[Freesurfer] Open research assistant position at Ohio State University

[Osher, David E.]

External Email - Use Caution

The Cognition and Brain Circuitry Laboratory at the Ohio State University is 
recruiting a research assistant. Primary duties include: conducting 
neuroscience research on the functional and structural architecture of the 
human brain, and its role in cognition; programming, running, and analyzing 
behavioral and brain-imaging experiments using functional magnetic resonance 
imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and 
behavioral assessments; scoring and coding data; performing statistical 
analyses using programs such as, MATLAB, Python, and shell scripting; 
recruiting research participants; maintaining participant databases; developing 
outreach letters. The position is available for one year with the possibility 
of extension based on satisfactory performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience (every one of our 
research assistants has successfully been admitted into doctoral programs!). We 
are seeking an aspiring, self-motivated researcher with strong 
coding/programming skills who is excited about the brain, cognitive 
neuroscience, and/or clinical disorders and demonstrates evidence of a serious 
interest in a career in the field.

If you are interested in being considered for this position, please apply 
online at 
https://secure-web.cisco.com/1w5xNz1auriZm4kg1U9EtUe0L6lVm2ZwBphpkQCXxqGqpgFK6SW5O-4oV7XY6yRH1mEvpiSChvzhUrC0fTO6IVw3x7nBi7J3i2t2TvOaOUgrQsSQaH2OM-VNYTqB6myp2NM9q6yp0IVyNBQA4gPCDoTSE5rtC-F-2nsSGow0dt1zJdJLgjXA2et_rGASaHjQzz9EAa_c91jymHlQToXIu-27T9RlJYfs-svpKQjhJJLjBFURLhFadYZopLaS0LLR9fNrtXv-phL_FjkGB6aNrXmcFAbeQC27n8TAJS20JhM2gzKAohdQ3Hrhrc3mBwdAYcP5DRZPbXbmmlI_PmT_PvQ/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2Fen-US%2FOSUCareers%2Fjob%2FResearch-Senior-Technician_R74514-1
 and submit a current CV and names of three references.


If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.


_
David E. Osher, Ph.D.
Assistant Professor of Psychology
The Ohio State University
davidosher.com<https://secure-web.cisco.com/1_NpgHtrxMaHWVU2jXBgnwwyBjoLFRWnvVowP4st8hUmPl8KSy2Nm1NwQsO1IWuh6yI53x4s3afapr93SOtgQwmrU5gFo8yaYsiAMkyQa5NY6AGAL5Ks32iE2Hg-RMvGtly4I8xoxip6a8lI1bW5-btO0wrYZfe9bfoUqXtsw2zm9VC24ogb8vclevP7d_BEcU8dyiVk2PXJzvQSMzKwvdVKwG7rrmL2Ot14hZIyPPbAySNLMPiMJ0gbFsIonfptAd4osFxgb_d3lZNTioxvhuKckuLfYaTNKpXuBggVdkYC2xBz1hZGEi9Dx4ZHWZnseWO1D0crAZKAjtSKKpYZNng/https%3A%2F%2Fwww.davidosher.com%2F>
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continue to communicate over unencrypted e-mail. 

[Freesurfer] Open research assistant position at Ohio State University

[Osher, David E.]

External Email - Use Caution

The Cognition and Brain Circuitry Laboratory at the Ohio State University is 
recruiting a research assistant. Primary duties include: conducting 
neuroscience research on the functional and structural architecture of the 
human brain, and its role in cognition; programming, running, and analyzing 
behavioral and brain-imaging experiments using functional magnetic resonance 
imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and 
behavioral assessments; scoring and coding data; performing statistical 
analyses using programs such as, MATLAB, Python, and shell scripting; 
recruiting research participants; maintaining participant databases; developing 
outreach letters. The position is available for one year with the possibility 
of extension based on satisfactory performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience (every one of our 
research assistants has successfully been admitted into doctoral programs!). We 
are seeking an aspiring, self-motivated researcher with strong 
coding/programming skills who is excited about the brain, cognitive 
neuroscience, and/or clinical disorders and demonstrates evidence of a serious 
interest in a career in the field.

If you are interested in being considered for these positions, please apply 
online at 
https://secure-web.cisco.com/1TciY0h9Hnogs0Vsz6IpkMg3S9JvHoraefFGDv9JWfB8mvIlucAJE9ulGkry9qT63OAfHCsMqIHsNzfSzcIxL8Cno70feKG9mJSeN07E5Tn8_y_wEQZxjZ9pgg_wrYvSGwz9KoiCbxloxQVszrBBAZfVAR7QAxd0j8LhEJczk8XTNEMPcvGzragjXAcnFTD_qlS4a1051SmwqsyqyejO0swGCLxb_jjBsniLSjp6EzD3R48dWcfU1M4WjF9NaL8Ix16ocyO9iYKZeI7DphPZ9imurfC1pHxqkSOXO-Xc2HLAvgc4cTZtiFK57N31SidMXKMAO3uxBHq_qEAsG_2veFw/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2Fen-US%2FOSUCareers%2Fjob%2FResearch-Senior-Technician_R74514-1
 and submit a current CV and names of three references.


If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.


_
David E. Osher, Ph.D.
Assistant Professor of Psychology
The Ohio State University
davidosher.com<https://secure-web.cisco.com/1-CVKBQsgAyt6sw0qCo0o_YrQ6nEs-h_DI1v27Nd4YqU306HOHFHCGlLs2xfbbSIxzyx-M3NQhrIztsKevdA540apkDlD8XZhLhceRJM49FGG8ENkVXvstpq721MxTBf-88TUsZK4dUmNbzrZwqheFfKRz22acoiBy96sd80vuYG2Usn96VZbkFb57CUCT0TsnzgIrbr7s4N_kX7sAeXwfUd0E4gpvW17QwJ5jhjAqg1l0Dn-5wtK-pTfdI1tr_qkUXuf0zd8VL-p2KbAuc_mKDRR5KY6Ux-k7CHCX8eONU85hbxkTLwIOI09YBM_1BoF/https%3A%2F%2Fwww.davidosher.com%2F>
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[Freesurfer] UnicodeEncodeError while running the recon-all

[David Lau]

External Email - Use Caution

Hi,


I tried to run Freesurfer (macOS-7.1.1) to the command line and the
terminal replied,


"DavidLaus-MacBook-Air:local davidlau$ recon-all -i
/Users/davidlau/Desktop/testing/1RAS.nii -subject
/Users/davidlau/Desktop/testing/$d done

Traceback (most recent call last):

  File "/Users/davidlau/Documents/freesurfer/python/scripts/rca-config",
line 143, in 

file.write(arg + '\n')

UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in
position 0: surrogates not allowed

ERROR: could not configure recon-all parameters"


A similar question has been retrieved from the mail list (20 Jul 2020) by
Molly and Andrew replied that there might be a non-unicode character
accidentlly passed to the command line and recommended manually typing out
the recon-all command. I've tried this several times but the same error
message popped out.


Any suggestions would be much appreciated.


David
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[Freesurfer] result question

[David]

External Email - Use Caution

Hi Freesurfer experts,

I'm very sorry to bother you, but I am very confused with the
following questions:

My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables

So I can get 6 classes: df, dm,mf, mm,hf,hm.

 I want to perform the difference between any of the classes
leves analysis with regressing out the effect of gender and two
Nvariables, but I don't know the rules for setting the contrasts for
the F-test.  The contrast matrix I used is:

1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0


My orders are as follows：


mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi lh --meas 
thickness --out lh_teach3.mgh
mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi rh --meas 
thickness --out rh_teach3.mgh


mri_glmfit --y lh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.lh --fwhm 10 --surface fsaverage lh --eres-save
mri_glmfit --y rh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.rh --fwhm 10 --surface fsaverage rh --eres-save


mri_glmfit-sim --glmdir group3.testA1_10sm.lh --cache 3 abs --cwp .05 --2spaces
mri_glmfit-sim --glmdir group3.testA1_10sm.rh --cache 3 abs --cwp .05 --2spaces

We obtained five differential brain regions and extracted their cortical 
thickness. And then put the extracted cortical thickness into SPSS for general 
linear model analysis, but two of the brain regions were not statistically 
significant.

Why? Is the contrast matrix I used wrong? Or other errors?


Any help will be very appreciated.

Best wishes

___
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[Freesurfer] segmentation of phantoms with own defined PVE priors

[Nederpelt, D.R. van (David)]

External Email - Use Caution

Hi Freesurfer developers,

I am trying to segment phantoms, but I would like to base the principle of the 
segmentation on a "freesurfer-like" pipeline/segmentation. This is to minimize 
differences between the segmentation pipeline of the phantoms compared to the 
patient/subject segmentation. I have predefined priors of the phantoms. Would 
you be able to provide me with some advice regarding this or maybe a 
collaboration?

Thank you very much in advance.

Best regards,
David

[cid:image002.png@01D40E30.3E299A80]

David R. van Nederpelt, MSc  | PhD Candidate
Radiology and Nuclear Medicine
Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ 
Amsterdam, the Netherlands
T: +31 20 444 6480 | E: 
d.vannederp...@amsterdamumc.nl<mailto:d.vannederp...@amsterdamumc.nl>
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[Freesurfer] Multiple comparison correction

[David]

External Email - Use Caution

Hi Freesurfer experts,

I'm very sorry to bother you, but I am very confused with the
following questions:

My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables

So I can get 6 classes: df, dm,mf, mm,hf,hm.

 I want to perform the difference between any of the classes
leves analysis with regressing out the effect of gender and two
Nvariables, but I don't know the rules for setting the contrasts for
the F-test.  The contrast matrix I used is:

1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0


My orders are as follows：


mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi lh --meas 
thickness --out lh_teach3.mgh
mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi rh --meas 
thickness --out rh_teach3.mgh


mri_glmfit --y lh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.lh --fwhm 10 --surface fsaverage lh --eres-save
mri_glmfit --y rh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.rh --fwhm 10 --surface fsaverage rh --eres-save


mri_glmfit-sim --glmdir group3.testA1_10sm.lh --cache 3 abs --cwp .05 --2spaces
mri_glmfit-sim --glmdir group3.testA1_10sm.rh --cache 3 abs --cwp .05 --2spaces

We obtained five differential brain regions and extracted their cortical 
thickness. And then put the extracted cortical thickness into SPSS for general 
linear model analysis, but two of the brain regions were not statistically 
significant.

Why? Is the contrast matrix I used wrong? Or other errors?


Any help will be very appreciated.

