Re: [Freesurfer] colour scale

[Trisanna Sprung-Much]

how else would you suggest I generate a colour bar? tksurfer doesn't appear
to be working for me either.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Sep 12, 2016 at 7:53 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks!
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang 
> wrote:
>
>> It appears you are running version 5.3. The upcoming 6.0 should fix it.
>>
>> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>> Hi there
>>
>> yup, so I had seen that. The issue is it looks like this and doesn't seem
>> to change no matter what changes I make in the GUI (heat vs colour map,
>> etc).
>>
>> Best
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang > > wrote:
>>
>>> There is a color bar button on the toolbar, or you can go to menu
>>> View->Show Color Scale.
>>>
>>> Ruopeng
>>>
>>>
>>> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>>>
>>> Hi there
>>>
>>> is there a way to view a colour scale bar in Freeview rather than
>>> Tksurfer, for instance, for a probability map? I can alter the Min and Max
>>> by "Configure Overlay" but cannot seem to display the bar next to my
>>> surface.
>>>
>>> Many thanks
>>>
>>> Trisanna
>>>
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>>
>>>
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Re: [Freesurfer] colour scale

[Trisanna Sprung-Much]

thanks!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang 
wrote:

> It appears you are running version 5.3. The upcoming 6.0 should fix it.
>
> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Hi there
>
> yup, so I had seen that. The issue is it looks like this and doesn't seem
> to change no matter what changes I make in the GUI (heat vs colour map,
> etc).
>
> Best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang 
> wrote:
>
>> There is a color bar button on the toolbar, or you can go to menu
>> View->Show Color Scale.
>>
>> Ruopeng
>>
>>
>> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>>
>> Hi there
>>
>> is there a way to view a colour scale bar in Freeview rather than
>> Tksurfer, for instance, for a probability map? I can alter the Min and Max
>> by "Configure Overlay" but cannot seem to display the bar next to my
>> surface.
>>
>> Many thanks
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
>> ___
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Re: [Freesurfer] colour scale

[Ruopeng Wang]

It appears you are running version 5.3. The upcoming 6.0 should fix it.

> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much 
>  wrote:
> 
> Hi there
> 
> yup, so I had seen that. The issue is it looks like this and doesn't seem to 
> change no matter what changes I make in the GUI (heat vs colour map, etc).
> 
> Best
> Trisanna
> 
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang  > wrote:
> There is a color bar button on the toolbar, or you can go to menu View->Show 
> Color Scale.
> 
> Ruopeng
> 
> 
> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>> Hi there
>> 
>> is there a way to view a colour scale bar in Freeview rather than Tksurfer, 
>> for instance, for a probability map? I can alter the Min and Max by 
>> "Configure Overlay" but cannot seem to display the bar next to my surface.
>> 
>> Many thanks
>> 
>> Trisanna
>> 
>> 
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> 
>> 
>> 
>> 
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[Freesurfer] Pial surface vs. aparc+aseg

[Nosal, Eryka [PSY]]

Hi,

I'm very new to Freesurfer, and I am trying to get subject-specific masks from 
the output of recon all that I can use on my functional data. I was going to 
isolate regions from the aparc+aseg files to create the ROIs. In my visual 
checks, I noticed that the pial surface often leaves off parts of the amygdala 
and hippocampus even though they are contained within the correct label of the 
aparc+aseg image. For my purposes, should I be concerned that these regions are 
not contained within the surface?

Sincerely,
Eryka Nosal
Research Tech
The University of Chicago
Department of Psychiatry & Behavioral Neuroscience
Clinical Neuroscience & Psychopharmacology Research Unit (CNPRU)
Phone: (773) 834-4113
Website: http://cnpru.bsd.uchicago.edu/research.html


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[Freesurfer] Job posting

[Ansgar Furst]

DEPARTMENT OF VETERANS AFFAIRS
Palo Alto WRIISC Special Postdoctoral Fellowship Program in Advanced
Neuroimaging

The Office of Academic Affiliations, Department of Veterans Affairs
(VA), is now accepting applications for a two-year Postdoctoral
Fellowship Training Program in advanced neuroimaging with an emphasis
on Traumatic Brain Injury (TBI), Posttraumatic stress disorder (PTSD),
cognitive impairment and chronic pain. The Fellowship can begin
between January 1st and August 31st, 2017. This is a joint fellowship
between VA Palo Alto War Related Illness and Injury Study Center
(WRIISC) and the Department of Psychiatry and Behavioral Sciences at
Stanford University. The VAPA-WRIISC-SFP site is linked to the two
other WRIISC fellowship sites (Washington, DC, East Orange, NJ) as
well as the VA Mental Illness Research, Education, and Clinical Center
(MIRECC) fellowship program (based at Palo Alto) for didactic,
academic, and research efforts. The Palo Alto WRIISC specializes in
integrating anatomical/functional Magnetic Resonance Imaging (MRI) and
Positron Emission Tomography (PET) to improve the
diagnostic/prognostic value of neuroimaging in the clinical setting.
The fellowship provides a unique opportunity to (a) receive training
in Diffusion Tensor Imaging (DTI), functional Magnetic Resonance
Imaging (fMRI), Voxel-based morphometry (VBM) and amyloid imaging from
a team of experienced neuroimagers and (b) relate neuroimaging
findings to clinical cases in consensus conferences with our team of
neurologists, nurse practitioners, psychiatrists & psychologists. We
are interested in the relationship between TBI/PTSD and a potentially
increased risk for Alzheimer’s disease and have recently received
funding to explore this question using amyloid PET imaging. Our team
of investigators is also part of the Alzheimer’s Disease Neuroimaging
Initiative (ADNI). There are additional opportunities to explore
projects in psychology and dementia with WRIISC, MIRECC, and Stanford
faculty. In collaboration with their mentors, fellows will develop and
conduct a research project, publish and present findings, participate
in grant writing, and utilize the latest technologies for research (5
MRI scanners including a brand new PET-MR unit).

Applicants must be US citizens. The ideal candidate will have a Ph.D.
in cognitive neuroscience, computer science, psychology, or a related
discipline. Prior experience in neuroimaging is essential. Experience
with Linux, MATLAB, SPM8/12, FreeSurfer v5.3.0 & FSL v5.0 is highly
desirable and programming skills would be a big plus.

A. To be eligible to apply for the WRIISC Fellowship Program you must
hold a PhD in one of the above described disciplines and be able to
provide evidence of U.S. citizenship.

B. Applications must be received by December 1st, 2016.  Applicants
must submit: a) a letter confirming they can fulfill the eligibility
requirements; b) a personal statement describing their interest in the
Fellowship; c) 3 letters of recommendation; and d) a current
curriculum vitae. These materials can be submitted directly to the PhD
Fellowship Program Director: Ansgar Furst, PhD at ansgar.fu...@va.gov.

