia
> wrote:
>
>> Kevin-
>> Yeah, either way.  In my "infinite" wisdom I thought that scrolling
>> slower
>> would help, but not so.
>>
>> Nick-
>> I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or
>> subjects directory.  Would it be somewhere else?  It looks like we're
>> using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site
>> shows a 1.0-8762 as the latest.  I'll see if we can update it today,
>> maybe
>> that will help.
>>
>> On the side...  why are my intensity values "infinite" for the following
>> subject?  I've briefly checked brainmask.mgz, and differing intensities
>> appear.  Any ideas?  Thanks.
>>
>> -Derin
>>
>> #
>> [EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006
>>
>> mri_segment brain.mgz wm.seg.mgz
>>
>> doing initial intensity segmentation...
>> using local statistics to label ambiguous voxels...
>> computing class statistics for intensity windows...
>> WM: nan +- nan [10.0 --> -10.0]
>> GM: nan +- nan [10.0 --> -10.0]
>> mri_segment: class statistics not finite - check input volume!
>> Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686
>> i386 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006
>>
>>
>>> Hm, I can't reproduce this.
>>>
>>> So, you load up a volume, and repeatedly press an arrow key to scroll
>>> through the slices? Or hold the button down?
>>>
>>> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote:
>>>> I've been experiencing some crashes/freezing using tkmedit lately, and
>>>> have been able to reproduce it pretty reliably.  It occurs when I
>>>> scroll
>>>> through the slices of the subject either using the arrows keys or
>>>> clicking
>>>> through on the toolbar.  It happens when viewing a variety of volumes
>>>> (brainmask, T1, etc), and from a variety of perspectives (coronal,
>>>> sagittal, etc); it  also happens on different subjects as well.  This
>>>> occurs no matter what workstation I use in the lab (networked
>>>> environment).  My X freezes up as well as the keyboard, but the mouse
>>>> doesn't.  I used to be able to restart my X remotely, but now tkmedit
>>>> locks up so bad I have to reboot.  Any ideas?
>>>>
>>>> Dell Precision 670 Workstations
>>>> CentOS 4.1 (32-bit)
>>>>
>>>>  freesurfer-Linux-centos4-stable-pub-v3.0.3 
>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>> FREESURFER_HOME /pkg/brainmap/freesurfer
>>>> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast
>>>> SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/
>>>> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions
>>>> MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin
>>>> MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib
>>>> PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0
>>>> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl
>>>> QTDIR   /usr/lib/qt-3.3
>>>> TCLLIBPATH  /pkg/brainmap/freesurfer/lib/tcltktixblt/lib
>>>> FSL_DIR /pkg/brainmap/freesurfer/fsl
>>>>
>>>> [EMAIL PROTECTED] ~]$ which tkmedit
>>>> /pkg/brainmap/freesurfer/bin//tkmedit
>>>>
>>>> cd /disk/k2/freesurfer/neuromorph_v1_flash/
>>>>
>>>> Thanks in advance.
>>>
>>>
>>> --
>>> Kevin Teich
>>>
>>
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Re: [Freesurfer] tkmedit crashes/freezes

[Derin Cobia]

Sorry, visual artifacts- yes (still there), crashing/freezing- no (but
I've been trying hard).  It's only been about an hour since the update,
I'll keep you posted.  So, should I worry about the artifacts affecting
output?  If I scroll through the slices long enough, they eventually all
disappear.

-Derin

> OK, so since you updated the graphics driver, you've had no problems
> with either the visual artifacts or the crashing/freezing? If there
> have been no problems, we'll assume the graphics driver fixed
> it. Otherwise, let us know.
>
> On Tue, Aug 29, 2006 at 01:24:09PM -0500, Derin Cobia wrote:
>> Bruce,
>>
>> No, I processed all of them the same way (converted files, -autorecon1,
>> etc).  The scan quality differs among them, but I tossed the really bad
>> ones.  Here is the xdebug file.  Also, is what I'm seeing in this slice
>> (see attached jpg) something to worry about?  If I scroll through other
>> slices, then come back to it, the artifacts are gone.  This happens
>> randomly on various slices on some of the subjects, but it never stays.
>>
>> I have updated the drivers for the video card, and haven't had any
>> issues
>> (yet).  I'll keep my eye on it.  Thanks for your help.
>>
>> -Derin
>>
>> > were these processed any differently? The .xdebug_tkmedit should be in
>> pwd
>> > wherever you ran it from.
>> >
>> > Bruce
>> >
>> >
>> > On Tue, 29 Aug 2006, Derin Cobia
>> > wrote:
>> >
>> >> Kevin-
>> >> Yeah, either way.  In my "infinite" wisdom I thought that scrolling
>> >> slower
>> >> would help, but not so.
>> >>
>> >> Nick-
>> >> I'm unable to locate a .xdebug_tkmedit file in either the freesurfer
>> or
>> >> subjects directory.  Would it be somewhere else?  It looks like we're
>> >> using the 1.0-8178 Nvidia driver for our Quadro FX card, but their
>> site
>> >> shows a 1.0-8762 as the latest.  I'll see if we can update it today,
>> >> maybe
>> >> that will help.
>> >>
>> >> On the side...  why are my intensity values "infinite" for the
>> following
>> >> subject?  I've briefly checked brainmask.mgz, and differing
>> intensities
>> >> appear.  Any ideas?  Thanks.
>> >>
>> >> -Derin
>> >>
>> >> #
>> >> [EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006
>> >>
>> >> mri_segment brain.mgz wm.seg.mgz
>> >>
>> >> doing initial intensity segmentation...
>> >> using local statistics to label ambiguous voxels...
>> >> computing class statistics for intensity windows...
>> >> WM: nan +- nan [10.0 --> -10.0]
>> >> GM: nan +- nan [10.0 --> -10.0]
>> >> mri_segment: class statistics not finite - check input volume!
>> >> Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686
>> i686
>> >> i386 GNU/Linux
>> >>
>> >> recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006
>> >>
>> >>
>> >>> Hm, I can't reproduce this.
>> >>>
>> >>> So, you load up a volume, and repeatedly press an arrow key to
>> scroll
>> >>> through the slices? Or hold the button down?
>> >>>
>> >>> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote:
>> >>>> I've been experiencing some crashes/freezing using tkmedit lately,
>> and
>> >>>> have been able to reproduce it pretty reliably.  It occurs when I
>> >>>> scroll
>> >>>> through the slices of the subject either using the arrows keys or
>> >>>> clicking
>> >>>> through on the toolbar.  It happens when viewing a variety of
>> volumes
>> >>>> (brainmask, T1, etc), and from a variety of perspectives (coronal,
>> >>>> sagittal, etc); it  also happens on different subjects as well.
>> This
>> >>>> occurs no matter what workstation I use in the lab (networked
>> >>>> environment).  My X freezes up as well as the keyboard, but the
>> mouse
>> >>>> doesn't.  I used to be able to restart my X remotely, but now
>> tkmedit
>> >>>> locks up so bad I have to re