Best wishes

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] freesufer

[David]

External Email - Use Caution

Hi Freesurfer experts,

I'm very sorry to bother you, but I am very confused with the
following questions:

My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables

So I can get 6 classes: df, dm,mf, mm,hf,hm.

 I want to perform the difference between any of the classes
leves analysis with regressing out the effect of gender and two
Nvariables, but I don't know the rules for setting the contrasts for
the F-test.  The contrast matrix I used is:

1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0


My orders are as follows：


mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi lh --meas 
thickness --out lh_teach3.mgh
mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi rh --meas 
thickness --out rh_teach3.mgh


mri_glmfit --y lh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.lh --fwhm 10 --surface fsaverage lh --eres-save
mri_glmfit --y rh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir 
group3.testA1_10sm.rh --fwhm 10 --surface fsaverage rh --eres-save


mri_glmfit-sim --glmdir group3.testA1_10sm.lh --cache 3 abs --cwp .05 --2spaces
mri_glmfit-sim --glmdir group3.testA1_10sm.rh --cache 3 abs --cwp .05 --2spaces

We obtained five differential brain regions and extracted their cortical 
thickness. And then put the extracted cortical thickness into SPSS for general 
linear model analysis, but two of the brain regions were not statistically 
significant.

Why? Is the contrast matrix I used wrong? Or other errors?


Any help will be very appreciated.

Best wishes___
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[Freesurfer] PostDoc (or qualified PhD) in Cognitive Computational Modeling (fMRI) in Copenhagen

[David Meder]

External Email - Use Caution

We are hiring a PostDoc (or qualified PhD student) on cognitive computational 
neuroimaging. 
This position is for you if you are interested in how the dopamine system works 
and like computational modeling. You would be part of a small and dynamic 
research project on the reward and motor systems in Parkinson’s Disease, 
embedded in the Movement Disorders research group at the Danish Research Centre 
for Magnetic Resonance.
And all of that in the most liveable city in the world.

For any inquiries or questions, write to dav...@drcmr.dk 
<mailto:dav...@drcmr.dk>.

Follow this link for all details and for the application: 
https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpCRc08SGhqteek4-saU0gK2d1IrYvxh7WrpMqHdVcUK2-4D4sRwCzlogvpv6l9SIuQXt9bNKMKHFPGMSqp35X6q94i-8-HN2geMcbuDxl4YButWlvPcpk9naaoLHc2xEtJsNI18nMEYJKeE72FNf8GdosRDpoK3obIehuVYRU14Pnq79ys7YEXFPuB25dvaR3g1mVBtgmL_7bFXDS15shWCkHuo4lEzL72_sZy0oTjS6WrVr3MisvAtfwwl4efoUsgplLJAYByZtUDuQb8Eij/https%3A%2F%2Fwww.drcmr.dk%2Fvacancies%2Fitem%2F1270-a-postdoc-or-qualified-phd-in-cognitive-computational-modeling-of-neuroimaging-data
 
<https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpCRc08SGhqteek4-saU0gK2d1IrYvxh7WrpMqHdVcUK2-4D4sRwCzlogvpv6l9SIuQXt9bNKMKHFPGMSqp35X6q94i-8-HN2geMcbuDxl4YButWlvPcpk9naaoLHc2xEtJsNI18nMEYJKeE72FNf8GdosRDpoK3obIehuVYRU14Pnq79ys7YEXFPuB25dvaR3g1mVBtgmL_7bFXDS15shWCkHuo4lEzL72_sZy0oTjS6WrVr3MisvAtfwwl4efoUsgplLJAYByZtUDuQb8Eij/https%3A%2F%2Fwww.drcmr.dk%2Fvacancies%2Fitem%2F1270-a-postdoc-or-qualified-phd-in-cognitive-computational-modeling-of-neuroimaging-data>
 

Deadline is Nov. 13th


David Meder
Research Fellow
Danish Research Centre for Magnetic Resonance DRCMR, Section 714
Copenhagen University Hospital Amager and Hvidovre
Kettegaard Alle 30, 2650 Hvidovre, Denmark

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[Freesurfer] SAMSEG longitudinal sbTIV bigger than cross-sectional

[Nederpelt, D.R. van (David)]

External Email - Use Caution

Dear SAMSEG developers,

We have a dataset with 55 subjects (MS patients and controls) scanned on three 
timepoints with yearly intervals.
When we ran the (SAMSEG) longitudinal pipeline we noticed that the sbTIV always 
had an increased volume (between 0.5 and 3.5% larger) compared to the sbTIV 
computed cross-sectionally. Do you have any idea how and why we may see these 
effects?

Thank you in advance!

Best regards,
David van Nederpelt | Amsterdam UMC

__
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[Freesurfer] Expand Zip file

[David Bjanes]

External Email - Use Caution

Hi all,

Trying to get open the *.zip file to install a Windows VM to run
FreeSurfer. I need a passcode to extract the contents of the Ubuntu VM.
Anyone know what that is?

Thanks!
David

**
David Bjånes, Ph.D.

Neilsen Foundation Fellow
Andersen Lab
Caltech
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[Freesurfer] Open research assistant position at Ohio State University (please share!)

[Osher, David E.]

External Email - Use Caution

The Cognition and Brain Circuitry Laboratory at the Ohio State University is 
recruiting a research assistant. Primary duties include: conducting 
neuroscience research on the functional and structural architecture of the 
human brain, and its role in cognition; programming, running, and analyzing 
behavioral and brain-imaging experiments using functional magnetic resonance 
imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and 
behavioral assessments; scoring and coding data; performing statistical 
analyses using programs such as, MATLAB, Python, and shell scripting; 
recruiting research participants; maintaining participant databases; developing 
outreach letters. The position is available for one year with the possibility 
of extension based on satisfactory performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience (every one of our 
research assistants has successfully been admitted into doctoral programs!). We 
are seeking an aspiring, self-motivated researcher with strong 
coding/programming skills who is excited about the brain, cognitive 
neuroscience, and/or clinical disorders and demonstrates evidence of a serious 
interest in a career in the field.

If you are interested in being considered for these positions, please apply 
online at 
https://secure-web.cisco.com/1a8p8qGhoqso6oYBkudeXI8_eqsXtlC6hqmGfFmjR86taA307VTHkS1oAKz8036JFzirncbV7AwQO_PxEPw4f7eJiJZJPu3S_zCJHrzJhvqw8djvRpW_fYBx3ZPk4nTvir7qY9OXROHo9t00C5gDKMmrUDvFjUBasrmmR6Zh8zGNqhFOqkTBKySNyI8c-HY1V0JQOYqlTZabDtpwTLNppXyT4vwgu22APN1JmOrTr_0h-pb7SgPkb-WnnBuzcyM-7PjuZEU304XAK-87RtqfwvuihJzaMeljcpN1EnZH65dNXcD5I4W29hBr11XzhRkUyYiOTrXjy58nI7K6nO0P2Gw/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2FOSUCareers%2Fjob%2FColumbus-Campus%2FResearch-Assistant-2---Social_R47050-1
 and submit a current CV and names of three references.


If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu<mailto:oshe...@osu.edu>

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.

_
David E. Osher, Ph.D.
Assistant Professor of Psychology
The Ohio State University
davidosher.com<https://secure-web.cisco.com/1lqk_MmIM3fJEV2RfMCA4jAX9cFL53d2oDdw2rc_wWO1FRN7ZSFZj2FlgPrP2BXLUKFcDPQrQ-N8oSyUtYFmMtTYLwzEWPuQdnKaQOe_QVJWGKYylr8EcZ6GyEnw_OaT14rP9na1dYjoCj_G5Eb6ts1WsfoONb6DXVdbbnMm-vAjoc6-3BaA0DpA7u2ll1XGygWqxphCzhni6FGwdjS5dcO8Kvj_Hgu3T2N140TgwifBMi5nmxWUj7TxHNZjJYGQlbHxfpiz4Bi1FTv9JSc-h7orXLe_B2_M1MVIrh0AayYeKEHIHIAsbWZL2xKlBtu-7/https%3A%2F%2Fwww.davidosher.com%2F>
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[Freesurfer] Multiple comparison correction

[David]

External Email - Use Caution

Hi Freesurfer experts,

I'm very sorry to bother you, but I am very confused with the
following questions:

My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables

So I can get 6 classes: df, dm,mf, mm,hf,hm.

 I want to perform the difference between any of the classes
leves analysis with regressing out the effect of gender and two
Nvariables, but I don't know the rules for setting the contrasts for
the F-test.  The contrast matrix I used is:

1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0
My orders are as follows：
mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi lh --meas area 
--out lh_teach.mgh
mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi rh --meas area 
--out rh_teach.mgh

mri_glmdir --y lh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx --glmdir 
group.area_sm.lh --fwhm 10 --surface fsaverage lh --eres-save

mri_glmdir --y rh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx --glmdir 
group.area_sm.rh --fwhm 10 --surface fsaverage rh --eres-save

mri_glmdir-sim --glmdir group.area_sm.lh --2spaces --cwp 0.05 --perm 100 
1.3 abs
mri_glmdir-sim --glmdir group.area_sm.rh --2spaces --cwp 0.05 --perm 100 
1.3 abs

   But there is no region of interest after running，
   Can I change the correction method or did I use it wrong


Any help will be very appreciated.