C. If the applicant is identified as the candidate of choice for this
site, they will be required to produce all documents listed in the
above section A and the following additional documents:

Transcripts from all educational institutions
VA Form 10-2850d, “Application for Health Professions Trainees.”

For more information, please contact Ansgar Furst, PhD at the WRIISC
Palo Alto Fellowship site, (650) 493-5000, "1", "1" then x68652 or
ansgar.fu...@va.gov.

See also: http://www.warrelatedillness.va.gov/

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Re: [Freesurfer] colour scale

[Ruopeng Wang]

There is a color bar button on the toolbar, or you can go to menu 
View->Show Color Scale.


Ruopeng

On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:

Hi there

is there a way to view a colour scale bar in Freeview rather than 
Tksurfer, for instance, for a probability map? I can alter the Min and 
Max by "Configure Overlay" but cannot seem to display the bar next to 
my surface.


Many thanks

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology




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[Freesurfer] Postdoc and Research Assistant openings in cognitive neuroscience at UCSF/Stanford

[Zhichao Xia]

Please respond to i...@brainlens.org

*Research Assistant Position at UCSF in California, USA on Multilingualism*

The Hoeft Lab (http://brainLENS.org  PI: Fumiko
Hoeft MD PhD) is looking for an exceptional research assistant interested
in the developmental cognitive neuroscience of multilingualism. This
NIH-funded research is in collaboration with Cammie McBride PhD of Chinese
Univ of Hong Kong, Ken Pugh PhD of Haskins/Yale/UConn, Linda Siegel of UBC,
Manolo Carreiras PhD of BCBL, Ioulia Kovelman PhD of U Michigan, and Yuuko
Uchikoshi EdD of UC Davis. The position is suited for a self-motivated,
organized and independent thinker, with good interpersonal and multitasking
skills, as well as proficiency in the English language and computer
software.  Neuroimaging, computational, statistical, programming, and
neuropsych testing skills are highly desired but not necessary. Native-like
proficiency in Spanish or Cantonese is a plus. A major strength of our lab
is that there are plenty of opportunities to conduct independent research,
to be first author on publications and to give conference presentations as
a novice RA (e.g. Myers et al. Psychol Sci ’14, Myers et al. SCAN ’16, Haft
et al. Curr Opin Behav Sci ’16).

The position begins in January but start date can be sooner and is
negotiable.
Please email i...@brainlens.org with a cover letter and your CV.

Please add “[RA job]” and your full name in the Subject of the email.
Qualified candidates will be asked to have 2-3 letters of reference
forwarded.



*Joint Postdoctocal Position at UCSF and Stanford University in California,
USA*

The Hoeft Lab (http://brainLENS.org  PI: Fumiko
Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for
Neurosciences in collaboration with the Stanford Mood and Anxiety Disorders
Lab in the Dept of Psychology (http://goo.gl/dc96Cx PI: Ian Gotlib PhD) is
looking for an exceptional postdoc in the field of affective neuroscience,
with advanced neuroimaging, psychophysiology, computational, programming
and organizational skills. Training in genetics is a plus.

The primary project that the postdoc will be responsible for is the
examination of intergenerational neuroimaging using a ‘natural’
cross-fostering design that allows dissociation of genetic, prenatal and
postnatal environment on brain networks that are transmitted across
generations. Related articles from our lab can be found here - Yamagata et
al. J Neurosci 2016 (http://goo.gl/vMK8iy), Ho et al. Trends in Neurosci
2016 (http://goo.gl/SyXLcK), and Scientific American (http://goo.gl/YTiH6D).
There are other funded opportunities to be involved in research that
examines the impact of anxiety and stereotype on psychophysiology and
cognitive processes.

The position can begin immediately.
Please email i...@brainlens.org with your CV, and with brief paragraphs of
research interests, career goals and why you feel you are a good fit for
the lab. Please add “[Postdoc job]” and your full name in the Subject of
the email. Qualified candidates will be asked to have 3 letters of
reference forwarded.

-- 
*Zhichao Xia*
National Key Laboratory of Cognitive Neuroscience and Learning &
IDG/McGovern Institute for Brain Research, Beijing Normal University
Center for Collaboration and Innovation in Brain and Learning Sciences,
Beijing Normal University
Division of Child and Adolescent Psychiatry, Department of Psychiatry, UCSF
Mobile: +1 (415) 712-3749; +86 13720002046
E-mail:  xiazc_...@163.com; xiazc@gmail.com;
zhichao@ucsf.edu
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Re: [Freesurfer] Analysis of rates or percent changes

[Katarina Trojacanec]

Hi Martin,


Thanks a lot.


Best, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Monday, September 12, 2016 7:58:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Katarina,


different time spacing is OK (not optimal, but OK). This 2-stage procedure 
first fits a line in each subject, independent on how many time points the 
subject has. Of course a linear fit from 4 time points will be more reliable 
than one from just 2 time points. This is not taken into consideration and 
therefore we usually recommend the Linear Mixed Effects modeling (where it is 
considered in the model). If most of your subjects have 4 time points and the 
spacing is similar (across subjects) you should be fine.


Other things I noticed:

- you should drop the --generic-time flag. I probably should change the help 
text to be more specific, but what it does it assigns a time of 1 2 3 4 to the 
time points (this is if you do repeated measures and there is no real time). So 
don't pass it.


- you can drop some of the --do... flags. Probably you are interested in the 
rate and one of the pct change flags. The average is just the average thickness 
(across time) for each subject. Not sure you want to analyze that. The 
--do-stack is a subject-specific stack of the time points, usually only used 
for debugging.


- the -stack-avg is not needed unless you want to analyze average thickness for 
each subject, rather you may want to create a stack for the rate or the pc1 or 
whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or 
whatever you use).


Best, Martin


On 09/12/2016 12:40 PM, Katarina Trojacanec wrote:

Hi,


I have a question about the analysis of rates or percent changes.


I use data with available scans at baseline (TP1) and the 6-month (TP2), 
12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of 
some of the data in the appropriate qdec table is given below:


fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr 
MMSE_TotScr FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06
ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12
ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24


The base is constructed using all four time points. The time variable is given 
in years. I am using long_stats_slopes for aseg.stats as follows:


long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats 
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit 
--do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg 
./qdec/long_AD_NL_TP1_2_3_4


(similarly for ?h.aparc.stats)


Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated 
approximately 6 months and TP3 and TP4 are separated approximately 12 months, 
are the annualized percent change or atrophy rates using this scenario 
reasonable (statistically?). Is it maybe more reasonable to apply the same 
scenario using three time points (for example TP1, TP3 and TP4 from the 
previous example and the template based only on these time points with the same 
approximate difference between all of them of 12 months, or TP1, TP2 and TP3 
from the previous example and the template based only on these time points with 
the same approximate difference between all of them of 6 months)?