[Freesurfer] nan issue

[Derin Cobia]

Bruce,

I worked my way backwards through the stream on each .mgz file.  The
aseg.mgz (and aseg.auto.mgz) file came up in pieces, some parts were
there, others weren't; brain.mgz was blank, there was nothing there, as
well as the values being 0; the same for norm.mgz.  However, both
brainmask & nu.mgz appeared normal, which makes me suspect the
talairach.lta file.  Is this bad output because of the talairach
registration?

-Derin
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[Freesurfer] Intensity/Conversion problem

[Derin Cobia]

I seem to be having some difficulty in converting my flash images into FS
format for processing.  After using mri_convert my orig.mgz files become
excessively bright compared to the original analyze file, thus creating
poor autorecon1 output, etc.  See the attached jpgs of before and after
shots.  Also, here's the command I'm using:
mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz
*subjectid*.img mri/orig/001.mgz
Am I doing something wrong?  Thanks.

-Derin


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Re: [Freesurfer] Intensity/Conversion problem

[Derin Cobia]

Bruce,

I've been getting values from around 188-255 in the wm.

-Derin


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Re: [Freesurfer] Intensity/Conversion problem

[Derin Cobia]

I believe I discovered the problem.  I had accidently linked to the 8-bit
.img files for the subjects instead of the 16-bit ones.  I've rerun
autorecon1 and everything looks good.

Any thoughts on the parcellated pial shot I sent?  It doesn't look correct
to me, but maybe I'm wrong.  Thanks!

-Derin

> Hi Derin,
>
> the attachment came through fine, but I need the unconformed (e.g.
> 001.mgz) volume in order to diagnose what went wrong.
>
> Bruce
> On Fri, 13 Oct 2006,
> Derin Cobia wrote:
>
>> Here is the orig.mgz file.  Been having trouble with attachments lately,
>> hopefully this works.  Thanks.
>>
>> -Derin
>>
>>> can you send us the image? This sounds like a bug. You should be able
>>> to
>>> specify the intensity scaling directly in mri_convert using -sc >> factor>
>>> On Fri, 13 Oct 2006, Derin Cobia wrote:
>>>
>>>> Bruce,
>>>>
>>>> I've been getting values from around 188-255 in the wm.
>>>>
>>>> -Derin
>>>>
>>>>
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>>>
>>
>

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[Freesurfer] mri_convert options

[Derin Cobia]

Hi,
Currently we've been converting from .img to .mgz format using the
following syntax:

mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz
s1501p.img mri/orig/001.mgz

It came to my attention today that the values we used for TI, TE, and TR
are all actually in ms, and correspond to the Siemen's Vision use of the
terms TI and TR for the MRPAGE sequence.  This is quite different from how
TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and
Trio Siemens platform.  Furthermore, we have actually been applying these
values to Vision FLASH data as well, for which TI is irrelevant, and the
TR and flip were different.  Basically, we have just been confused in our
use of mri_convert.

So, this raises a couple questions:
1) Are the TI, TE, TR and flip parameters important to mri_convert?  How
are they used?  Are they used in any manner in the subsequent Freesurfer
processing stream?  We wonder if they are not important, since the current
documention lists TR as an option, but doesn't mention TI, TE, or flip as
options.
2) If these parameters are important in some manner how would the use of
such grossly incorrect values affect the results?

So basically, we are wondering what parameters, if any, are truly
necessary as part of mri_convert?  And do we (gasp) need to consider
rerunning the stream from stage 1...

Thanks!
Derin

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Re: [Freesurfer] Scan quality

[Derin Cobia]

  I attempted to get them relatively close to the same size, the surfaced
one is at Zoom "2" in FS (the orig is viewed using MoJo); I didn't alter
brightness or anything.  I was just worried this would make my results
(volume in particular) problematic.  Thanks Bruce.

-Derin


> Hi Derin,
>
> the surfaces look reasonable, although the images aren't that great. Is
> the one with surfaces overlaid windowed up relative to the other one? It
> looks noisier, but maybe that's because you turned the brightness up.
> Still, if they are old data there's not much you can do
>
> cheers,
> Bruce
>
>
> On Mon, 6 Nov 2006, Derin
> Cobia wrote:
>
>> Should I expect this kind of quality/resolution from my FS images based
>> on
>> the original scan (see attached images)?  These are older scans that
>> I've
>> been given, and I just want to make sure that the image quality isn't
>> introducing any unnecessary error, or is not "good enough" for FS.
>> Thanks.
>>
>> -Derin
>>
>>
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[Freesurfer] Scan quality & FS

[Derin Cobia]

Some of the scans I work with are of the same subject, but differ only in
the length of time they were in the scanner.  Obviously the scans of
longer length (everything else being equal) will yield better quality;
however, I'm interested in a kind of "bang-for-your-buck" approach.  Is
there a point where some amount of diminishing returns occurs with respect
to FS processing and scan quality?  Therefore, my main question:

1) Is there anything in the FS processing stream that would be a
reasonable heuristic for determining if one scan processes better than
another (all things being equal beside length of time being scanned)?  For
example, # of topological defects to correct, length of processing, amount
of manual correction, or just visual quality?