Best wishes,___
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[Freesurfer] mri_glmfit error

[David]

External Email - Use Caution

Hello FreeSurfer Developers,
my fsgd is this：
GroupDescriptorFile 1
Title post compane
Class d
Class m
Class h

RescaleFlag 1
DemeanFlag 1
Variables gender Age Edu
Input bd1 d 0 15 8
Input bd2 d 1 19 13
Input bd7 d 0 17 11
Input bd8 d 1 19 13
Input bd6 m 1 22 12
Input bd9 m 1 26 7
Input bd10 m 0 53 15
Input bd11 m 1 56 4
Input hc3 h 0 45 7
Input hc4 h 1 18 13
Input hc1 h 0 52 7
Input hc2 h 1 24 10


When I run Three Groups (One Factor/Three Levels), three Covariates,my MTX is

1 -1 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0
It’s wrong,What should I do

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



 ERROR: READ THIS -
--vv-
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y rh_teach66.mgh --fsgd glmteach66.fsgd --C glmteach66.mtx 
--glmdir group66.area_66sm.rh --fwhm 10 --surface fsaverage rh --eres-save
  2. The terminal output of this program (ie, everything it prints to the 
screen)
  3. The FSGD file (glmteach66.fsgd)
  4. The design matrix group66.area_66sm.rh/Xg.dat
Attempting to diagnose further
WARNING: Class d has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
WARNING: Class m has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
WARNING: Class h has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
SumSq: Min=1.491914 (col 10), Max=2.676059 (col 11)
 ... could not determine the cause of the problem
--


ERROR: cannot find residual group66.area_66sm.lh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
ERROR: cannot find residual group66.area_66sm.rh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
glm66.sh: line 14: --perm-resid: command not found
---
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[Freesurfer] qdec analysis error

[David]

External Email - Use Caution

Hello FreeSurfer Developers,

I have a problem. Can you help me

freesurfer version : 6.0.0

Load qdec when I run qdec.table.dat, the data is loaded correctly, but when I 
design, I choose discrete and continuous factors for analysis
The error log is as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
1 bd1 d Male 15.00 8.00
2 bd2 d Female 19.00 13.00
3 bd3 d Male 25.00 9.00
4 bd4 d Male 17.00 12.00
5 bd5 d Male 16.00 10.00
6 bd6 m Female 22.00 12.00
7 bd7 d Male 17.00 11.00
8 bd8 d Female 19.00 13.00
9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
1  d
2  m
3  h
2  gender  discrete 2
1  Male
2  Female
3  age  continuous 0
4  edu  continuous 0
Continuous Factors: Mean:   StdDev:
--- -   ---
age22.293 9.015
edu11.374 2.827

Number of subjects:   99
Number of factors:4 (2 discrete, 2 continuous)
Number of classes:6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR is '/media/root/Backup_Plus2/new/RECON'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 

Re: [Freesurfer] Custom Freeview Color Map (not Lookup Table)

[Keator, David (Psychiatry & Human Behavior)]

External Email - Use Caution

Hi Ruopeng,

I have the colormap I’m interested in using.  It’s a 256 colormap with RGB 
values.  I could save it as a binary colormap if I know the precise format or 
an ascii formatted colormap.

Thanks,
Dave


From:  on behalf of "Wang, Ruopeng" 

Reply-To: Freesurfer support list 
Date: Monday, March 14, 2022 at 7:59 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Custom Freeview Color Map (not Lookup Table)

There isn’t a way to do that at the moment. So you want to use a continuous 
spectrum with 256 color stops as the color map?

Ruopeng


On Mar 11, 2022, at 6:06 PM, Keator, David (Psychiatry & Human Behavior) 
mailto:dbkea...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

I’d like to load in a custom color map to be used in color percentile-scaled 
functional images into FreeView (version 3.0; Build Aug 11, 2020).  I can’t 
seem to find a reference for defining and loading a custom color map.  I have 
done this for custom lookup tables and that’s all fine but now I’d like to 
define a ~256 RGB colors and use that in place of the standard color maps (e.g. 
Jet, NIH, PET, etc.).

Thanks,
Dave


David Keator, M.S., Ph.D.
Research Professor
Psychiatry and Human Behavior
Operations Director
Neuroscience Imaging Center
University of California, Irvine
Irvine Hall rm. 163 – Zot 3960
Irvine, CA. 92697
Office: 949-824-7870




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[Freesurfer] Custom Freeview Color Map (not Lookup Table)

[Keator, David (Psychiatry & Human Behavior)]

External Email - Use Caution

Hi,

I’d like to load in a custom color map to be used in color percentile-scaled 
functional images into FreeView (version 3.0; Build Aug 11, 2020).  I can’t 
seem to find a reference for defining and loading a custom color map.  I have 
done this for custom lookup tables and that’s all fine but now I’d like to 
define a ~256 RGB colors and use that in place of the standard color maps (e.g. 
Jet, NIH, PET, etc.).

Thanks,
Dave


David Keator, M.S., Ph.D.
Research Professor
Psychiatry and Human Behavior
Operations Director
Neuroscience Imaging Center
University of California, Irvine
Irvine Hall rm. 163 – Zot 3960
Irvine, CA. 92697
Office: 949-824-7870




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[Freesurfer] sulc surface error: unit mismatch between FreeSurfer 5.3.0 and 6.0.1

[Guerreiro Fernandes-3, F.D. (Francisco David)]

External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to correlate the sulcal depth information present in the ?h.sulc 
files with activation in particular brain regions during  an overt language 
task in an fMRI paradigm. For this matter, a dataset was gathered throughout 
the years with several subjects and the cortical reconstruction process (as 
described in: 
https://secure-web.cisco.com/1nqW39ubw2AyrvIfDDZNWB66KB47XSeO6tS5QZO8RBYGIE_HEX0L_9ky5BplO2g3f5Yype5vdBj4W0De7S1NBLNdvHFPI1k0DayuUt2hc8j52YzXFhR7ng6pxJ4WM9WsiFPnfTnLRWLH7RHeMEPW8DMqOq4bEtJHfRx81pXgSbL9KqbThH3rR-G7j34pXg15cg8R__sP3dfS4Te9UczFajxl3ED3vYroskCPgsbZZfvIqegttwogROzyTE40I9jKEPHbTC0ad0azXoFQhZh0312sG9dthj8QouCdrRS3UGD3lb7Z6ZEAyu8iwXtIgnOzh1aGKos3EBeMGRghRHiFnXQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all)
 was performed at the time of data acquisition. However, for subjects where 
recon-all was run in different FreeSurfer versions (5.3.0 or 6.0.1), I get an 
order of magnitude difference in the sulc values in the ?h.sulc volumes.

I've searched the list and the official FreeSurfer Release Notes 
(https://secure-web.cisco.com/1vUPpLJpZFWtBAPAZsBnTOCfqihx6dgklkyFygBvPMdyx7egogmPbZrtHwz8GVBBctGuDY99I9NnZfKG1jKUmWJ5aqaEOn1QU0WGVi-mGQOpV_8hc-GGg1nVkplvhR_AH0QLrM9rYmeJJ6WOfAhGJftjmZSK4fsKHwYrZ8Bro6e82ktqUL4ijtCobfRW5TMxI7SXZpDjHhN6rEdoBdi6VWw5qx1fbGGZtLa8NHhcwjbuVf0h0E97zMwPFyXEVb3ZhTCkNu5-wVG3pexTcTvG1AxBkIiCsEyxQk236UYmFDDNazzSD6x3TTLqWsj4PH4KVbLl6uVvzEMJ9lVLZqLbtcA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes)
 and found no information of a change of magnitude in sulc values. Does anyone 
have any thoughts on how to trouble-shoot this one?

1) FreeSurfer versions: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 & 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
2) Platform: Linux blue 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 
(2015-08-04) x86_64 GNU/Linux


Kind Regards,
Francisco D. Guerreiro Fernandes

[Description: Universitair Medisch Centrum Utrecht]

Francisco David Guerreiro Fernandes, PhD Candidate   |   BCI Group   |   UMC 
Utrecht Brain Center
Dept. Neurology & Neurosurgery   |   University Medical Center Utrecht
Room STR 4.119   |   Heidelberglaan 100   |   3584CX Utrecht   |   The 
Netherlands
Email: 
f.guerreirofernande...@umcutrecht.nl<mailto:f.guerreirofernande...@umcutrecht.nl>
   |   Tel: +31 88 75 50080


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[Freesurfer] surface based group analysis

[David]

External Email - Use Caution

Hello FreeSurfer Developers,

Hello, I would like to ask if there are other correction methods besides 
multiple comparison correction when surface based group analysis.___
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[Freesurfer] Total volumes SAMSEG

[Nederpelt, D.R. van (David)]

External Email - Use Caution

Dear SAMSEG developers,

Is there an easy way/specific function to compute the total volumes (GM, WM and 
Total Brain) after the cross sectional processing pipeline has been run?
I currently add the volumes specified here: MorphometryStats - Free Surfer Wiki 
(harvard.edu)<https://secure-web.cisco.com/1TiZSqlkmJdSG6YomLyN1O5wCUsd9cdQzzIoKCQYS9WpviPI49_lorZ_PTx-cok1PIeuP8aWJ0IV6NMrcGfHODM2PLpH9RCWg-ln0Jg3_V6zwsh77nVZB4eIAR3Y-sri82P9wc_X4NwGgnapiZ_giZMZuqHSwm3ql2xGpURyF3CTBTmybLP1w9Cv7SbWp2TZhZkZnRB9yYZHo-e9S5TPVgg_igr4Am5G0FC_cGgwpO0coHVaAsMKqmpERVazbMNtYaLa3U6l0NChbwkbKfwL0wA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMorphometryStats>
However, adding the WM volumes (lhCerebralWhiteMatter + rhCerebralWhiteMatter + 
WM hypointensities) results in lower volumesthan  the volumes found with 
FreeSurfer.

Thank you very much in advance!

Best regards,
David

[cid:image002.png@01D40E30.3E299A80]

David van Nederpelt, MSc.  | PhD Candidate
Radiology and Nuclear Medicine
Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ 
Amsterdam, the Netherlands
T: +31 20 444 6480 | E: 
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 / 
http://secure-web.cisco.com/1IDr1ToLQ00j-N7JGdkZizZ2EY4BfRaX-Ni0bhB33BkT_pJtmXKSQPSMX7LC04i3XB25FIoQpS4c_HfkEnw0O4HnZHVeFZnjWlyvnLDpUtZEiNM6HuERtm38DavT5BeAk0oe-wdTltFJz-I_5X7zeKtdUCpEzNaVBHAWUanrgYP9J2kmbUAB5nit7Tc82Zn-yHVegPRrVelTY4YQXRQMrxKdxnk5ISJ8uEz9Is_0f1yW5wTAXW64kL_J69XAWvjftdLIPyEGnAaBwomnxBjlrUw/http%3A%2F%2Fwww.amc.nl<http://secure-web.cisco.com/1wXJqt2HAZw1ZuD0nu0MtMhTFzaeK7O7CKFnLDqQmLsmS7l58-5sLp7UrEJJotSs2KHUEEDV0wnmawamcCbpdNxUYXyFRDmrCfVvAXYfn1z-X9oG_nKEEFfwxmSVlx3I2kiIhTAkw9tUfJaxHxMIJ8gpAVRPW_bFZUlAPQio1cFqorbuXJ4Jfho8WDOlD0apweEUKAcB6GHhQNmK-dB4Hmj7e_xkh5FcgWtJxGKnfr6Co4r4i8Y7WkBy0rslsakHVrM6fP8pup9FvmcHEnjwcSg/http%3A%2F%2Fwww.amc.nl%2F>
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Re: [Freesurfer] Does segmentation depend on input orientation {Disarmed} {Disarmed}

[Nederpelt, D. van (David)]

External Email - Use Caution

Thank you for your reply. What I fail to understand is why this would happen. 
Since, you only flip the orientation (and if I understand correctly freesurfer 
uses its "own" orientation LIA). The program should start at the same point.