Best Regards,


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia




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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu
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contains patient 

[Freesurfer] colour scale

[Trisanna Sprung-Much]

Hi there

is there a way to view a colour scale bar in Freeview rather than Tksurfer,
for instance, for a probability map? I can alter the Min and Max by
"Configure Overlay" but cannot seem to display the bar next to my surface.

Many thanks

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

[Douglas N Greve]

I think the problem is the initialization. I noticed you used 
--init-header. This should only be used if the two volumes were acquired 
during the same session and the direction cosines (ie, geometry) info is 
accurate for both. Is this the case? I noticed that the input has 
"preproc" in the name, so I'm a bit suspicious. You can try --init-fsl 
instead


On 09/12/2016 01:36 PM, A Nunes wrote:
> Hi Doug
>
> I can't see any errors in the log file, and with other datasets I did 
> not have this issue. My register.dat is:
>
> 50664
> 3.00
> 4.50
> 0.15
> 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 
> 3.139470825195312e+02
> 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01 
> 2.150849456787109e+02
> -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02 
> 4.339286499023438e+02
> 0 0 0 1
> round
>
> and my register.dat.log is:
>
> setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
> cd /Users/adonay/Desktop/data/prepo_cpac
> /Applications/freesurfer/bin/bbregister --s 50664 --mov 
> 50664_preprocessed.nii.gz --init-header --reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold
>
> $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
> Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 
> 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64
> FREESURFER_HOME /Applications/freesurfer
> mri_convert 50664_preprocessed.nii.gz 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
> mri_convert 50664_preprocessed.nii.gz 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
>  
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 50664_preprocessed.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, -0, 0)
> j_ras = (-0, 1, 0)
> k_ras = (-0, -0, 1)
> writing to 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii...
> tkregister2_cmdl --s 50664 --mov 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
>  
> --regheader --reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
>  
> --noedit
> tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target  volume orig
> movable volume 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
> reg file 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
> LoadVol0
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
> INFO: loading target 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz
> Ttarg: 
> -1.000   0.000   0.000   128.000;
>  0.000   0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> INFO: loading movable 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
> Tmov: 
> -3.000   0.000   0.000   96.000;
>  0.000   0.000   4.500  -63.000;
>  0.000  -3.000   0.000   96.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 1, float2int = 0
> Computing reg from header (and possibly input matrix)
>  Input registration matrix (computed) 
>  1.000   0.000   0.000   307.685;
>  0.000   0.000   1.000   216.216;
>  0.000  -1.000   0.000   435.341;
>  0.000   0.000   0.000   1.000;
> ---
>  Input registration matrix 
>  1.000   0.000   0.000   307.685;
>  0.000   0.000   1.000   216.216;
>  0.000  -1.000   0.000   435.341;
>  0.000   0.000   0.000   1.000;
> Determinant 1
> subject = 50664
> RegMat ---
>  1.000   0.000   0.000   307.685;
>  0.000   0.000   1.000   216.216;
>  0.000  -1.000   0.000   435.341;
>  0.000   0.000   0.000   1.000;
> mri_segreg --mov 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
>  
> --init-reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
>  
> --out-reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat
>  
> --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 
> 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
> $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
> setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
> cd /Users/adonay/Desktop/data/prepo_cpac
> mri_segreg --mov 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
>  
> --init-reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
>  
> --out-reg 
> /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat
>  
> --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 

[Freesurfer] convert FSFAST files to gifti format

[Sabin Khadka]

Hi all,

Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz)
files to convert into gifti format? I've tried mris_convert but it does not
work.

Thanks for help.

Cheers,
Sabin Khadka
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Re: [Freesurfer] mris_anatomical_stats

[Arkadiy Maksimovskiy]

Hi Bruce,

Thank you so much for this suggestion.

In case anyone searches for this thread in the future, I am writing back to
report that it worked and thickness indices remain the same (although other
indices, which are of no interest to me for this analysis, did change).

Best,
Arkadiy
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Re: [Freesurfer] Qdec Error: Couldn't open qcache file

[Jana Dinges]

I have already solved the problem.
Thank you for your support.

Best regards
Jana Dinges

-- 
Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail gesendet.Am 07.09.16, 23:57, Douglas N Greve  schrieb:

  
*Can you send the terminal output for recon-all -s subjid -qcache*


On 09/01/2016 02:53 PM, Jana Dinges wrote:
> Dear freesurfer community,
> we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have
> been experiencing some problems with the final analysis steps.
> We are using the qdec. Uploading of the data table has been successful. When we
> try to use the “Analyze” command (design) in the qdec, we get the following
> error message:
> Error in Analyze: Couldn’t open file
> /data/projects/oertelmatura/Neurodegeneration_MCI/AK38/surf/lh.thickness.fwhm10.fsaverage.mgz or mgh
> Obviously, the file was not created during preprocessing*although we ran (recon-all -s subjid -qcache)* for every subject.
> We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for
> your comments.
> Yours sincerely,
> JanaXXX
>
>
> ___
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] ERROR again

[Douglas N Greve]