I understand some of this is related to what structure(s) I'm interested
in measuring, but was wondering about it in a general fashion.  This may
come in handy down the road for us because many of our subjects are
individuals with schizophrenia, and being in an enclosed space (let alone
the time it takes to yield a high-quality scan) is traumatic enough for
them.  Thanks for any input.

-Derin
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Re: [Freesurfer] Bad surfaces?

[Derin Cobia]

Bruce,

Are the things I'm noticing due to using 3.0.3 for everything (including
topology fixer) up to final surfaces, then using 3.0.4?  So I guess the
other "odd" surfaces are acceptable to trust (excluding the medial temp
lobe)?

Thanks!

Derin

> Hi Derin,
>
> it's pretty much impossible to tell if surfaces are crossing from a 2d
> slice. This looks like there was an incorrectly fixed topological defect
> in the hippocampus. You could manually correct it in the wm.mgz volume,
> but we don't really care about the surfaces in this region (cerebral
> cortex)
>
> cheers,
> Bruce
> On Wed, 31 Jan 2007, Derin Cobia wrote:
>
>> I reran our subjects from "final_surfaces" on through autorecon3 using
>> 3.0.4 to correct for the pial surface crossover at the midline (as
>> recommended by Bruce).  Most things look fine, except that there are
>> many
>> portions of the surfaces that appear to "bunch" together.  In one
>> extreme
>> example it appears that the white and pial surface cross.  I've attached
>> some jpgs to demonstrate what I mean.  The close-up is r medial temporal
>> area, while the other shows the "bunching" in the l superior portion,
>> and
>> at the midline.  I understand that the crossing is not correct, but do
>> the
>> other surfaces look appropriate?  Thanks.
>>
>> -Derin
>>
>>
>

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Re: [Freesurfer] Bad surfaces?

[Derin Cobia]

Aseg looks good, here's another example of what I'm finding.  It's
posterior midline (~PreCuneus area).  Sometimes this happens on the outer
cortical surfaces too.  Thanks.

-Derin

> not really sure. Does the aseg look good? We don't usually see that kind
> of defect.
> On Wed, 31 Jan 2007, Derin Cobia wrote:
>
>> Bruce,
>>
>> Are the things I'm noticing due to using 3.0.3 for everything (including
>> topology fixer) up to final surfaces, then using 3.0.4?  So I guess the
>> other "odd" surfaces are acceptable to trust (excluding the medial temp
>> lobe)?
>>
>> Thanks!
>>
>> Derin
>>
>>> Hi Derin,
>>>
>>> it's pretty much impossible to tell if surfaces are crossing from a 2d
>>> slice. This looks like there was an incorrectly fixed topological
>>> defect
>>> in the hippocampus. You could manually correct it in the wm.mgz volume,
>>> but we don't really care about the surfaces in this region (cerebral
>>> cortex)
>>>
>>> cheers,
>>> Bruce
>>> On Wed, 31 Jan 2007, Derin Cobia wrote:
>>>
>>>> I reran our subjects from "final_surfaces" on through autorecon3 using
>>>> 3.0.4 to correct for the pial surface crossover at the midline (as
>>>> recommended by Bruce).  Most things look fine, except that there are
>>>> many
>>>> portions of the surfaces that appear to "bunch" together.  In one
>>>> extreme
>>>> example it appears that the white and pial surface cross.  I've
>>>> attached
>>>> some jpgs to demonstrate what I mean.  The close-up is r medial
>>>> temporal
>>>> area, while the other shows the "bunching" in the l superior portion,
>>>> and
>>>> at the midline.  I understand that the crossing is not correct, but do
>>>> the
>>>> other surfaces look appropriate?  Thanks.
>>>>
>>>> -Derin
>>>>
>>>>
>>>
>>
>>
>>
>
<>
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[Freesurfer] total brain volume

[Derin Cobia]

I would like to calculate total brain volume (defined as: total white,
gray, and subcortical altogether).  Should I take the BrainSegVol and
minus out cerebellum and ventricles, or add the white and gray matter
volumes from mris_anatomical_stats (it seems I remember hearing that white
matter from mris_anatomical_stats is not reliable)?  Thanks.

-Derin


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Re: [Freesurfer] total brain volume

[Derin Cobia]

Bruce,

So if I downloaded the dev version of the program I could use it to get
the volumes from subjects processed with 3.0.3?  And would adding these
volumes together generate the total volume I'm looking for (including
subcoritical)?  Thanks!

-Derin

> Hi Derin,
>
> the aseg labeling of cortical gm is not that accurate - the surfaces are
> quiet a bit more so. We have a new tool for generating the estimate of the
> gm and wm volume from the surfaces called mris_volume and mris_wm_volume.
> I
> think Doug or Nick has integrated it into the dev version of recon-all.
>
> cheers,
> Bruce
>
>
> On Fri, 2 Feb 2007, Derin Cobia wrote:
>
>> I would like to calculate total brain volume (defined as: total white,
>> gray, and subcortical altogether).  Should I take the BrainSegVol and
>> minus out cerebellum and ventricles, or add the white and gray matter
>> volumes from mris_anatomical_stats (it seems I remember hearing that
>> white
>> matter from mris_anatomical_stats is not reliable)?  Thanks.
>>
>> -Derin
>>
>>
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>>
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Re: [Freesurfer] total brain volume

[Derin Cobia]

Is there any way I can get mris_wm_volume?  If not, what's the next best
thing?  Can I use the aseg.stats estimates?