If I apply mri_convert to both input image,s in this case "001.mgz", and 
reorientate these to the LIA convention, they are exactly the same.
I would therefore expect the output to be the same as well. Why would the 
starting point differ?

Best,
David

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: maandag 7 december 2020 16:21
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Does segmentation depend on input orientation 
{Disarmed}

Yes, this can happen  (and happens to almost all neuroimaging packages).  As 
with any optimization program, where it ends up depends a little on where it 
starts.
On 12/3/2020 6:31 AM, Nederpelt, D. van (David) wrote:

External Email - Use Caution
Hi,

I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and 
once on this image converted to LAS orientation
I would expect the output (especially in volume) to be equal, because 
freesurfer reconverts it to its own orientation if I understood correctly. 
However, I found that the segmentation and output volumes differed depending on 
the input orientation.

So while in fact both images are actually the same, the output differs. What 
would be the reason for this difference in output?

Any help would be much appreciated

Kind regards,


[cid:image002.png@01D40E30.3E299A80]

David van Nederpelt, MSc.  | PhD Candidate
Radiology and Nuclear Medicine
Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ 
Amsterdam, the Netherlands
E: d.vannederp...@amsterdamumc.nl<mailto:d.vannederp...@amsterdamumc.nl>
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[Freesurfer] Does segmentation depend on input orientation {Disarmed}

[Nederpelt, D. van (David)]

External Email - Use Caution

Hi,

I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and 
once on this image converted to LAS orientation
I would expect the output (especially in volume) to be equal, because 
freesurfer reconverts it to its own orientation if I understood correctly. 
However, I found that the segmentation and output volumes differed depending on 
the input orientation.

So while in fact both images are actually the same, the output differs. What 
would be the reason for this difference in output?

Any help would be much appreciated

Kind regards,


[cid:image002.png@01D40E30.3E299A80]

David van Nederpelt, MSc.  | PhD Candidate
Radiology and Nuclear Medicine
Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ 
Amsterdam, the Netherlands
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[Freesurfer] qdec replacement

[Pagliaccio, David (NYSPI)]

External Email - Use Caution

Hello
I was just wondering if there were any updates on a FSv7 replacement for QDEC 
for vertex-wise cortical thickness analyses? Or if there were any 
recommendations for analyses in other programs?
Thanks!
David



--
David Pagliaccio, Ph.D.
Assistant Professor of Clinical Neurobiology (in Psychiatry)
Columbia University Irving Medical Center

Assistant Research Scientist
Division of Child and Adolescent Psychiatry
New York State Psychiatric Institute
1051 Riverside Drive
New York, NY 10032
phone: 646-774-5556
Email: 
david.pagliac...@nyspi.columbia.edu<mailto:david.pagliac...@nyspi.columbia.edu>
Pronouns: he/him

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[Freesurfer] Open research assistant position at Ohio State University

[Osher, David E.]

External Email - Use Caution

The Cognition and Brain Circuitry Laboratory at the Ohio State University is 
recruiting a research assistant. Primary duties include: conducting 
neuroscience research on the functional and structural architecture of the 
human brain, and its role in cognition; programming, running, and analyzing 
behavioral and brain-imaging experiments using functional magnetic resonance 
imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and 
behavioral assessments; scoring and coding data; performing statistical 
analyses using programs such as, MATLAB, Python, and shell scripting; 
recruiting research participants; maintaining participant databases; developing 
outreach letters. The position is available for one year with the possibility 
of extension based on satisfactory performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience. We are seeking an 
aspiring, self-motivated researcher with strong coding/programming skills who 
is excited about the brain, cognitive neuroscience, and/or clinical disorders 
and demonstrates evidence of a serious interest in a career in the field.

If you are interested in being considered for these positions, please apply 
online at https://www.jobsatosu.com/postings/103123 and submit a current CV and 
names of three references.


If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu<mailto:oshe...@osu.edu>

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.


_
David E. Osher, Ph.D.
Assistant Professor of Psychology
The Ohio State University
davidosher.com<https://www.davidosher.com/>
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[Freesurfer] POSTDOC POSITION - modeling the functional and structural architecture of the visual system

[Osher, David E.]

External Email - Use Caution

POSTDOCTORAL SCHOLAR
We are recruiting a Post Doctoral Scholar in the Cognition and Brain Circuitry 
Laboratory of Dr. David Osher at the Ohio State University.  The Post Doctoral 
Scholar will plan, design, and conduct research using computational models to 
investigate the functional and structural architecture of the brain.  This 
position is available for one year with the possibility of extension based on 
satisfactory performance and availability of funds.

Required qualifications include Ph.D. in cognitive neuroscience, psychology, or 
related field; research experience in neuroimaging methods (magnetic resonance 
imaging (MRI), functional magnetic resonance imaging (fMRI), diffusion-weighted 
(DWI,) and/or functional connectivity). Desired qualifications include 
proficiency in coding; interest in any or all of the following: understanding 
the functional and structural architecture of the brain, computational modeling 
of individual differences in brain and behavior (especially in attention and 
perception), training and neural plasticity, and computational models of the 
human visual system.

If you are interested in being considered for this position, please apply 
online at https://www.jobsatosu.com, under job listing #459936 and submit a 
current CV and names of three references.

If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu<mailto:oshe...@osu.edu>

OSU is located in Columbus, Ohio and is home to a vibrant community of 
cognitive neuroscientists, computational modelers, and vision scientists in the 
Psychology Department and Center for Cognitive and Brain Sciences.  Postdocs 
will have access to state-of-the-art MRI and EEG facilities located inside the 
Psychology building.

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.


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[Freesurfer] Two research assistant positions

[Osher, David E.]

External Email - Use Caution

RESEARCH ASSISTANT
We are recruiting 2 technical research assistants in the Cognition and Brain 
Circuitry Laboratory of Dr. David Osher at the Ohio State University. Primary 
duties for both positions include: conducting neuroscience research on the 
functional and structural architecture of the human brain, and its role in 
cognition; programming, running, and analyzing behavioral and brain-imaging 
experiments using functional magnetic resonance imaging (fMRI), diffusion 
weighted imaging (DWI), functional connectivity, and behavioral assessments; 
scoring and coding data; performing statistical analyses using programs such 
as, MATLAB, Python, and shell scripting; recruiting research participants; 
maintaining participant databases; developing outreach letters. Positions are 
available for one year with the possibility of extension based on satisfactory 
performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience. We are seeking an 
aspiring, self-motivated researcher with strong coding/programming skills who 
is excited about the brain, cognitive neuroscience, and/or clinical disorders 
and demonstrates evidence of a serious interest in a career in the field.

If you are interested in being considered for these positions, please apply 
online at https://www.jobsatosu.com, under job listing #459935 (100%) and/or 
#459934 (75%) and submit a current CV and names of three references.

If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu<mailto:oshe...@osu.edu>

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.



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[Freesurfer] version 7 docker container

[David Pagliaccio]

External Email - Use Caution

Hello
I was wondering if Freesurfer version 7 will be released as a container on
docker hub?
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[Freesurfer] Error running recon-all

[David Schwantner]

External Email - Use Caution

Thank you in advance for the assistance!

I am running the following command:

 recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all

The log is at
https://github.com/dschwant/mri_to_3d/blob/master/202004090853_error_recon-all.log,
and the nii file is at
https://github.com/dschwant/mri_to_3d/blob/master/202004_DS_Brain_MRI/1131_T2_raw.nii.gz
.

Here is the tail of the log. As you can see, I am running it in Ubuntu
18.04.4 under the Windows Subsystem for Linux.

...
searching rotation angles z=[-9  5], y=[-22 -8]
searching scale 1 Z rot 5.3  global minimum found at slice 139.0, rotations
(-14.14, -1.42)
final transformation (x=139.0, yr=-14.141, zr=-1.420):
 0.96940   0.02478  -0.24423   8.04082;
-0.02403   0.99969   0.00605  -41.07934;
 0.24430   0.0   0.96970   18.40543;
 0.0   0.0   0.0   1.0;
mri_cc: no WM voxels found with norm > 40 -- check skull stripping

No such file or directory
Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07 15:22:00 PST
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s DS_T2 exited with ERRORS at Thu Apr  9 11:19:24 DST 2020
...


Is it just not enough "details" in the nifti file? I am trying the next
larger one now.
----
David - dschw...@gmail.com

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[Freesurfer] Error running "recon-all"

[David Schwantner]

External Email - Use Caution

Thank you in advance for the assistance!

I am running the following command:

 recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all

I have attached the log file. Here is the tail. As you can see, I am
running it in Ubuntu 18.04.4 under the Windows Subsystem for Linux.

...
searching rotation angles z=[-9  5], y=[-22 -8]
searching scale 1 Z rot 5.3  global minimum found at slice 139.0, rotations
(-14.14, -1.42)
final transformation (x=139.0, yr=-14.141, zr=-1.420):
 0.96940   0.02478  -0.24423   8.04082;
-0.02403   0.99969   0.00605  -41.07934;
 0.24430   0.0   0.96970   18.40543;
 0.0   0.0   0.0   1.0;
mri_cc: no WM voxels found with norm > 40 -- check skull stripping

No such file or directory
Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07 15:22:00 PST
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s DS_T2 exited with ERRORS at Thu Apr  9 11:19:24 DST 2020
...


What other information would be helpful in determining what I need to do to
make this work?
----
David Schwantner
dschw...@gmail.com
(858) 518-7263



recon-all.log
Description: Binary data
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Re: [Freesurfer] Contents of Freesurfer digest...

[David Kamson]

External Email - Use Caution

Martin, thank you for these comments. These are extremely valuable!

Although my patients had tumors, these are cured (this is why I have so few of 
them…) and have no residual mass effect/deformity beyond biopsy tracks / small 
resection cavities. Thus far, I was able to get pretty accurate looking 
segmentations of deep nuclei on aseg. Segmentation issues were associated with 
the surface structures (e.g.  dura/falx being misclassified as gray or brain 
tissue adjacent to resection cavities are correctly classified as brain but 
GM/WM often misclassified).

I’m OK restricting the analysis to ventricular and deep GM volume, since what 
I’m trying to measure is marked atrophy of these structure after chemotherapy 
which I guess is in the range of 1-5%/year. The changes are mostly marked 
enough to enable a visual qualitative analysis, however, quantitative data 
would be clinically more helpful to clarify when, and how much change to expect 
after treatment.