normalization means to subtract the mean and divide by the stddev


On 09/12/2016 02:04 PM, Seung Gul Kang wrote:
> Dear  Douglas Greve and FS team,
>
> I send this e-mail again since I was afraid that you would not receive 
> my previous e-mail.
> I am sorry if you got the previous e-mail and are figuring this 
> problem out.
>
> I am looking forward to receive your reply regarding to the solution.
>
> Thank you.
>
> Best,
> Seung-Gul
>
> ---
> *Seung Gul Kang, M.D., Ph.D. *
>
> *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil 
> Medical Center, Gachon University, School of Medicine, 21, 
> Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
> *Research scholar*; Sleep Disorders Clinical Research Program, 
> Department of Psychiatry, Massachusetts General Hospital, Harvard 
> Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA
> *Collaboration researcher*; Division of Sleep & Circadian Disorders, 
> Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, 
> Boston MA 02115
>
> -- Forwarded message --
> From: *Seung Gul Kang*  >
> Date: 2016-09-10 17:49 GMT-04:00
> Subject: Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly 
> scaled, condno = 22801.1
> To: Freesurfer support list  >
>
>
> Dear Douglas Greve,
>
> Thank you so much for your answer.
> But, unfortunately it did not work.
>
> The problem develops when I put bhth (global thickness) as a covariate.
> (I want to control age, sex, BDINS, and bhth for the comparison 
> between two groups.)
> If I don't put bhth as a covariate, there is no problem.
> And, inerestingly, if I put only bhth as a covariate (without putting 
> other covariates), the error does not develop.
>
> Does the normalization mean the log (bhth)?
> I changed the bhth into log (bhth) and ran qdec again. However, the 
> error appeared again as below.
> (Actually, the bhth already shows normal distribution in spss.)
> I am afraid that normalization would not be solution.
> Please see the file 1 (my FSGD file) and 2 (FSGD file made in qdec 
> folder).
>
> Normalized matrix condition is 16920.4
> Design matrix --
>  1.000   0.000   0.000   0.000 27.000   0.000   0.000   0.000   3.000 
>   0.000 0.000   0.000   0.415   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   28.000   0.000   0.000 
>   0.000 4.000   0.000   0.000   0.000   0.387   0.000;
>  1.000   0.000   0.000   0.000 25.000   0.000   0.000   0.000   1.000 
>   0.000 0.000   0.000   0.400   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   26.000   0.000   0.000 
>   0.000 7.000   0.000   0.000   0.000   0.399   0.000;
>  1.000   0.000   0.000   0.000 35.000   0.000   0.000   0.000   1.000 
>   0.000 0.000   0.000   0.390   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000 30.000   0.000   0.000   0.000   0.000 
>   0.000 0.000   0.000   0.376   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   24.000   0.000   0.000 
>   0.000 0.000   0.000   0.000   0.000   0.385   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   24.000   0.000   0.000 
>   0.000 1.000   0.000   0.000   0.000   0.379   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   28.000   0.000   0.000 
>   0.000 0.000   0.000   0.000   0.000   0.372   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   33.000   0.000   0.000 
>   0.000 2.000   0.000   0.000   0.000   0.379   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   45.000   0.000   0.000 
>   0.000 0.000   0.000   0.000   0.000   0.362   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   38.000   0.000   0.000 
>   0.000 0.000   0.000   0.000   0.000   0.362   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   24.000   0.000   0.000 
>   0.000 0.000   0.000   0.000   0.000   0.394   0.000;
>  1.000   0.000   0.000   0.000 28.000   0.000   0.000   0.000   0.000 
>   0.000 0.000   0.000   0.364   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000 30.000   0.000   0.000   0.000   0.000 
>   0.000 0.000   0.000   0.390   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000 39.000   0.000   0.000   0.000   3.000 
>   0.000 0.000   0.000   0.348   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   48.000   0.000   0.000 
>   0.000 4.000   0.000   0.000   0.000   0.382   0.000;
>  1.000   0.000   0.000   0.000 32.000   0.000   0.000   0.000   3.000 
>   0.000 0.000   0.000   0.374   0.000   0.000   0.000;
>  1.000   0.000   0.000   0.000 32.000   0.000   0.000   0.000   4.000 
>   0.000 0.000   0.000   0.399   0.000   0.000   0.000;
>  0.000   0.000   1.000   0.000 0.000   0.000   31.000   0.000   0.000 
>   0.000 2.000   0.000   0.000   0.000   0.376   0.000;
>  1.000   0.000   0.000   0.000 33.000   0.000   0.000   0.000   1.000 
>   0.000 0.000   0.000   

Re: [Freesurfer] Analysis of rates or percent changes

[Martin Reuter]

Hi Katarina,


different time spacing is OK (not optimal, but OK). This 2-stage 
procedure first fits a line in each subject, independent on how many 
time points the subject has. Of course a linear fit from 4 time points 
will be more reliable than one from just 2 time points. This is not 
taken into consideration and therefore we usually recommend the Linear 
Mixed Effects modeling (where it is considered in the model). If most of 
your subjects have 4 time points and the spacing is similar (across 
subjects) you should be fine.



Other things I noticed:

- you should drop the --generic-time flag. I probably should change the 
help text to be more specific, but what it does it assigns a time of 1 2 
3 4 to the time points (this is if you do repeated measures and there is 
no real time). So don't pass it.



- you can drop some of the --do... flags. Probably you are interested in 
the rate and one of the pct change flags. The average is just the 
average thickness (across time) for each subject. Not sure you want to 
analyze that. The --do-stack is a subject-specific stack of the time 
points, usually only used for debugging.



- the -stack-avg is not needed unless you want to analyze average 
thickness for each subject, rather you may want to create a stack for 
the rate or the pc1 or whatever, to pass it into the stats tool (like 
mri_glmfit, or R, SPSS or whatever you use).



Best, Martin


On 09/12/2016 12:40 PM, Katarina Trojacanec wrote:


Hi,


I have a question about the analysis of rates or percent changes.


I use data with available scans at baseline (TP1) and the 6-month 
(TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. 
An example of some of the data in the appropriate qdec table is given 
below:



fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr 
MMSE_TotScr FAQ_TotScr visit1_2_3_4

ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06
ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F xx xx m12
ADNI_sub2_m24 ADNI_base2 2 76 y AD F xx xx m24

The base is constructed using all four time points. The time variable 
is given in years. I am using long_stats_slopes for aseg.stats as follows:



long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat 
--stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate 
--do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years 
--stack-avg ./qdec/long_AD_NL_TP1_2_3_4



(similarly for ?h.aparc.stats)


Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated 
approximately 6 months and TP3 and TP4 are separated approximately 12 
months, are the annualized percent change or atrophy rates using this 
scenario reasonable (statistically?). Is it maybe more reasonable to 
apply the same scenario using three time points (for example TP1, TP3 
and TP4 from the previous example and the template based only on these 
time points with the same approximate difference between all of them 
of 12 months, or TP1, TP2 and TP3 from the previous example and the 
template based only on these time points with the same approximate 
difference between all of them of 6 months)?