-Derin

>
> I have not implemented it in recon-all yet.
>
> doug
>
>
>
>
> On Fri, 2 Feb 2007, Bruce Fischl wrote:
>
>> you would need to add in whatever subcortical components you wanted to
>> include, as they are excluded from the wm volume
>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>
>>> Bruce,
>>>
>>> So if I downloaded the dev version of the program I could use it to get
>>> the volumes from subjects processed with 3.0.3?  And would adding these
>>> volumes together generate the total volume I'm looking for (including
>>> subcoritical)?  Thanks!
>>>
>>> -Derin
>>>
>>>> Hi Derin,
>>>>
>>>> the aseg labeling of cortical gm is not that accurate - the surfaces
>>>> are
>>>> quiet a bit more so. We have a new tool for generating the estimate of
>>>> the
>>>> gm and wm volume from the surfaces called mris_volume and
>>>> mris_wm_volume.
>>>> I
>>>> think Doug or Nick has integrated it into the dev version of
>>>> recon-all.
>>>>
>>>> cheers,
>>>> Bruce
>>>>
>>>>
>>>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>>>
>>>>> I would like to calculate total brain volume (defined as: total
>>>>> white,
>>>>> gray, and subcortical altogether).  Should I take the BrainSegVol and
>>>>> minus out cerebellum and ventricles, or add the white and gray matter
>>>>> volumes from mris_anatomical_stats (it seems I remember hearing that
>>>>> white
>>>>> matter from mris_anatomical_stats is not reliable)?  Thanks.
>>>>>
>>>>> -Derin
>>>>>
>>>>>
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>>>>>
>>>>>
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>>>
>>>
>>>
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>>
>>
>
> --
> 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
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Re: [Freesurfer] total brain volume

[Derin Cobia]

CentOS 4 (32-bit).  Thanks!

-Derin

> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume?  If not, what's the next best
>> thing?  Can I use the aseg.stats estimates?
>>
>> -Derin
>>
>>>
>>> I have not implemented it in recon-all yet.
>>>
>>> doug
>>>
>>>
>>>
>>>
>>> On Fri, 2 Feb 2007, Bruce Fischl wrote:
>>>
>>>> you would need to add in whatever subcortical components you wanted to
>>>> include, as they are excluded from the wm volume
>>>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>>>
>>>>> Bruce,
>>>>>
>>>>> So if I downloaded the dev version of the program I could use it to
>>>>> get
>>>>> the volumes from subjects processed with 3.0.3?  And would adding
>>>>> these
>>>>> volumes together generate the total volume I'm looking for (including
>>>>> subcoritical)?  Thanks!
>>>>>
>>>>> -Derin
>>>>>
>>>>>> Hi Derin,
>>>>>>
>>>>>> the aseg labeling of cortical gm is not that accurate - the surfaces
>>>>>> are
>>>>>> quiet a bit more so. We have a new tool for generating the estimate
>>>>>> of
>>>>>> the
>>>>>> gm and wm volume from the surfaces called mris_volume and
>>>>>> mris_wm_volume.
>>>>>> I
>>>>>> think Doug or Nick has integrated it into the dev version of
>>>>>> recon-all.
>>>>>>
>>>>>> cheers,
>>>>>> Bruce
>>>>>>
>>>>>>
>>>>>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>>>>>
>>>>>>> I would like to calculate total brain volume (defined as: total
>>>>>>> white,
>>>>>>> gray, and subcortical altogether).  Should I take the BrainSegVol
>>>>>>> and
>>>>>>> minus out cerebellum and ventricles, or add the white and gray
>>>>>>> matter
>>>>>>> volumes from mris_anatomical_stats (it seems I remember hearing
>>>>>>> that
>>>>>>> white
>>>>>>> matter from mris_anatomical_stats is not reliable)?  Thanks.
>>>>>>>
>>>>>>> -Derin
>>>>>>>
>>>>>>>
>>>>>>> ___
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>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>>
>>> --
>>> 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
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>>
>>
>>
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Re: [Freesurfer] total brain volume

[Derin Cobia]

I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs.  Am I missing something?  Do I
need to run mris_volume for a different surface?  Thanks.

-Derin

> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume?  If not, what's the next best
>> thing?  Can I use the aseg.stats estimates?
>>
>> -Derin
>>
>>>
>>> I have not implemented it in recon-all yet.
>>>
>>> doug
>>>
>>>
>>>
>>>
>>> On Fri, 2 Feb 2007, Bruce Fischl wrote:
>>>
>>>> you would need to add in whatever subcortical components you wanted to
>>>> include, as they are excluded from the wm volume
>>>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>>>
>>>>> Bruce,
>>>>>
>>>>> So if I downloaded the dev version of the program I could use it to
>>>>> get
>>>>> the volumes from subjects processed with 3.0.3?  And would adding
>>>>> these
>>>>> volumes together generate the total volume I'm looking for (including
>>>>> subcoritical)?  Thanks!
>>>>>
>>>>> -Derin
>>>>>
>>>>>> Hi Derin,
>>>>>>
>>>>>> the aseg labeling of cortical gm is not that accurate - the surfaces
>>>>>> are
>>>>>> quiet a bit more so. We have a new tool for generating the estimate
>>>>>> of
>>>>>> the
>>>>>> gm and wm volume from the surfaces called mris_volume and
>>>>>> mris_wm_volume.
>>>>>> I
>>>>>> think Doug or Nick has integrated it into the dev version of
>>>>>> recon-all.
>>>>>>
>>>>>> cheers,
>>>>>> Bruce
>>>>>>
>>>>>>
>>>>>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>>>>>
>>>>>>> I would like to calculate total brain volume (defined as: total
>>>>>>> white,
>>>>>>> gray, and subcortical altogether).  Should I take the BrainSegVol
>>>>>>> and
>>>>>>> minus out cerebellum and ventricles, or add the white and gray
>>>>>>> matter
>>>>>>> volumes from mris_anatomical_stats (it seems I remember hearing
>>>>>>> that
>>>>>>> white
>>>>>>> matter from mris_anatomical_stats is not reliable)?  Thanks.
>>>>>>>
>>>>>>> -Derin
>>>>>>>
>>>>>>>
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>>>>>>>
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>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>>
>>> --
>>> 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
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>>
>>
>>
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[Fwd: Re: [Freesurfer] total brain volume]

[Derin Cobia]

Not sure if this went through the first time yesterday, here it is again. 
Thanks.