Do you think increasing the number of time points analyzed (I have 4-6 scans 
per year for each patient) could eliminate the noise from head 
positioning/slicing as long as the volumetric trends remain consistent? Again, 
the data would be normalized per individual and I would not use absolute volume 
for any comparative analysis.

Thank you again. This message board is of incredible value!

Best regards,
David




--

Message: 1
Date: Wed, 09 Oct 2019 10:48:48 +0200
From: Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Questions re slice thickness, aseg and
longitudinal analysis
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu<mailto:7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="UTF-8"

Hi David,

I am not very optimistic:

5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You
will certainly get something, but it can be very unreliable and
completely wrong. Especially longitudinally these thick slices will
induce large variance due to different head positioning (and different
slice angulations) in the scanner.

Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
not work if tumor lesions are present.

About your questions:

1. Surfaces update the aseg, but if you are only interested in the
volumes, you can skip this expensive step (potentially at the cost of
slightly higher noise levels in your measurements).

2. I think not (see above). 5mm is too low.

3. Theoretically yes, but I have never tested if the scripts will do
it. You could run up to the aseg in the cross, then create base (up to
aseg) and then run the longs up to aseg. Not even sure you really need
the base aseg. You might be able to just run the initial base
registration step, obtain the transformations and median norm.mgz
image, could be sufficient for the long runs.

4. No. Gad images won't work.

Best, Martin


   External Email - Use Caution
Freesurfers,

First of all, I'd like to express my gratitude to the community for
the support that keeps researchers like myself afloat!


I have a unique set of oncology patients that I want to evaluate for
brain atrophy in a retrospective longitudinal analysis.
I was thinking about using Aseg.auto results to assess longitudinal
volume changes, but before I invest all the time I wanted to check
with the community whether this makes any sense at all:

The dataset that looks like this:
- 22 patients (no control dataset [yet])
- 10-25 MRIs per patient acquired over 2-8 years in relatively
uniform intervals
- Patients had most of their scans on the same scanner, but
scanners differed widely between patients
- All patients have axial T1 post gadolinium scans of 1x1x5mm
resolution (3D acquisition available in <10%)
- About 80% of scans have an axial pre-contrast T1 sequence
- All scans are skullstripped (third party algorithm)

I'm looking for crude changes, no subtleties; volumes of interest
are:
- Whole brain volume
- White matter volume
- Ventricular volume (mainly lateral ventricle)
- Subcortical gray matter volume (whole thalamus most importantly)

I ran a few test analyses and to my surprise I was able to generate
pretty acceptable surfaces, however, topology fixing took about 24H
per scan, and I feel aseg.auto contained all the volumetric data I
was really interested in.

My concrete questions are:
1) Does the full autorecon pipeline affect Aseg.auto? If there is no
benefit, I could reduce the per scan analysis time from 28 hours to
1-2 h.
2) Would this low-resolution dataset be accepted by reviewers if used
for Aseg? Should I do any quantitative validation beyond a visual
quality analysis of Aseg?
3) Can I perform a longitudinal analysis only for the Aseg resu

[Freesurfer] Questions re slice thickness, aseg and longitudinal analysis

[David Kamson]

External Email - Use Caution

Freesurfers,


First of all, I'd like to express my gratitude to the community for the support 
that keeps researchers like myself afloat!



I have a unique set of oncology patients that I want to evaluate for brain 
atrophy in a retrospective longitudinal analysis.

I was thinking about using Aseg.auto results to assess longitudinal volume 
changes, but before I invest all the time I wanted to check with the community 
whether this makes any sense at all:


The dataset that looks like this:

- 22 patients (no control dataset [yet])

- 10-25 MRIs per patient acquired over 2-8 years in relatively uniform intervals

- Patients had most of their scans on the same scanner, but scanners differed 
widely between patients

- All patients have axial T1 post gadolinium scans of 1x1x5mm resolution (3D 
acquisition available in <10%)

- About 80% of scans have an axial pre-contrast T1 sequence

- All scans are skullstripped (third party algorithm)


I'm looking for crude changes, no subtleties; volumes of interest are:

- Whole brain volume

- White matter volume

- Ventricular volume (mainly lateral ventricle)

- Subcortical gray matter volume (whole thalamus most importantly)


I ran a few test analyses and to my surprise I was able to generate pretty 
acceptable surfaces, however, topology fixing took about 24H per scan, and I 
feel aseg.auto contained all the volumetric data I was really interested in.


My concrete questions are:

1) Does the full autorecon pipeline affect Aseg.auto? If there is no benefit, I 
could reduce the per scan analysis time from 28 hours to 1-2 h.

2) Would this low-resolution dataset be accepted by reviewers if used for Aseg? 
Should I do any quantitative validation beyond a visual quality analysis of 
Aseg?

3) Can I perform a longitudinal analysis only for the Aseg results?

4) Is it OK to use T1-gad images for the analysis?


I'd appreciate any input!


Best regards,

David O. Kamson, MD PhD

Neuro-oncology fellow

Johns Hopkins Hospital &

National Institutes of Health


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[Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

[David S Lee]

External Email - Use Caution

Hello FreeSurfer Experts,

I wanted to re-post this question (posted June 4th), yet did not receive
your guidance:

I have visually checked 116 subjects that have been processed using
Freesurfer's latest hippocampal/amygdala subfield segmentation
algorithm (Development
version 20180518
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala>)
and came across 5 cases that failed the QC. My T1s had been processed using
FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev
version.

- 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but
in the volumetric output, there are values for the regions.

- 2 subjects' medical nuclei masks are located in the Putamen region (more
superior/detached from the rest of the amygdala).

I found the exact same inquiry RE: AAA region posted on April 30, 2019, but
I did not see any response.

What would be your recommended course of action to resolve these issues?
Is there a way to see volumetric measures in the freeview GUI (when
clicking a region) to possibly manually trace the missing regions?

Thank you for your time,


-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

[David S Lee]

External Email - Use Caution

Hello FreeSurfer Experts,

I have visually checked 116 subjects that have been processed using
Freesurfer's
latest hippocampal/amygdala subfield segmentation algorithm (Development
version 20180518
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala>)
and came across 5 cases that failed the QC. My T1s had been processed using
FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev
version.

- 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but
in the volumetric output, there are values for the regions.

- 2 subjects' medical nuclei masks are located in the Putamen region (more
superior/detached from the rest of the amygdala).

I found the exact same inquiry RE: AAA region posted on April 30, 2019, but
I did not see any response.

What would be your recommended course of action to resolve these issues?
Is there a way to see volumetric measures in the freeview GUI (when
clicking a region) to possibly manually trace the missing regions?

Thank you for your time,


-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] ExploreDTI Workshop in May@Budapest

[Szabolcs David]

External Email - Use Caution

ExploreDTI Workshop -  A course on processing, analyzing, and visualizing
diffusion MRI data
When: 27-29 May, 2019
Where: Budapest, Hungary
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs

>
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[Freesurfer] extracting the version of FreeSurfer used to process some data

[David Groppe]

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Hi FreeSurfers,
   I'm working with some data that has been collected and processed with
FreeSurfer over several years. Consequently, some individuals have been
processed with different versions of FreeSurfer. Is there a file in an
individual's subject directory that specifies which version of FreeSurfer
was used to create it?
   much thanks,
   -David
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[Freesurfer] GM and WM intensity thresholds (Manual Edits)

[David S Lee]

External Email - Use Caution

Hello FreeSurfer Experts!

I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w
scans through recon-all pipeline. The correction has solved many
segmentation errors which reduced the time spent on manual editing. I have
several questions related to this:

1. I am aware of the "3T" flag that can be supplied to recon-all command.
It seems redundant to use this flag for already-bias-corrected 3T scans
(testing from my end also confirms this), but do you recommend any other
bias-correction steps?

2. What are the minimum and maximum intensity thresholds set for GM and WM
during recon-all? In the official control point tutorial
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0>,
it suggests that WM should be "close" to intensity of 110, but I wanted to
know the exact thresholds to perform more accurate manual editing.

3. If these GM and WM intensity parameters can be changed from default, do
you recommend doing so?

If there is a documentation I can refer to find answers (I've failed to
find one so far), please let me know.

Thank you for your time as always,

-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Gray Matter Manual Edit Reverting

[David S Lee]

External Email - Use Caution

Hello Bruce,

Thank you for the quick response.

I unchecked "do not draw on voxels in the range of" in the "Recon Edit"
window, and I was able to get the clone to work nicely.

Thank you for your time!

David

On Mon, Nov 19, 2018 at 1:38 PM David S Lee  wrote:

> Hello Experts,
>
> I am currently using FreeSurfer version 6.0 to make manual edits to T1w
> images. In an earlier version 5.3,  when GM has been erroneously removed, I
> used the "clone tool" to bring back voxels based on the original T1w.
> However, this tool seems to be not working in 6.0. Would you be able to
> help me troubleshoot this? If there is a better alternative to revert GM
> removal, please let me know!
>
> Thank you for your help.
>
> --
> David S. Lee
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin - Madison
> (608) 890-1115
>


-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] Gray Matter Manual Edit Reverting

[David S Lee]

External Email - Use Caution

Hello Experts,

I am currently using FreeSurfer version 6.0 to make manual edits to T1w
images. In an earlier version 5.3,  when GM has been erroneously removed, I
used the "clone tool" to bring back voxels based on the original T1w.
However, this tool seems to be not working in 6.0. Would you be able to
help me troubleshoot this? If there is a better alternative to revert GM
removal, please let me know!

Thank you for your help.

-- 
David S. Lee
Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream

[Pagliaccio, David (NYSPI)]

External Email - Use Caution

Hello,
Our lab has been running a set of data from a pre/post-treatment study through 
the FreeSurfer v6 pipeline. I was comparing the pre-treatment structural values 
initially run through the cross-sectional pipeline with the same pre-treatment 
data later run through the longitudinal pipeline and was seeing the same issue 
as has been previously posted about (msg52994). Particularly, one cortical 
region of interest shows on average 0.24mm (8.8%) larger cortical thickness 
values processed in the longitudinal pipeline vs. the cross-sectional pipeline. 
While all participant’s data showed increased thickness in this area with the 
longitudinal vs. cross-sectional pipeline, this was not at all consistent 
across participants (ranging from 0.08 to 0.47mm differences [3-18%]). While 
the longitudinal pipeline would increase reliability and sensitivity comparing 
the pre to post-scans, we are just very concerned about these major and 
inconsistent differences analyzing the same baseline data with the different 
pipelines. Particularly, we have some attrition so most participants have 2 but 
some have only 1 scan and thus this feels like it could introduce systematic 
bias in overall thickness.
Any input would be appreciated!
David
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[Freesurfer] 3T Intensity Normalization (Re-Submission)

[David S Lee]

External Email - Use Caution

Hello Experts,

I believe -3T Flag can be used with "recon-all" on scans collected by 3T
scanners. I believe it performs intensity normalization to set white matter
intensity threshold at 110. I am hoping to learn more about the flag option
as it produces slightly better output for me.