Best Regards,


*Katarina Trojacanec, M.Sc.*
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Getting Waveform from Label - dim mismatch

[Douglas N Greve]

you need to transfer the label into the space of subject 401 using 
mri_label2label. Currently, the label is in fsaverage space which is why 
you get the mismatch


On 09/12/2016 12:53 PM, ERIK JAHNER wrote:
> (sorry if you got this multiple times this morning I had some server 
> issues)
>
> I had not seen a post based on this email, so I am resending it. It is 
> my understanding that I can use freesurfer and FSfast to get 
> activation levels after data has been smoothed across the surface 
> instead of 3D volume. Is the mir_segstats only able to use the 3D 
> volume and not the surface data stored within vertices? Sorry if this 
> questions is obvious to everyone. I want to basically get the average 
> activation for a set of vertices at each time point included in a 
> label from the surface mapped functional data. See below for 
> additional details of the parameters I entered.
>
> Thanks
> Erik Jahner
>
>> On Sep 9, 2016, at 8:20 AM, ERIK JAHNER > > wrote:
>>
>>
>>> Dear Freesurfer experts,
>>>
>>> I am attempting to get the waveform from a subject (401)using the 
>>> preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means 
>>> of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). 
>>>  This label was created from the subjects “sphere.reg" file.
>>>
>>> I am using the following command:
>>>
>>> mri_segstats
>>> --slabel 401 lh 
>>> /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label
>>>  
>>>
>>> --avgwf out.dat
>>> --id 1
>>> --i 
>>> /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
>>>  
>>>
>>>
>>> However I am getting the following error:
>>>
>>> ERROR: dimension mismatch between input volume and seg
>>>   input 163842 1 1
>>>   seg   140104 1 1
>>>
>>> Obviously there is something wrong with my file dimensions. But, I 
>>> am unsure of how to fix this. I checked some of the files in my 
>>> subject anatomical folder like the thickness file and they also have 
>>> 140104 1 1 as the dimensions. But, as would be predicted the 
>>> "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 
>>> 163842 1 1 210. Is there an easy way to fix this problem? I am 
>>> unsure what I did to create this discrepancy.
>>>
>>> Thanks for your continued support,
>>> Erik Jahner
>
>
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Tracula movement

[Anastasia Yendiki]

You're right that this looks fine. Can you upload the entire DWI series 
for me here? Nifti is fine. Thanks!


https://gate.nmr.mgh.harvard.edu/filedrop2/

On Mon, 12 Sep 2016, Lars M. Rimol wrote:



 Re: [Freesurfer] Tracula movement

Anastasia Yendiki Mon, 12 Sep 2016 04:24:56 -0700

Hi Lars - This sounds like the subject was trying to climb out of
the scanner: 3cm average translational motion and 24% of the slices in
the series have drop-out. How do the images look?

a.y


Hi,

I don't have a lot of experience looking at dwi scans, but they don't seem
crazy to me. I have attached screenshots of the dwi, FA, and brain_anat_mni
images, and the gross anatomy looks fine to me. There are stripes in
brain_anat_mni, which I would guess indicate motion..

Thank you!


sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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[Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

[A Nunes]

Hi Doug

I can't see any errors in the log file, and with other datasets I did not
have this issue. My register.dat is:

50664
3.00
4.50
0.15
9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02
3.139470825195312e+02
1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01
2.150849456787109e+02
-2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02
4.339286499023438e+02
0 0 0 1
round

and my register.dat.log is:

setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
cd /Users/adonay/Desktop/data/prepo_cpac
/Applications/freesurfer/bin/bbregister --s 50664 --mov
50664_preprocessed.nii.gz --init-header --reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 20:21:34
PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64
FREESURFER_HOME /Applications/freesurfer
mri_convert 50664_preprocessed.nii.gz
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
mri_convert 50664_preprocessed.nii.gz
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 50664_preprocessed.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
writing to
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii...
tkregister2_cmdl --s 50664 --mov
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
--regheader --reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
--noedit
tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
reg file
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz
Ttarg: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
Tmov: 
-3.000   0.000   0.000   96.000;
 0.000   0.000   4.500  -63.000;
 0.000  -3.000   0.000   96.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
 Input registration matrix (computed) 
 1.000   0.000   0.000   307.685;
 0.000   0.000   1.000   216.216;
 0.000  -1.000   0.000   435.341;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.000   0.000   307.685;
 0.000   0.000   1.000   216.216;
 0.000  -1.000   0.000   435.341;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = 50664
RegMat ---
 1.000   0.000   0.000   307.685;
 0.000   0.000   1.000   216.216;
 0.000  -1.000   0.000   435.341;
 0.000   0.000   0.000   1.000;
mri_segreg --mov
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
--init-reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
--out-reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
cd /Users/adonay/Desktop/data/prepo_cpac
mri_segreg --mov
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
--init-reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
--out-reg
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname  Darwin
hostname sc-155014
machine  x86_64
user adonay
movvol
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/template.nii
regfile
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/reg.init.dat
subject 50664
dof 6
outregfile
/Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregister.14726/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.50
PenaltyCenter 0.00
surfname white
GMProjFrac 0.50
WMProjAbs 2.00
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100

[Freesurfer] Getting Waveform from Label - dim mismatch

[ERIK JAHNER]

(sorry if you got this multiple times this morning I had some server issues)

I had not seen a post based on this email, so I am resending it. It is my 
understanding that I can use freesurfer and FSfast to get activation levels 
after data has been smoothed across the surface instead of 3D volume. Is the 
mir_segstats only able to use the 3D volume and not the surface data stored 
within vertices? Sorry if this questions is obvious to everyone. I want to 
basically get the average activation for a set of vertices at each time point 
included in a label from the surface mapped functional data. See below for 
additional details of the parameters I entered. 

Thanks 
Erik Jahner

> On Sep 9, 2016, at 8:20 AM, ERIK JAHNER  > wrote:
> 
> 
>> Dear Freesurfer experts,
>> 
>> I am attempting to get the waveform from a subject (401)using the 
>> preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a 
>> label I created from the icosahedron 3 (lh.ic3.tri_vertex_638).  This label 
>> was created from the subjects “sphere.reg" file. 
>> 
>> I am using the following command: 
>> 
>> mri_segstats 
>> --slabel 401 lh 
>> /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label
>>  
>> --avgwf out.dat 
>> --id 1 
>> --i 
>> /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
>>   
>> 
>> However I am getting the following error:
>> 
>> ERROR: dimension mismatch between input volume and seg
>>   input 163842 1 1
>>   seg   140104 1 1
>> 
>> Obviously there is something wrong with my file dimensions. But, I am unsure 
>> of how to fix this. I checked some of the files in my subject anatomical 
>> folder like the thickness file and they also have 140104 1 1 as the 
>> dimensions. But, as would be predicted the 
>> "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 
>> 210. Is there an easy way to fix this problem? I am unsure what I did to 
>> create this discrepancy.
>> 
>> Thanks for your continued support,
>> Erik Jahner
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[Freesurfer] Analysis of rates or percent changes

[Katarina Trojacanec]

Hi,


I have a question about the analysis of rates or percent changes.


I use data with available scans at baseline (TP1) and the 6-month (TP2), 
12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of 
some of the data in the appropriate qdec table is given below:


fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr 
MMSE_TotScr FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06
ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12
ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24


The base is constructed using all four time points. The time variable is given 
in years. I am using long_stats_slopes for aseg.stats as follows:


long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats 
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit 
--do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg 
./qdec/long_AD_NL_TP1_2_3_4


(similarly for ?h.aparc.stats)


Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated 
approximately 6 months and TP3 and TP4 are separated approximately 12 months, 
are the annualized percent change or atrophy rates using this scenario 
reasonable (statistically?). Is it maybe more reasonable to apply the same 
scenario using three time points (for example TP1, TP3 and TP4 from the 
previous example and the template based only on these time points with the same 
approximate difference between all of them of 12 months, or TP1, TP2 and TP3 
from the previous example and the template based only on these time points with 
the same approximate difference between all of them of 6 months)?