I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs.  Am I missing something?  Do I
need to run mris_volume for a different surface?  Thanks.

-Derin


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Re: [Fwd: Re: [Freesurfer] total brain volume]

[Derin Cobia]

Then is there a reason to use mris_volume when I can just do
mris_anatomical_stats and forget the math?

So, if I take the ?h.pial volume then add in the subcortical structure
volumes from aseg.stats (as you mentioned earlier) then that would give me
the estimated whole brain volume?  Thanks Bruce!

-Derin

> you would need to subtract the ?h.white volume from the ?h.pial to get
> gm volume
>
> On Tue, 6 Feb 2007, Derin Cobia wrote:
>
>> Not sure if this went through the first time yesterday, here it is
>> again.
>> Thanks.
>>
>>
>> I've noticed that the gray matter volume output from
>> mris_anatomical_stats
>> (lh) vs. mris_volume (lh.pial) differs.  Am I missing something?  Do I
>> need to run mris_volume for a different surface?  Thanks.
>>
>> -Derin
>>
>>
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Re: [Fwd: Re: [Freesurfer] total brain volume]

[Derin Cobia]

For one of our projects.  We're using cortical gray matter for another
(which I wanted to clarify).

-Derin

> On Tue, 6 Feb 2007, Derin Cobia
> wrote:
>
>> Then is there a reason to use mris_volume when I can just do
>> mris_anatomical_stats and forget the math?
>>
>> So, if I take the ?h.pial volume then add in the subcortical structure
>> volumes from aseg.stats (as you mentioned earlier) then that would give
>> me
>> the estimated whole brain volume?  Thanks Bruce!
>>
>> -Derin
>>
>>> you would need to subtract the ?h.white volume from the ?h.pial to get
>>> gm volume
>>>
>>> On Tue, 6 Feb 2007, Derin Cobia wrote:
>>>
>>>> Not sure if this went through the first time yesterday, here it is
>>>> again.
>>>> Thanks.
>>>>
>>>>
>>>> I've noticed that the gray matter volume output from
>>>> mris_anatomical_stats
>>>> (lh) vs. mris_volume (lh.pial) differs.  Am I missing something?  Do I
>>>> need to run mris_volume for a different surface?  Thanks.
>>>>
>>>> -Derin
>>>>
>>>>
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>>
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[Freesurfer] pial editing

[Derin Cobia]

I have a question regarding editing the pial surface.  Many times it
includes bright spots, such as fat or vessels.  Should I be editing this
out?  I'm pretty clear on getting rid of included dura, but if I spent the
time to edit out every little bright spot, it would be pretty time
intensive.  Would leaving these little "extras" skew my data?  Is there
some balance I can strike when editing?  Thanks!

-Derin
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[Freesurfer] missing cerebellum

[Derin Cobia]

I noticed that one of our subjects made it through the processing stream
(successfully) with the cerebellum missing, thus creating a bad aseg.mgz. 
I filled it back in, and was wondering if I needed to reprocess it
completely under autorecon2 and 3 again, or just run -aseg and whatever
else it needed.  Thanks.

-Derin
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[Freesurfer] autorecon1 failures

[Derin Cobia]

Two questions for two different subjects during autorecon1:

1. The initial skull strip on this subject left too much extra-cerebral
material.  Subsequent attempts at using the wsatlas or manual adjustment
of the wsthresh have resulted in this error:

*WATERSHED**
preflooding height equal to 25 percent
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  1960516

  Find the largest 110-component...mriSegmentReallocateVoxels: could
not alloc 1048381 voxels for sno 8343
Cannot allocate memory
done
  And identify it as the main brain basin...Segmentation fault
Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686
i686 i386 GNU/Linux

recon-all exited with ERRORS at Mon Apr  2 15:02:05 CDT 2007
#--

Are there too many voxels?  I've looked, but couldn't find any information
on how to fix this one.


2. This subject continues to fail with errors during intensity
normalization.Here is the output:

#
[EMAIL PROTECTED] Intensity Normalization Mon Apr  2 15:46:47 EDT 2007
/disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri

 mri_normalize -g 1 nu.mgz T1.mgz

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 0.830  -0.117  -0.004  -3.656;
 0.116   0.833  -0.323  -26.577;
 0.004   0.028   0.075   84.152;
 0.000   0.000   0.000   1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize: could not find any valid peaks
mri_normalize: normalization failed
Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Apr  2 15:46:49 EDT 2007
#-

I've checked the talairach.xfm and it is bad.  It seems I remember someone
on the list saying that a -nold flag could fix this, but I couldn't find
any info on the wiki about it.  Any suggestions?  Can I still salvage this
subject?

Thanks for all of your help!

-Derin
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Re: [Freesurfer] autorecon1 failures

[Derin Cobia]

The talairach looks really bad, stretched beyond recognition and smeared,
so I think I'll try renaming.  What about the 1st subject I mentioned? 
Talairach bad with this one too?  Thanks.