Would you be able to guide me to a documentation on this -3T flag?

Thank you!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] FreeSurfer Manual Edit Sequence

[David S Lee]

External Email - Use Caution

Hello Experts,

When performing manual edits on brain masks, white matter, and gray matter,
do I have to strictly follow the sequences(process stages) listed here
<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>?

For instance, the link suggests that "autorecon2-pial is used after editing
brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before
"autorecon2-wm"?

Thank you for your time,
-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] ExploreDTI Workshop in September 2018

[Szabolcs David]

External Email - Use Caution

 ExploreDTI Workshop -  A course on processing, analyzing, and visualizing
diffusion MRI data
When: 10-12 September, 2018
Where: Utrecht, Netherlands
Details: http://www.exploredti.com/workshop

See you soon in the early Dutch autumn ;)

Best,
Szabolcs
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] ASEG Extraction Inquiry

[David S Lee]

External Email - Use Caution

Hi FreeSurfer Experts,

I have extracted ASEG volumes using "asegstats2table" and have a few
questions about the output.

1. I get values of "0" for Left and Right "WM-hypointensities" as well as
"non-WM-hypointensities". Does the ASEG segmentation for WM-hypointensities
only produce whole brain measures (Left and Right combined) ?

2. Most measures are separated by Left and Right, but some are not. So, are
these values pertinent to both hemispheres (whole brain?)

3. Is there a reference page I can check to see what each of the measures
mean (i.e. atlas)?

Thank you for your time!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] transforming functional volumes to MNI without resampling

[David Beeler]

External Email - Use Caution

Alright thanks, mri_coreg looks a little better than bbregister. But similar to 
bbregister, using 6 dof results in a brain that is a little too small and using 
12 dof has both scaling and translation issues.


What would be the way to use CVS? I tried using the m3z from mri_cvs_register 
as described in my first message, but got those weird artifacts 
(http://web.mit.edu/dsbeeler/www/images/m3z-mni.png).


DB


 



Douglas N. Greve wrote:


Use mri_coreg instead of bbregister. Make sure to use 12 DOF. You could
use CVS as well since that is non-linear



> 


On 05/07/2018 04:11 PM, David Beeler wrote:
>
>
> Hi Doug,
> Ok so if I am understanding correctly, SPM or FSL will be better at
> registering functional data to CVS or MNI space for group analyses than
> freesurfer will be because they have the capability of doing nonlinear
> registrations. If that's the case I may give SPM a shot and compare the
> results.
> But if I were to use freesurfer to do this registration, is there something
> better than the following commands?:
> bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --bold
>
> mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg
> --no-resample --nearest
> Adding --12 to bbregister and using the same mri_vol2vol as above actually
> makes the transformation much worse, is there something I'm missing? I will
> use SPM if I have to, but I feel like there is probably something smarter I
> could be doing with freesurfer. And for clarification, is the --12 flag in
> bbregister making the registration affine (ie accounting for translation,
> rotation, scaling, and sheers)?
> Thanks again for your help, much appreciated!
> DB
> 
> Douglas N. Greve wrote:
> If that is really what you want to do, you should use a tool appropriate
> for this type of analysis (eg, SPM and FSL have non-linear intersubject
> registration)
> ----
>
> On 05/04/2018 01:13 PM, David Beeler wrote:
> >
> >
> > Hi Doug,
> >
> > funcVol is an individual functional resting state scan. We are doing
> > some clustering analyses and trying to visually compare the clustering
> > across subjects (I would be a bit sketched out trying to quantify the
> > overlap between subjects due to individual differences in anatomy,
> > etc, but just looking at it might give us a clue on what is going on).
> > We do all our analyses in the individual subject's native space, but
> > it's hard to see what the similarities / differences are.
> >
> > If not bbregister, what would be the correct way to align all subjects
> > to a common space?
> >
> > Thanks,
> > DB
> > 
> > Douglas N. Greve wrote:
> > What is funcVol? An individual functional? If so, then use --12 (12 dof
> > to account for scaling). In general, we don't recommend doing cross
> > subject registration with BBR as it is really not appropriate for that
> > kind of thing.
> > 
> > On 05/03/2018 01:30 PM, David Beeler wrote:
> >
> > Hi,
> >
> > I'm trying to register and transform some raw functional data
> > (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low
> > res dimensions.
> >
> > I have tried:
> > bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl
> > --bold
> > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg
> > --no-resample --nearest
> > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg
> > --no-resample
> >
> > And this looks pretty good, but not perfect... the functional data is
> > oriented correctly but the brain seems to be a centimeter or two
> > smaller in multiple dimensions, see:
> >
> > http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png
> >
> > I'm not too surprised since the MNI brain is blurry and oddly round,
> > but presumably there is a way to do this transformation more
> > accurately. I've run mri_cvs_register for this subject using the --mni
> > flag:
> >
> > mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir
> >
> > And for other applications I use this m3z file to transform volumes
> > between MNI orig.mgz and individual subject orig.mgz, but is there a
> >

Re: [Freesurfer] transforming functional volumes to MNI without resampling

[David Beeler]

External Email - Use Caution

Hi Doug,


Ok so if I am understanding correctly, SPM or FSL will be better at registering 
functional data to CVS or MNI space for group analyses than freesurfer will be 
because they have the capability of doing nonlinear registrations. If that's 
the case I may give SPM a shot and compare the results.


But if I were to use freesurfer to do this registration, is there something 
better than the following commands?:


bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --bold


mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample --nearest


Adding --12 to bbregister and using the same mri_vol2vol as above actually 
makes the transformation much worse, is there something I'm missing? I will use 
SPM if I have to, but I feel like there is probably something smarter I could 
be doing with freesurfer. And for clarification, is the --12 flag in bbregister 
making the registration affine (ie accounting for translation, rotation, 
scaling, and sheers)?


Thanks again for your help, much appreciated!

DB



Douglas N. Greve wrote:


If that is really what you want to do, you should use a tool appropriate
for this type of analysis (eg, SPM and FSL have non-linear intersubject
registration)



On 05/04/2018 01:13 PM, David Beeler wrote: > > > Hi Doug, > > funcVol is an 
individual functional resting state scan. We are doing > some clustering 
analyses and trying to visually compare the clustering > across subjects (I 
would be a bit sketched out trying to quantify the > overlap between subjects 
due to individual differences in anatomy, > etc, but just looking at it might 
give us a clue on what is going on). > We do all our analyses in the individual 
subject's native space, but > it's hard to see what the similarities / 
differences are. > > If not bbregister, what would be the correct way to align 
all subjects > to a common space? > > Thanks, > DB > 
 > 
Douglas N. Greve wrote: > What is funcVol? An individual functional? If so, 
then use --12 (12 dof > to account for scaling). In general, we don't recommend 
doing cross > subject registration with BBR as it is really not appropriate for 
that > kind of thing. > 
---- > On 
05/03/2018 01:30 PM, David Beeler wrote: > > Hi, > > I'm trying to register and 
transform some raw functional data > (108x108x72x175, 2mm iso voxels) to MNI 
space, while keeping the low > res dimensions. > > I have tried: > bbregister 
--s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl > --bold > 
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > 
--no-resample --nearest > mri_vol2vol --mov funcVol --reg func2mni.lta --o 
funcVolMNI --fstarg > --no-resample > > And this looks pretty good, but not 
perfect... the functional data is > oriented correctly but the brain seems to 
be a centimeter or two > smaller in multiple dimensions, see: > > 
http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png > > I'm not too 
surprised since the MNI brain is blurry and oddly round, > but presumably there 
is a way to do this transformation more > accurately. I've run mri_cvs_register 
for this subject using the --mni > flag: > > mri_cvs_register --openmp 8 --mni 
--mov $subjID --outdir $mniDir > > And for other applications I use this m3z 
file to transform volumes > between MNI orig.mgz and individual subject 
orig.mgz, but is there a > way to use it to transform functional data to MNI 
space while keeping > the functional dimensions? > > I could do: > > 
mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > --reg 
register.dof6.lta --nearest --o template-in-anat.nii.gz > > mri_vol2vol 
--noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > --mov 
template-in-anat.nii.gz --m3z > $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
--o > template-in-MNI-m3z.nii.gz --nearest > > But not only is this unideal 
because it requires upsampling the > functional data to 256x256x256, it also 
gets these funky wavy distortions: > > 
http://web.mit.edu/dsbeeler/www/images/m3z-mni.png > > > Any thoughts are 
appreciated, thanks! > > -DB > > > 
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Re: [Freesurfer] transforming functional volumes to MNI without resampling

[David Beeler]

External Email - Use Caution

Hi Doug,

funcVol is an individual functional resting state scan. We are doing some 
clustering analyses and trying to visually compare the clustering across 
subjects (I would be a bit sketched out trying to quantify the overlap between 
subjects due to individual differences in anatomy, etc, but just looking at it 
might give us a clue on what is going on). We do all our analyses in the 
individual subject's native space, but it's hard to see what the similarities / 
differences are.

If not bbregister, what would be the correct way to align all subjects to a 
common space?

Thanks,
DB



Douglas N. Greve wrote:


What is funcVol? An individual functional? If so, then use --12 (12 dof
to account for scaling). In general, we don't recommend doing cross
subject registration with BBR as it is really not appropriate for that
kind of thing.




On 05/03/2018 01:30 PM, David Beeler wrote:

Hi,

I'm trying to register and transform some raw functional data (108x108x72x175, 
2mm iso voxels) to MNI space, while keeping the low res dimensions.

I have tried:
bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample --nearest
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample

And this looks pretty good, but not perfect... the functional data is oriented 
correctly but the brain seems to be a centimeter or two smaller in multiple 
dimensions, see:

http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png

I'm not too surprised since the MNI brain is blurry and oddly round, but 
presumably there is a way to do this transformation more accurately. I've run 
mri_cvs_register for this subject using the --mni flag:

mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir

And for other applications I use this m3z file to transform volumes between MNI 
orig.mgz and individual subject orig.mgz, but is there a way to use it to 
transform functional data to MNI space while keeping the functional dimensions?