Best Regards,


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table

[Douglas N Greve]

you can find it here fsaverage/surf/?h.white.avg.area.mgh



On 09/12/2016 11:26 AM, Claudia Dacquino claudia.dacqu...@gmail.com 
[martinos-tech] wrote:
> Thanks Doug!
> Yes, I realized I was wrong and I wrote to the freesurfer list too.
> Just another question,as you were so prompt in replying... Where can I 
> find the average surface area of the inputsubjects?
> Thanks.
> Clauia
>
>
> 2016-09-12 17:15 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu 
>  [martinos-tech] 
> >:
>
> Hi Claudia, it is better to post these things to the freesurfer
> list as
> martinos-tech is no longer active. The total cortical surface area
> (65416.6mm2) is incorrect. The total should be 82219.960938. The
> reported value is the actual surface area of the fsaverage white
> surface. However, the average white surface has a much lower surface
> area than areas of any of the input subjects because the surface
> coordinate averaging causes minor folding to be smoothed out. To get
> around this, we keep track of the average surface area of the input
> subjects (rather than the surface area of the average surface, if
> that
> is not too confusing). The size of the cluster reported
> (76467.08mm2) is
> accurate.
>
> doug
>
> On 09/12/2016 07:52 AM, Claudia Dacquino
> claudia.dacqu...@gmail.com 
>
> [martinos-tech] wrote:
> >
> > Hi all,
> >
> > I've run GLM surface analysis and I've got a summary table like
> this:
> >
> >
> > # Cluster Growing Summary (mri_surfcluster)
> >
> > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
> >
> > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> >
> > # CreationTime 2016/09/12-08:47:18-GMT
> >
> > # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh
> --csd
> >
> 
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd
>
> > --mask lh.Compr.glmdir/mask.mgh --cwsig
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot
> aparc
> > --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat
> > --cwpvalthresh 0.05 --o
> > lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni
> > --bonferroni 2 --surf white
> >
> > # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts
> >
> > # sysname Linux
> >
> > # hostname Piras-TC2
> >
> > # machine x86_64
> >
> > # FixVertexAreaFlag 1
> >
> > # FixSurfClusterArea 1
> >
> > #
> >
> > # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh
> >
> > # Frame Number 0
> >
> > # srcsubj fsaverage
> >
> > # hemi lh
> >
> > # surface white
> >
> > # annot aparc
> >
> > # SUBJECTS_DIR /media/TREKSTOR/SUBJ
> >
> > # SearchSpace_mm2 65416.6
> >
> > # SearchSpace_vtx 149953
> >
> > # Bonferroni 2
> >
> > # Minimum Threshold 4
> >
> > # Maximum Threshold infinity
> >
> > # Threshold Sign pos
> >
> > # AdjustThreshWhenOneTail 1
> >
> > # CW PValue Threshold: 0.05
> >
> > # Area Threshold 0 mm^2
> >
> > # CSD thresh 4.00
> >
> > # CSD nreps 1
> >
> > # CSD simtype null-z
> >
> > # CSD contrast NA
> >
> > # CSD confint 90.00
> >
> > # Overall max 1e+10 at vertex 3
> >
> > # Overall min 0 at vertex 8
> >
> > # NClusters 1
> >
> > # Total Cortical Surface Area 65416.6 (mm^2)
> >
> > # FixMNI = 0
> >
> > #
> >
> > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
> > CWPLow CWPHi NVtxs Annot
> >
> > 1 100.000 3 76467.08 -22.1 41.5 24.1 0.00020
> > 0.0 0.00040 149953 rostralmiddlefrontal
> >
> >
> > Is it possible to have a Cluster Size (76467.08 mm2) greater
> than the
> > Total Cortical Surface (65416.6 mm2).
> >
> > Are there some errors in this?
> >
> > Thanks a lot to all of you.
> >
> > Claudia
> >
> >
> > --
> >
> > Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
> >
> > Laboratorio di Neuropsichiatria
> >
> > Dipartimento di Neurologia Clinica e Comportamentale
> >
> > IRCCS Fondazione Santa Lucia
> >
> > via Ardeatina 306 - 00179 Roma
> >
> > Tel. +39 (0)6 51501358
> >
> > Fax +39 (0)6 51501575
> >
> > web: http://www.neuropsichiatrialab.com
> 

[Freesurfer] visualize corrected results

[Caroline Beelen]

Dear FS,

I have a question on visualizing results from GLM analysis... How can I 
visualize corrected results in Freeview after having applied bonferroni/FDR 
correction (somewhere else)?
I saw it is not possible (error: masking file missing) -and was told it is not 
necessary- to apply monte carlo simulation on results obtained via aparc-files 
from DK-atlas.

Thank you very much!

Regards, Caroline

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table

[Douglas N Greve]

Hi Claudia, it is better to post these things to the freesurfer list as 
martinos-tech is no longer active. The total cortical surface area 
(65416.6mm2) is incorrect. The total should be 82219.960938. The 
reported value is the actual surface area of the fsaverage white 
surface. However, the average white surface has a much lower surface 
area than areas of any of the input subjects because the surface 
coordinate averaging causes minor folding to be smoothed out. To get 
around this, we keep track of the average surface area of the input 
subjects (rather than the surface area of the average surface, if that 
is not too confusing). The size of the cluster reported (76467.08mm2) is 
accurate.