-Derin

> Hi Derin,
>
> the bad talairach is probably messing everything up. You can either
> correct it manually with tkregister2, or remove/rename the talairach.xfm
> and talairach.auto.xfm use recon-all with -notalairach so it won't be
> rebuilt. Nick: is there a flag to ignore the tal xform even if it's there?
> Something like -badtalairach?
>
> cheers,
> Bruce
>
> On Mon, 2 Apr 2007, Derin Cobia wrote:
>
>> Two questions for two different subjects during autorecon1:
>>
>> 1. The initial skull strip on this subject left too much extra-cerebral
>> material.  Subsequent attempts at using the wsatlas or manual adjustment
>> of the wsthresh have resulted in this error:
>>
>> *WATERSHED**
>> preflooding height equal to 25 percent
>> Sorting...
>>  T1-weighted MRI image
>>  modification of the preflooding height to 15 percent
>>  Count how many 110 voxels are present :  1960516
>>
>>  Find the largest 110-component...mriSegmentReallocateVoxels: could
>> not alloc 1048381 voxels for sno 8343
>> Cannot allocate memory
>> done
>>  And identify it as the main brain basin...Segmentation fault
>> Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006
>> i686
>> i686 i386 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Apr  2 15:02:05 CDT 2007
>> #--
>>
>> Are there too many voxels?  I've looked, but couldn't find any
>> information
>> on how to fix this one.
>>
>>
>> 2. This subject continues to fail with errors during intensity
>> normalization.Here is the output:
>>
>> #
>> [EMAIL PROTECTED] Intensity Normalization Mon Apr  2 15:46:47 EDT 2007
>> /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri
>>
>> mri_normalize -g 1 nu.mgz T1.mgz
>>
>> using max gradient = 1.000
>> reading from nu.mgz...
>> normalizing image...
>> talairach transform
>> 0.830  -0.117  -0.004  -3.656;
>> 0.116   0.833  -0.323  -26.577;
>> 0.004   0.028   0.075   84.152;
>> 0.000   0.000   0.000   1.000;
>> INFO: Modifying talairach volume c_(r,a,s) based on average_305
>> MRInormalize: could not find any valid peaks
>> mri_normalize: normalization failed
>> Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64
>> x86_64 x86_64 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Apr  2 15:46:49 EDT 2007
>> #-
>>
>> I've checked the talairach.xfm and it is bad.  It seems I remember
>> someone
>> on the list saying that a -nold flag could fix this, but I couldn't find
>> any info on the wiki about it.  Any suggestions?  Can I still salvage
>> this
>> subject?
>>
>> Thanks for all of your help!
>>
>> -Derin
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>>
>>
>>
>

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Re: [Freesurfer] bad white surface

[Derin Cobia]

The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary
appropriately.  What should I try next?

-Derin

> this is probably a topology fixing problem. Look at the ?h.orig.nofix and
> see how it is
> On Fri, 13 Apr 2007, Derin Cobia wrote:
>
>> Did you mean wm.mgz?  It looks fine.  The orig surface is not good
>> either.
>> Here's a pic.
>>
>> -Derin
>>
>>
>>
>>> Hi Derin,
>>>
>>> What does the orig surface look like?  and the wm?  Are those correct?
>>>
>>> Jenni
>>>
>>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>>>
>>>> I have two subjects where the white surface does not follow the
>>>> gray-white
>>>> gradient (see attached pic for example).  Is there any way to fix
>>>> this?
>>>> I'm assuming it has to do with the limitations of my scan too (it's
>>>> FLASH
>>>> data).  I'm running 3.0.4, thanks.
>>>>
>>>> -Derin
>>>>
>>>>
>>>
>>
>

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Re: [Freesurfer] bad white surface

[Derin Cobia]

What should I erase?  Sorry, I did mean to say I saw the surface errors
overlaid on the volume, but couldn't discern any in the wm.mgz alone. 
It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1
acquisition, 1x1x1 mm^3 voxels.  Nothing fancy, maybe that's the
problem...

-Derin

> it looks like there is an (incorrect) connection in the wm.mgz from the
> temporal lobe across the insula. The data also looks really noisy - what
> is the acquisition? You'll need to erase some stuff form the wm.mgz I
> think.
>
> On Fri, 13 Apr 2007, Derin Cobia wrote:
>
>> Here is a pic of the inflated.nofix, how do I know what to edit?  I've
>> checked the wm.mgz and it looks fine (at least I can't see any errors).
>> Maybe I'm missing something, I've attached a shot of it as well.
>> Thanks.
>>
>> -Derin
>>
>>> look at the ?h.inflated.nofix to see what is causing the defect, and
>>> correct the wm.mgz manually to remove it. Jenni: can you point Derin at
>>> the
>>> appropriate wiki page?
>>>
>>> thanks,
>>> Bruce
>>>
>>>
>>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>>>
>>>> The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary
>>>> appropriately.  What should I try next?
>>>>
>>>> -Derin
>>>>
>>>>> this is probably a topology fixing problem. Look at the ?h.orig.nofix
>>>>> and
>>>>> see how it is
>>>>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>>>>>
>>>>>> Did you mean wm.mgz?  It looks fine.  The orig surface is not good
>>>>>> either.
>>>>>> Here's a pic.
>>>>>>
>>>>>> -Derin
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Derin,
>>>>>>>
>>>>>>> What does the orig surface look like?  and the wm?  Are those
>>>>>>> correct?
>>>>>>>
>>>>>>> Jenni
>>>>>>>
>>>>>>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>>>>>>>
>>>>>>>> I have two subjects where the white surface does not follow the
>>>>>>>> gray-white
>>>>>>>> gradient (see attached pic for example).  Is there any way to fix
>>>>>>>> this?
>>>>>>>> I'm assuming it has to do with the limitations of my scan too
>>>>>>>> (it's
>>>>>>>> FLASH
>>>>>>>> data).  I'm running 3.0.4, thanks.
>>>>>>>>
>>>>>>>> -Derin
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
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>>>
>>
>

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Re: [Freesurfer] bad white surface

[Derin Cobia]

Thanks Nick.  I am familiar with those pages, but none of those defects
are apparent in this subject (e.g., no misclassifications, lesions, or
failure to have the ventricles filled).  The surface just appears to jump
from one section to another over blank space (or over gm in the
brainmask.mgz volume).  Maybe I'll have to scrap this one.  Thanks again.