I could do:

mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --reg 
register.dof6.lta --nearest --o template-in-anat.nii.gz

mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --mov 
template-in-anat.nii.gz --m3z $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
--o template-in-MNI-m3z.nii.gz --nearest

But not only is this unideal because it requires upsampling the functional data 
to 256x256x256, it also gets these funky wavy distortions:

http://web.mit.edu/dsbeeler/www/images/m3z-mni.png


Any thoughts are appreciated, thanks!

-DB
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[Freesurfer] (Follow-Up) Interaction Contrast

[David S Lee]

External Email - Use Caution

Dear Douglas,


Thank you for your guidance.


I am following-up on your response with regards to setting up DODS
matrix to test interaction between two continous covariates. If I
understand your recommendation correctly (please correct me if I am
wrong), I am averegaing slopes for the new interaction covairate
(age*weight), while regressing out slope estimates for age and weight.
I am curious to know why regressing out the two original covariates is
recommended.


Thanks for your time!


David

_


You need to put in age, weight, AND age*weight. If you have two classes and
use DODS, then the contrast would be

0 0 0 0 0 0 0.5 0.5

On 4/13/18 8:02 PM, David S Lee wrote:

Hi Douglas,

Thank you for your reply.


To follow up, I am setting up GLM analysis with 1 categorical variable and
1 continuous variable (age X weight). Myfsgd looks like this:

/GroupDescriptorFile 1/
/Title Cortical Thickness Interaction between Age and Weight/
/Class class1 plus blue/
/Class class2 circle green/
/Variable   Demean Age X Demean Weight/
/Input001Class1500/
/Input002Class2433/
/.../


I want to test for an interaction between age and weight while controlling
forgroup. Instead ofputting-inage and weight separately, I multiply them to
test for interaction. Can you tell me if following contrast vector will
correctly test for this?

/0 0 0.5 0.5/
/
/
Thank you for your time,
/
/
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115 <tel:%28608%29%20890-1115>


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[Freesurfer] transforming functional volumes to MNI without resampling

[David Beeler]

External Email - Use Caution

Hi,

I'm trying to register and transform some raw functional data (108x108x72x175, 
2mm iso voxels) to MNI space, while keeping the low res dimensions.

I have tried:
bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample --nearest
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample

And this looks pretty good, but not perfect... the functional data is oriented 
correctly but the brain seems to be a centimeter or two smaller in multiple 
dimensions, see:

http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png

I'm not too surprised since the MNI brain is blurry and oddly round, but 
presumably there is a way to do this transformation more accurately. I've run 
mri_cvs_register for this subject using the --mni flag:

mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir

And for other applications I use this m3z file to transform volumes between MNI 
orig.mgz and individual subject orig.mgz, but is there a way to use it to 
transform functional data to MNI space while keeping the functional dimensions?

I could do:

mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --reg 
register.dof6.lta --nearest --o template-in-anat.nii.gz

mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --mov 
template-in-anat.nii.gz --m3z $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
--o template-in-MNI-m3z.nii.gz --nearest

But not only is this unideal because it requires upsampling the functional data 
to 256x256x256, it also gets these funky wavy distortions:

http://web.mit.edu/dsbeeler/www/images/m3z-mni.png


Any thoughts are appreciated, thanks!

-DB
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[Freesurfer] QDEC Interaction of Two Covariates

[David S Lee]

External Email - Use Caution

Hi FreeSurfer Experts,

I want to test the relationship between cortical thickness and two
continuous covariates (interaction) while controlling for one categorical
variable. In QDEC, I can only choose one covariate, so I created a new
variable that is a dot product (covariate1*covariate2) of the two to
represent interaction. After analyzing, when I look at the data points at a
single voxel, there is no visual indication of interaction. There also is
no fitted line.

Am I utilizing QDEC correctly?

Thank you for your help!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] Group Analysis Contrast (Follow-up)

[David S Lee]

Hi Douglas,

Thank you for your reply.

To follow up, I am setting up GLM analysis with 1 categorical variable and
1 continuous variable (age X weight). My fsgd looks like this:

*GroupDescriptorFile 1*
*Title Cortical Thickness Interaction between Age and Weight*
*Class class1 plus blue*
*Class class2 circle green*
*Variable   Demean Age X Demean Weight*
*Input 001 Class1 500*
*Input 002 Class2 433*
*...*

I want to test for an interaction between age and weight while controlling
for group. Instead of putting-in age and weight separately, I multiply them
to test for interaction. Can you tell me if following contrast vector will
correctly test for this?

*0 0 0.5 0.5*

Thank you for your time,

--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] RV: "preproc-sess" with intermediate volume

[David Sánchez Bestué]

Thank you very much!!

De: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve 
<dgr...@mgh.harvard.edu>
Enviado: jueves, 12 de abril de 2018 16:39
Para: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] RV: "preproc-sess" with intermediate volume

Hi David, move your intermediate volume to

session_1/ifsd/001/orig.mgz

then try


-bbr-int ifsd orig



On 04/12/2018 04:10 AM, David Sánchez Bestué wrote:
> Dear all,
>
> I have a problem with the command:
> "preproc-sess"
>
> I wanted to use the Registration option to add an intermediate volume.
> The only documentation I could find about it was the one that appears
> with the command: "preproc-sess --help"
>
> Registration options
>   -init-fsl : use fsl to initialize bbr registration
>   -init-spm : use spm to initialize bbr registration (needs matlab)
>   -init-header : use geometry to initialize bbr registration
>   -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem
>
>
> I used the last flag in my line as follows:
>
> preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5
> -per-run -bbr-int ifsd istem
>
> I got this error:
>
> ERROR: could not determine file for ifsd/001/istem
>
>
> It seems that the path is not working but I do not why. The relevant
> paths are this:
>
> session_1/bold/001/f.nii
> session_1/ifsd/001/istem/orig.mgz
>
> Any help would be really appreciated!
>
> Thank you all
>
> Bests,
>
> David
>
>
>
>
>
>
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[Freesurfer] Group Analysis Design Matrix

[David S Lee]

Hi FreeSurfer Experts,

I have two groups (Male and Female) and two covariates (Age and Weight). I
want to test change of cortical thickness with age and weight, after
removing effects of Group. In other words, is there an interaction between
age and weight, regressing out the effects of groups.

How can I set up my Design Matrix to test this?

Thank you,

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] RV: "preproc-sess" with intermediate volume

[David Sánchez Bestué]

Dear all,

I have a problem with the command:
"preproc-sess"

I wanted to use the Registration option to add an intermediate volume. The only 
documentation I could find about it was the one that appears with the command: 
"preproc-sess --help"

Registration options
  -init-fsl : use fsl to initialize bbr registration
  -init-spm : use spm to initialize bbr registration (needs matlab)
  -init-header : use geometry to initialize bbr registration
  -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem


I used the last flag in my line as follows:

preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run 
-bbr-int ifsd istem

I got this error:

ERROR: could not determine file for ifsd/001/istem


It seems that the path is not working but I do not why. The relevant paths are 
this:

session_1/bold/001/f.nii
session_1/ifsd/001/istem/orig.mgz

Any help would be really appreciated!

Thank you all

Bests,

David




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Re: [Freesurfer] Surface label to volume and then back to surface

[David Beeler]

Hi Doug, thanks for the explanation! Also --projfrac-max -.1 1 .1 is a big 
improvement, I think it should be good for my purposes. Feeling good about this 
now!

Cheers,
DB
___

On 04/11/2018 12:44 PM, David Beeler wrote:

> Hi Doug, thanks for the response! So it looks like my initial 
> transform from surface label to anatomical volume wasn't working 
> because my template.nii.gz and brainmask were in a different space 
> than the functional data I was processing. This happened because I was 
> taking the raw f.nii.gz, doing some transformations first, and saving 
> it to a file called f_reg.nii.gz. I was then trying to run 
> preproc-sess using the -i flag to specify this f_reg.nii.gz, but when 
> preproc runs mktemplate-sess it still uses f.nii.gz to make the 
> template, regardless of what the -i or -mcin flags say. I just added a 
> line in the if($DoTemplate) section of preproc-sess to have the option 
> of adding a -funcstem and it worked fine. I have now updated my 
> preprocessing to run all the commands individually instead of using 
> preproc-sess at all, and I'm probably going to send another message to 
> this list later making sure I'm doing that correctly. Additionally, 
> Re: "I think you could do it with a single call to mri_label2vol using 
> --regheader and specifying the func template." This works great! 
> Thanks for the shortcut. I got the surface label direct to functional 
> volume transform working with: mri_vol2vol --regheader --mov 
> $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ 
> $MEANFUNCDIR/meanfunc.nii.gz --o 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --nearest But I'm still 
> not entirely sure exactly what information is contained in regheader 
> (or where I can view this information). The reason I have been using 
> regheader instead of register.dof6.lta is that my functional data is 
> aligned to the anatomical prior to running preprocessing, and my 
> understanding was that using regheader would just downsample (similar 
> to mri_convert) and I wouldn't need to specify a registration file. Is 
> this a flawed understanding of regheader?

Regheader assumes that the two volumes "share a RAS space". This is a 
little hard to explain. Each volume has some geometry information in it 
that determines where a voxel is in RAS (right, anterior, superior) 
space. --regheader assumes that the RAS space is the same, so, if the 
RAS for voxel in volume 1 is the samseg as that of a voxel in volume2, 
then they must represent the same place anatomically. If you have 
already resampled your functional data into the 1mm, 256^3 anatomical 
space, then --regheader should work ok

> So transforming to functional space seems to be okay now, but 
> transforming back to the surface is still not perfect. I tried 
> mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz 
> --regheader $SUBJID --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/regheadersurface.nii.gz and also bbregister --s $SUBJID 
> --reg $OUTPUTDIR/testreg.lta --mov $MEANFUNCDIR/meanfunc.nii.gz 
> --init-fsl --bold mri_vol2surf --mov 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg 
> $OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/testregsurface.nii.gz Which both give essentially the same 
> result: Original Label: 
> http://web.mit.edu/dsbeeler/www/images/MTlabel.png Back to Surface 
> Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png This is 
> actually much better than it was, but is there a way to get rid of the 
> patchiness?