doug


On 09/12/2016 07:52 AM, Claudia Dacquino claudia.dacqu...@gmail.com 
[martinos-tech] wrote:
>
> Hi all,
>
> I've run GLM surface analysis and I've got a summary table like this:
>
>
> # Cluster Growing Summary (mri_surfcluster)
>
> # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
>
> # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
>
> # CreationTime 2016/09/12-08:47:18-GMT
>
> # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd 
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd
>  
> --mask lh.Compr.glmdir/mask.mgh --cwsig 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc 
> --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat 
> --cwpvalthresh 0.05 --o 
> lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni 
> --bonferroni 2 --surf white
>
> # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts
>
> # sysname  Linux
>
> # hostname Piras-TC2
>
> # machine  x86_64
>
> # FixVertexAreaFlag 1
>
> # FixSurfClusterArea 1
>
> #
>
> # Input  lh.Compr.glmdir/SZSI-SZNO/sig.mgh
>
> # Frame Number  0
>
> # srcsubj fsaverage
>
> # hemi lh
>
> # surface white
>
> # annot aparc
>
> # SUBJECTS_DIR /media/TREKSTOR/SUBJ
>
> # SearchSpace_mm2 65416.6
>
> # SearchSpace_vtx 149953
>
> # Bonferroni 2
>
> # Minimum Threshold 4
>
> # Maximum Threshold infinity
>
> # Threshold Signpos
>
> # AdjustThreshWhenOneTail 1
>
> # CW PValue Threshold: 0.05
>
> # Area Threshold0 mm^2
>
> # CSD thresh  4.00
>
> # CSD nreps1
>
> # CSD simtype  null-z
>
> # CSD contrast NA
>
> # CSD confint  90.00
>
> # Overall max 1e+10 at vertex 3
>
> # Overall min 0 at vertex 8
>
> # NClusters  1
>
> # Total Cortical Surface Area 65416.6 (mm^2)
>
> # FixMNI = 0
>
> #
>
> # ClusterNo  Max   VtxMax Size(mm^2)  MNIX   MNIY   MNIZCWP   
>  CWPLowCWPHi   NVtxs   Annot
>
>1 100.000   3  76467.08-22.1   41.5   24.1  0.00020 
>  0.0  0.00040  149953  rostralmiddlefrontal
>
>
> Is it possible to have a Cluster Size (76467.08 mm2) greater than the 
> Total Cortical Surface (65416.6  mm2).
>
> Are there some errors in this?
>
> Thanks a lot to all of you.
>
> Claudia
>
>
> -- 
>
> Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
>
> Laboratorio di Neuropsichiatria
>
> Dipartimento di Neurologia Clinica e Comportamentale
>
> IRCCS Fondazione Santa Lucia
>
> via Ardeatina 306 - 00179 Roma
>
> Tel. +39 (0)6 51501358
>
> Fax +39 (0)6 51501575
>
> web: http://www.neuropsichiatrialab.com 
> 
>
>
>
> __._,_.___
> 
> Posted by: Claudia Dacquino 
> 
> Reply via web post 
> 
>  
>   •   Reply to sender 
> 
>  
>   •   Reply to group 
> 
>  
>   •   Start a New Topic 
> 
>  
>   •   Messages in this topic 
> 
>  
> (1)
>
> 

Re: [Freesurfer] mris_anatomical_stats

[Bruce Fischl]

I think that would be ok, but an easy way to test it is to try it on 
another subject first with their actual wm.mgz, then with the one from 
fsaverage to check that the thickness is the same.

cheers
Bruce
On Sun, 11 Sep 2016, 
Arkadiy Maksimovskiy wrote:

> Dear Freesurfer Experts,
> 
> I am trying to run mris_anatomical_stats in order to extra thickness data 
> from my participants' label files. However, I only have access to a 
> subj_recon data (without wm.mgz in that
> folder).
> 
> Does anyone know if there is a way to extract the thickness measures for 
> every participant's label, without having the wm.mgz file? Would it be okay 
> to copy that file from
> fsaverage, in order ot bypass this issue, or would that mess up the 
> calculations of the thickness of the participants' labels?
> 
> Thank you in advance for your help,
> 
> Arkadiy
> 
>
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Re: [Freesurfer] Coordinates of particular volumes

[Bruce Fischl]

Hi Aziz,

make sure $FREESURFER_HOME/matlab is in your matlab path.

cheers
Bruce
On Mon, 12 Sep 
2016, Aziz Nanthaamornphong wrote:




Which the version of Matlab has a 'MRIread' function? I got this error
message from my installed Matlab (v. 8.4.0). 
"Undefined function 'MRIread' for input arguments of type 'char'." 

Best Regards,
Aziz.

On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl 
wrote:
  yup, or mri_Info called form the command line. If you use
  MRIread on the aseg.mgz you can extract e.g. the left
  hippocampus using matlab via:


  mri = MRIread('aseg.mgz');
  find(mri.vol == 17);
  then compute the ras coords of those indices using ind2sub

  cheers
  Bruce

  On Sun, 4 Sep 2016, Ruyuan Zhang wrote:


Hi, Aziz

 You can use MRIread function to read in a
volume (i.e. brainmask.mgz).
You will get a structure, which contains a field
called ras2vox.

cheers

ruyuan

On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote:
      Hi,
For example, I want to know the list of x, y, z
coordinates of a left
hippocampus volume. 

As you mentioned "ras2vox" matrices, hoe can I see
or get these
matrices?

Thank you.
Aziz

On Monday, 5 September 2016, Bruce Fischl

wrote:
      Hi Aziz

      can you elaborate? What coordinates do you
want? What are
      you trying to do with them? The .mgz format
contains
      ras2vox matrices that let you go from voxel
indices to RAS
      coordinates and such.


      cheers
      Bruce


      On Sun, 4 Sep 2016, Aziz Nanthaamornphong
wrote:

            Dear Freesurfer experts,
            How can we get the coordinates (X, Y, Z)
of a
            particular volume? I couldn't
            find any functions or command to do
that. 

            Thank you in advance.

            Aziz.




--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information
Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz




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--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz


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[Freesurfer] Troubles witg GLM Surface-based Cluster Summary Table

[Claudia Dacquino]

Hi all,

I've run GLM surface analysis and I've got a summary table like this:


# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $

# $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $

# CreationTime 2016/09/12-08:47:18-GMT

# cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm15/pos/th40/mc-z.csd --mask lh.Compr.glmdir/mask.mgh --cwsig
lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig
lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum
lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn
lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot
lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc
--csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat --cwpvalthresh
0.05 --o lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh
--no-fixmni --bonferroni 2 --surf white

# cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts

# sysname  Linux

# hostname Piras-TC2

# machine  x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input  lh.Compr.glmdir/SZSI-SZNO/sig.mgh

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# annot aparc

# SUBJECTS_DIR /media/TREKSTOR/SUBJ

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 149953

# Bonferroni 2

# Minimum Threshold 4

# Maximum Threshold infinity

# Threshold Signpos

# AdjustThreshWhenOneTail 1

# CW PValue Threshold: 0.05

# Area Threshold0 mm^2

# CSD thresh  4.00

# CSD nreps1

# CSD simtype  null-z

# CSD contrast NA

# CSD confint  90.00

# Overall max 1e+10 at vertex 3

# Overall min 0 at vertex 8

# NClusters  1

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
   CWPHi   NVtxs   Annot

   1 100.000   3  76467.08-22.1   41.5   24.1  0.00020
 0.0  0.00040  149953  rostralmiddlefrontal


Is it possible to have a Cluster Size (76467.08 mm2) greater than the Total
Cortical Surface (65416.6  mm2).