-Derin

> Derin,
>
> The tutorial pages showing which defects to look for and how to fix them
> start here:
>
>  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
>
> this includes white matter edits:
>
>  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
>
> Nick
>
>
> On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote:
>> Here is a pic of the inflated.nofix, how do I know what to edit?  I've
>> checked the wm.mgz and it looks fine (at least I can't see any errors).
>> Maybe I'm missing something, I've attached a shot of it as well.
>> Thanks.
>>
>> -Derin
>>
>> > look at the ?h.inflated.nofix to see what is causing the defect, and
>> > correct the wm.mgz manually to remove it. Jenni: can you point Derin
>> at
>> > the
>> > appropriate wiki page?
>> >
>> > thanks,
>> > Bruce
>> >
>> >
>> > On Fri, 13 Apr 2007, Derin Cobia wrote:
>> >
>> >> The ?h.orig.nofix looks ok, meaning it follows the white-gray
>> boundary
>> >> appropriately.  What should I try next?
>> >>
>> >> -Derin
>> >>
>> >>> this is probably a topology fixing problem. Look at the
>> ?h.orig.nofix
>> >>> and
>> >>> see how it is
>> >>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>> >>>
>> >>>> Did you mean wm.mgz?  It looks fine.  The orig surface is not good
>> >>>> either.
>> >>>> Here's a pic.
>> >>>>
>> >>>> -Derin
>> >>>>
>> >>>>
>> >>>>
>> >>>>> Hi Derin,
>> >>>>>
>> >>>>> What does the orig surface look like?  and the wm?  Are those
>> >>>>> correct?
>> >>>>>
>> >>>>> Jenni
>> >>>>>
>> >>>>> On Fri, 13 Apr 2007, Derin Cobia wrote:
>> >>>>>
>> >>>>>> I have two subjects where the white surface does not follow the
>> >>>>>> gray-white
>> >>>>>> gradient (see attached pic for example).  Is there any way to fix
>> >>>>>> this?
>> >>>>>> I'm assuming it has to do with the limitations of my scan too
>> (it's
>> >>>>>> FLASH
>> >>>>>> data).  I'm running 3.0.4, thanks.
>> >>>>>>
>> >>>>>> -Derin
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>
>> >>>
>> >>
>> >>
>> >>
>> > ___
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>> >
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Re: [Freesurfer] Subgenual surfaces

[Derin Cobia]

Is this something the rest of us need to worry about?  I've been checking
some of my data and don't believe I'm finding the same problem as Alex. 
Thanks.

-Derin

> Hi Alex,
>
> sorry, this is an unintended consequence of the code that prevents the
> surface from deforming into non-cortical structures. I'll see if I can
> fix it and get you a new version.
>
> cheers,
> Bruce
> On Thu, 19 Apr 2007, Alexander Fornito
> wrote:
>
>> Hi,
>> I've been consistently getting errors in surface reconstruction in the
>> subgenual area of the cingulate - the grey matter gets missed
>> completely,
>> and instead, both the pial and white surfaces run along the grey/white
>> boundary (see attached). The aseg seems to be ok, labelling the region
>> as
>> cerebral cortex (also see attached). I've tried control points and
>> various
>> other fixes but can't seem to adjust it. Any suggestions re: what to do?
>> this happens consistently on just about all my images (they are Phillips
>> 3T).
>> Thanks,
>> Alex
>>
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[Freesurfer] aparc2aseg error

[Derin Cobia]

I'm getting the following error on several of my subjects during the
aparc2aseg stage:

_
[EMAIL PROTECTED] AParc-to-ASeg Sat Jun  9 12:19:58 EDT 2007
/disk/eli/freesurfer/conte_flash/5111

 mri_aparc2aseg --s 5111 --ribbon

SUBJECTS_DIR /disk/eli/freesurfer/conte_flash
subject 5111
outvol /disk/eli/freesurfer/conte_flash/5111/mri/aparc+aseg.mgz
useribbon 1
baseoffset 0

Reading lh white surface
 /disk/eli/freesurfer/conte_flash/5111/surf/lh.white

Building hash of lh white

Reading lh pial surface
 /disk/eli/freesurfer/conte_flash/5111/surf/lh.pial

Building hash of lh pial
ERROR: lh white and pial have a different number of vertices (190233,189041)
Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jun  9 12:20:07 EDT 2007
___

Do I need to reprocess from a certain stage on, or redo the whole thing? 
What would have caused this (it didn't happen with some other subjects
during the same process batch).  I couldn't find any info on this in the
archive or wiki, I'm running 3.0.4.

Thanks,

Derin
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[Freesurfer] Volume calculation

[Derin Cobia]

How is the volume of each cortical structure (and hemisphere) calculated? 
It seems I remember from somewhere that it is the thickness x average
surface area of the tesselated triangles?  Is this right? What I'm most
interested in is how the cortical gray matter volume from
mris_anatomical_stats is calculated.  Is it the average thickness of the
whole hemisphere x surface area, or is by adding up the volumes of all the
parcellated structures from the atlas?  I remember reading about it
earlier, but couldn't find any info in the list archive or on the wiki. 
Thanks.

-Derin
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[Freesurfer] tksurfer display tcl error & FS training

[Derin Cobia]

Two questions:

1.  We installed the latest version of 32-bit FS on several workstations
running CentOS 5.1 in our lab.  However, once we ran the CentOS updates
(~280 of them through up2date), tkmedit now fails to open and tksurfer
exhibits behavior exactly as described in this message from the mail
archive:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html
Having attempted to troubleshoot it I discovered that a blt lib was
missing, but even with re-installation of this tksurfer continues to not
display correctly.  I believe it's a tcl problem, but I don't understand
why performing incremental updates to CentOS would break FS.  More
importantly, I'm not sure which of the updates does "the breaking" so I
can just avoid it.  Any ideas?

2.  We are in the process of training new research assistants in how to
use FS.  Typically we have approached this in a more qualitative way by
working side-by-side with them to guide their edits and processing.  I was
wondering if there is a quantitative way of comparing their work that you
(or others) have used when training "new recruits" in FS.  Maybe something
like was done in the Han et al (2006) paper, such as compare their
thickness (or other) maps with someone we know does well with manual
interventions?  In essence, we're trying to think of a rigorous way to
train new people in FS, thanks!

-Derin
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Re: [Freesurfer] tksurfer display tcl error & FS training

[Derin Cobia]

Nick,

Yes, our tcltktixblt directory was intact and set correctly.  The reason I
thought it was a BLT lib was it came up missing when I ran fs_lib check. 
At any rate, the DefaultDepth is already at 24 in our xorg.conf file and
the problem persists.  Any other thoughts what might be occurring?  Would
you like me to submit my output as well?

Also, any thoughts from anyone with regard to question #2 (see below)? 
Thanks.

-Derin


On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote:

Derin,

To answer your first question, the solution to that particular problem
that you reference was not to install the BLT libs (as they are included
with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and
found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by
changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the
file /etc/X11/xorg.conf file.

Nick

Two questions:

1.  We installed the latest version of 32-bit FS on several workstations
running CentOS 5.1 in our lab.  However, once we ran the CentOS updates
(~280 of them through up2date), tkmedit now fails to open and tksurfer
exhibits behavior exactly as described in this message from the mail
archive:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html
Having attempted to troubleshoot it I discovered that a blt lib was
missing, but even with re-installation of this tksurfer continues to not
display correctly.  I believe it's a tcl problem, but I don't understand
why performing incremental updates to CentOS would break FS.  More
importantly, I'm not sure which of the updates does "the breaking" so I
can just avoid it.  Any ideas?

2.  We are in the process of training new research assistants in how to
use FS.  Typically we have approached this in a more qualitative way by
working side-by-side with them to guide their edits and processing.  I was
wondering if there is a quantitative way of comparing their work that you
(or others) have used when training "new recruits" in FS.  Maybe something
like was done in the Han et al (2006) paper, such as compare their
thickness (or other) maps with someone we know does well with manual
interventions?  In essence, we're trying to think of a rigorous way to
train new people in FS, thanks!

-Derin
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Re: [Freesurfer] tksurfer display tcl error & FS training

[Derin Cobia]

Nick,

Here's the output:

[EMAIL PROTECTED] conte_mprage]$ ldd `which tkmedit.bin`
linux-gate.so.1 =>  (0x0059)
libtix8.1.8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so
(0x001c3000)
libtk8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x00e8b000)
libtcl8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so
(0x006c6000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x0011)
libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000)
libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000)
libz.so.1 => /usr/lib/libz.so.1 (0x0067b000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000)
libdl.so.2 => /lib/libdl.so.2 (0x0065c000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00662000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0768)
libm.so.6 => /lib/libm.so.6 (0x00633000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000)
libc.so.6 => /lib/libc.so.6 (0x0023a000)
libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000)
libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x0019)
libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000)
libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000)
/lib/ld-linux.so.2 (0x004cb000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x00438000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x0045f000)

[EMAIL PROTECTED] conte_mprage]$ ldd `which tksurfer.bin`
linux-gate.so.1 =>  (0x00f6e000)
libtix8.1.8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so
(0x002e6000)
libtk8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x003ce000)
libtcl8.4.so =>
/pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so
(0x0011)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x006f7000)
libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000)
libz.so.1 => /usr/lib/libz.so.1 (0x0067b000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000)
libdl.so.2 => /lib/libdl.so.2 (0x0065c000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00662000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0768)
libm.so.6 => /lib/libm.so.6 (0x00633000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000)
libc.so.6 => /lib/libc.so.6 (0x004ee000)
libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000)
libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000)
libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x00259000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000)
/lib/ld-linux.so.2 (0x004cb000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x001ad000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x001b6000)

For our network:
$FREESURFER_HOME=/pkg/brainmap/freesurfer

Thanks,

Derin




On Oct 9, 2008, at 3:40 PM, Nick Schmansky wrote:

Derin,

Can you do this:

 source $FREESURFER_HOME/bin/tcl_setup

then send me the output of:

 ldd `which tkmedit.bin`

and

 ldd `which tksurfer.bin`

I will be looking to see if the proper tcl/tk/tix/blt libs are being
used (those in freesurfer/lib/tcltktixblt).

Nick


On Thu, 2008-10-09 at 11:15 -0500, Derin Cobia wrote:
Nick,

Yes, our tcltktixblt directory was intact and set correctly.  The reason I
thought it was a BLT lib was it came up missing when I ran fs_lib check.
At any rate, the DefaultDepth is already at 24 in our xorg.conf file and
the problem persists.  Any other thoughts what might be occurring?  Would
you like me to submit my output as well?

Also, any thoughts from anyone with regard to question #2 (see below)?
Thanks.

-Derin


On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote:

Derin,

To answer your first question, the solution to that particular problem
that you reference was not to install the BLT libs (as they are included
with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and
found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by
changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the
file /etc/X11/xorg.conf file.

Nick

Two questions:

1.  We installed the latest version of 32-bit FS on several workstations
running CentOS 5.1 in our lab.  However, once we ran the CentOS updates
(~280 of them through up2date), tkmedit now fails to open and tksurfer
exhibits behavior exactly as described in this message from the mai