Are there some errors in this?

Thanks a lot to all of you.

Claudia


-- 

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com

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Re: [Freesurfer] Tracula movement

[Anastasia Yendiki]

Hi Lars - This sounds like the subject was trying to climb out of the 
scanner: 3cm average translational motion and 24% of the slices in the 
series have drop-out. How do the images look?


a.y

On Mon, 12 Sep 2016, Lars M. Rimol wrote:


HI,
Is there a rule-of-thumb upper level of acceptable head motion? The tutorial
gives these values as examples:

AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
0.489419 0.00398925 0 1
I have a subject with 

AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
30.018
0.209
24
1.6


I plan, of course, to use the index described in Yendiki et al. (2013) but
would such high levels nevertheless be considered disqualifying a priori?  



Thank you!



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Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis

[Matyáš Kuhn]

Hi Doug,

Yes I did and the registration looks good to me (no axial shift in the 
images) - but I am little confused. In the command for check the 
registration:


/tkregister2 --mov $SUBJECTS_DIR/568/mri/mni152.orig.mgz \
--targ 
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz \

--reg $SUBJECTS_DIR/568/mri/mni152.orig.mgz.reg /

I am comparing images of subject in MNI space and the MNI template, 
right? Why there is also the registration file?


In mri_label2vol I am using /mri/transforms/reg.mni152.2mm.dat for 
tranform aparc+aseg to MNI. Which transformation to use? Or should I 
combine somehow the transformations?  The result with the 
..transforms/reg.mni152.2mm.dat is still shifted.


Or should I try some other way to get aparc+aseg to MNI?

Thank you for any help,

Matyas

/PhD student,//
//CEITEC MU, Brno//
//Czech republic/


Dne 9.9.2016 v 18:53 Douglas Greve napsal(a):

Did you verify that the result of mni152reg is accurate? It should have
printed out a command line to check it


On 9/9/16 5:58 AM, Matyáš Kuhn wrote:

Hi FreeSurfer experts,

We would like to use Destrieux atlas for masking DLPFC in subjects, who
uderwent fMRI and we used SPM to process the data. We want to find peaks
in individuals according to some regions from the atlas (create
individual mask). The problem I am facing is to get
aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM
and Freesurfer.

I followed some discussions on mailing list and tried this:

mni152reg --s $SUB

mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \
   --temp /.../spm/spmT_0001.nii \
   --reg
$SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \
   --o aseg.$SUB.mni152.nii

The process ended without errors, but while watching results in freeview
- the results are not correctly aligned. Is FSL (which is part of
mni152reg procedure) using some other MNI template than SPM?
Any suggestions will be most appreciated.

The freeview snapshot is here:
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG


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Re: [Freesurfer] Coordinates of particular volumes

[Aziz Nanthaamornphong]

Which the version of Matlab has a 'MRIread' function? I got this error
message from my installed Matlab (v. 8.4.0).

"Undefined function 'MRIread' for input arguments of type 'char'."

Best Regards,
Aziz.

On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl 
wrote:

> yup, or mri_Info called form the command line. If you use MRIread on the
> aseg.mgz you can extract e.g. the left hippocampus using matlab via:
>
>
> mri = MRIread('aseg.mgz');
> find(mri.vol == 17);
> then compute the ras coords of those indices using ind2sub
>
> cheers
> Bruce
>
>
> On Sun, 4 Sep 2016, Ruyuan Zhang wrote:
>
>
>> Hi, Aziz
>>
>>  You can use MRIread function to read in a volume (i.e.
>> brainmask.mgz).
>> You will get a structure, which contains a field called ras2vox.
>>
>> cheers
>>
>> ruyuan
>>
>> On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote:
>>   Hi,
>> For example, I want to know the list of x, y, z coordinates of a left
>> hippocampus volume.
>>
>> As you mentioned "ras2vox" matrices, hoe can I see or get these
>> matrices?
>>
>> Thank you.
>> Aziz
>>
>> On Monday, 5 September 2016, Bruce Fischl 
>> wrote:
>>   Hi Aziz
>>
>>   can you elaborate? What coordinates do you want? What are
>>   you trying to do with them? The .mgz format contains
>>   ras2vox matrices that let you go from voxel indices to RAS
>>   coordinates and such.
>>
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 4 Sep 2016, Aziz Nanthaamornphong wrote:
>>
>> Dear Freesurfer experts,
>> How can we get the coordinates (X, Y, Z) of a
>> particular volume? I couldn't
>> find any functions or command to do that.
>>
>> Thank you in advance.
>>
>> Aziz.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
>>
>> ___
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>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mai
>> l
>> contains patient information, please contact the Partners Compliance
>> HelpLin
>> e at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in er
>> ror
>> but does not contain patient information, please contact the sender and
>> prop
>> erly
>> dispose of the e-mail.
>>
>>
>>
>>
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-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] white and pial surface crossin in the lingual gyrus

[Alain Imaging]

Thanks a lot Bruce,


I will try it for sure!


Best


Alain


De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Bruce Fischl 

Envoyé : vendredi 9 septembre 2016 17:28:06
À : Freesurfer support list
Objet : Re: [Freesurfer] white and pial surface crossin in the lingual gyrus

Hi Alain

I'm pretty sure that this is a bug in 5.3 that is fixed in dev and will
not be an issue in 6.0. You can test this by downloading and trying out
dev if you like.

cheers
Bruce
On Fri, 9 Sep 2016, Alain Imaging wrote:

>
> Hello everybody,
>
>
> I am gladly starting my freesurfer adventure after the awesome last course
> in Copenhagen, but I have quickly realized that troubleshooting on your own
> is not as easy as with experts going around in a room.
>
>
> I was looking for errors after having run the recon all and I stumbled upon
> this crossing between white and pial surface in the lingual gyrus (see
> attached Figure1, green arrow).
>
>
> It seems to me that the problem may arise from the fact that in the WM
> volume (see attached Figure2) there are areas that have been categorized as
> WM hypointensities, and in particular on the right, the problem could be
> that the white matter surface, instead of going around these brighter
> voxels, just goes straight down (I hope I have explained myself). Is the
> fixing to this problem changing the value of those voxels (part of them, of
> course) in the WM volume ?  If I look at the WM seg I see that indeed they
> are left out from the mask. Or should I do something else ?
>
>
> I am working with freesurfer version Linux-centos6_x86_64-stable-pub-v5.3.0,
> with Linux version 3.10.0-327.4.5.el7.x86_64 (Red Hat 4.8.3-9).
>
>
> Thanks in advance for any suggestion
>
>
> Alain
>
>
>
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