The patchiness is caused by something else. When you run vol2surf, you 
can try --projfrac-max -.1 1 .1 That should reduce the patchiness. If it 
is still not tolerable, then let me know

> Again, thanks for all the useful info!
> David
> __
> Hi David, I've tried to answer your questions below.
>
> doug
> On 03/30/2018 01:48 PM, David Beeler wrote:
> > Hi all,
> > Sorry in advance, this is a bit of an annoying one!
> >
> > I am trying to use freesurfer's automatically generated MT label as a 
> > parcel to constrain activity measured during a functional MT 
> > localizer. I am currently doing my analysis in the volume and I'd like 
> > to transform the MT surface label into the subject's volume functional 
> > space (i.e. the same space as the sig.nii.gz for a particular 
> > contrast), take the voxels in sig.nii.gz that are within the MT label, 
> > and project them back onto the surface (preferably to be viewed as an 
> > overlay with freeview). I will eventually run the analysis on the 
> > surface as well (making this much less roundabout, but I also use 
> > volume parcels so understanding how to corre

Re: [Freesurfer] Surface label to volume and then back to surface

[David Beeler]

Hi Doug, thanks for the response!

So it looks like my initial transform from surface label to anatomical volume 
wasn't working because my template.nii.gz and brainmask were in a different 
space than the functional data I was processing. This happened because I was 
taking the raw f.nii.gz, doing some transformations first, and saving it to a 
file called f_reg.nii.gz. I was then trying to run preproc-sess using the -i 
flag to specify this f_reg.nii.gz, but when preproc runs mktemplate-sess it 
still uses f.nii.gz to make the template, regardless of what the -i or -mcin 
flags say. I just added a line in the if($DoTemplate) section of preproc-sess 
to have the option of adding a -funcstem and it worked fine. I have now updated 
my preprocessing to run all the commands individually instead of using 
preproc-sess at all, and I'm probably going to send another message to this 
list later making sure I'm doing that correctly.

Additionally, Re: "I think you could do it with a single call to
mri_label2vol using --regheader and specifying the func template."

This works great! Thanks for the shortcut. I got the surface label direct to 
functional volume transform working with:

mri_vol2vol --regheader --mov $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ 
$MEANFUNCDIR/meanfunc.nii.gz --o $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz 
--nearest

But I'm still not entirely sure exactly what information is contained in 
regheader (or where I can view this information). The reason I have been using 
regheader instead of register.dof6.lta is that my functional data is aligned to 
the anatomical prior to running preprocessing, and my understanding was that 
using regheader would just downsample (similar to mri_convert) and I wouldn't 
need to specify a registration file. Is this a flawed understanding of 
regheader?

So transforming to functional space seems to be okay now, but transforming back 
to the surface is still not perfect.

I tried
mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --regheader 
$SUBJID --projfrac 0.5 --interp nearest --hemi rh --o 
$OUTPUTDIR/regheadersurface.nii.gz

and also

bbregister --s $SUBJID --reg $OUTPUTDIR/testreg.lta --mov 
$MEANFUNCDIR/meanfunc.nii.gz --init-fsl --bold

mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg 
$OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o 
$OUTPUTDIR/testregsurface.nii.gz

Which both give essentially the same result:
Original Label: http://web.mit.edu/dsbeeler/www/images/MTlabel.png
Back to Surface Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png
This is actually much better than it was, but is there a way to get rid of the 
patchiness?


Again, thanks for all the useful info!

David

__


Hi David, I've tried to answer your questions below.

doug


On 03/30/2018 01:48 PM, David Beeler wrote:
> Hi all,
> Sorry in advance, this is a bit of an annoying one!
>
> I am trying to use freesurfer's automatically generated MT label as a
> parcel to constrain activity measured during a functional MT
> localizer. I am currently doing my analysis in the volume and I'd like
> to transform the MT surface label into the subject's volume functional
> space (i.e. the same space as the sig.nii.gz for a particular
> contrast), take the voxels in sig.nii.gz that are within the MT label,
> and project them back onto the surface (preferably to be viewed as an
> overlay with freeview). I will eventually run the analysis on the
> surface as well (making this much less roundabout, but I also use
> volume parcels so understanding how to correctly go between the volume
> and surface is important to me).
>
> In my pipeline I start off by running preproc-sess, then I register
> and transform my preprocessed functional data (fmcpr.nii.gz) to the
> subject's anatomical (without upsampling). After doing mkanalysis and
> mkcontrast, I run selxavg on this volume. So the functional data is
> aligned with the anatomical, but still has low res dimensions.
>
> If it's not too much to ask, would it be possible to provide the
> specific commands to do all these transformations properly? I'll
> provide some of the commands I've tried below so you can see where I'm
> going wrong:
>
> First I want to transform the MT label to the functional volume. I've
> tried:
>
> mri_label2vol --subject $SUBJID --label
> $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o
> $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp
> $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh
>
> ...which I would expect to put the label in high resolution anatomical
> volume space (orig.mgz), but it doesn't fill the graymatter ribbon
> nicely at all.
I  would have expected this to work. Can you send a pic? I just ran it
myself, and it seemed to do ok.
>
> I then use mri_vol2vol to transform to functiona

[Freesurfer] Surface label to volume and then back to surface

[David Beeler]

Hi all,
Sorry in advance, this is a bit of an annoying one!

I am trying to use freesurfer's automatically generated MT label as a parcel to 
constrain activity measured during a functional MT localizer. I am currently 
doing my analysis in the volume and I'd like to transform the MT surface label 
into the subject's volume functional space (i.e. the same space as the 
sig.nii.gz for a particular contrast), take the voxels in sig.nii.gz that are 
within the MT label, and project them back onto the surface (preferably to be 
viewed as an overlay with freeview). I will eventually run the analysis on the 
surface as well (making this much less roundabout, but I also use volume 
parcels so understanding how to correctly go between the volume and surface is 
important to me).

In my pipeline I start off by running preproc-sess, then I register and 
transform my preprocessed functional data (fmcpr.nii.gz) to the subject's 
anatomical (without upsampling). After doing mkanalysis and mkcontrast, I run 
selxavg on this volume. So the functional data is aligned with the anatomical, 
but still has low res dimensions.

If it's not too much to ask, would it be possible to provide the specific 
commands to do all these transformations properly? I'll provide some of the 
commands I've tried below so you can see where I'm going wrong:

First I want to transform the MT label to the functional volume. I've tried:

mri_label2vol --subject $SUBJID --label $SUBJECTS_DIR/$SUBJID/label/rh.MT.label 
--o $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp 
$SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh

...which I would expect to put the label in high resolution anatomical volume 
space (orig.mgz), but it doesn't fill the graymatter ribbon nicely at all.

I then use mri_vol2vol to transform to functional/sig.nii.gz space (I could 
also just downsample with mri_convert since I've already aligned my sig.nii.gz 
to my anatomical, this gives me the same result). I am using regheader here, is 
this okay?

mri_vol2vol --regheader --mov $OUTPUTDIR.rh.MT.volume.anat.nii.gz --targ 
meanfunc.nii.gz --o rh.MT.volume.func.nii.gz --nearest

...and this works pretty well, but it's a little sparse so I may need to dilate 
it with mri_morphology. I think this step is fine.

Next I use matlab to take the voxels in sig.nii.gz that are also in 
rh.MT.volume.func.nii.gz and I save that as a new volume, say 
constrainedsig.nii.gz. Now I want to transform constrainedsig.nii.gz to the 
surface. I have tried going directly using the register.dof6.lta generated from 
preproc-sess:

mri_vol2surf --mov constrainedsig.nii.gz --reg register.dof6.lta --projfrac 0.5 
--interp nearest --hemi rh --o $OUTPUTDIR/constrainedsig_surface.nii.gz

... and this is in the right area, but its shape doesn't match the shape of the 
original label. So I've also tried backtracking and doing another vol2vol and 
then vol2surf with regheader:

mri_vol2vol --regheader --mov constrainedsig.nii.gz --targ 
$SUBJECTS_DIR/$SUBJID/mri/orig.mgz --o 
$OUTPUTDIR/constainedsig_anatvolume.nii.gz

mri_vol2surf --mov constrainedsig_anatvolume.nii.gz --hemi rh --regheader S02 
--o $OUTPUTDIR/constrainedsig_anatsurface

...and while this ends up in the right place, it is really patchy (looking kind 
of like twisty zebra stripes). Seems to me like it has the wrong dimensions or 
something, but mri_info says it's the same dimensions as the volume I 
originally created with mri_label2vol.

Any help is much appreciated, thanks!
David
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[Freesurfer] "preproc-sess" with intermediate volume

[David Sánchez Bestué]

Dear all,

I have a problem with the command:
"preproc-sess"

I wanted to use the Registration option to add an intermediate volume. The only 
documentation I could find about it was the one that appears with the command: 
"preproc-sess --help"

Registration options
  -init-fsl : use fsl to initialize bbr registration
  -init-spm : use spm to initialize bbr registration (needs matlab)
  -init-header : use geometry to initialize bbr registration
  -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem


I used the last flag in my line as follows:

preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run 
-bbr-int ifsd istem

I got this error:

ERROR: could not determine file for ifsd/001/istem


It seems that the path is not working but I do not why. The relevant paths are 
this:

session_1/bold/001/f.nii
session_1/ifsd/001/istem/orig.mgz

Any help would be really appreciated!

Thank you all

Bests,

David




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Re: [Freesurfer] Registering functional data between scan sessions

[David Beeler]

Awesome, thanks Doug!


For clarity, I got it working with:


bbregister --s  --mov  --reg day1func-to-day1anat.lta 
--init-fsl --bold

bbregister --s  --mov  --reg day2func-to-day2anat.lta 
--init-fsl --bold

bbregister --s  --mov $SUBJECTS_DIR//mri/brain.mgz 
--reg day1anat-to-day2anat.lta --init-fsl --t1

mri_concatenate_lta day1func-to-day1anat.lta day1anat-to-day2anat.lta 
test/day1func-to-day2anat.lta

mri_concatenate_lta -invert2 day1func-to-day2anat.lta day2func-to-day2anat.lta 
day1func-to-day2func.lta

mri_vol2vol --mov  --targ  --reg 
day1func-to-day2func.lta --o day1func-in-day2func.nii.gz


Cheers,

DB
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[Freesurfer] Registering functional data between scan sessions

[David Beeler]

Hi,

I have some functional data for the same localizer (dimensions 80x80x38x246) 
that was acquired in the same subject on two separate days. I would like day 
1's raw data to be spatially aligned to the anatomical taken on day 2, but 
still have the low resolution dimensions of functional space. This question has 
been asked a couple times before in various forms, but I can't seem to find a 
clear answer of how to do this correctly.

Anatomicals were collected on both days, so I figured I could do something like 
this:

mri_vol2vol --nearest --regheader --mov day1-f.nii.gz --targ 
$SUBJECTS_DIR/S03/mri/brain.mgz --o day1-f-in-day1-3danat.nii.gz

bbregister --s S03_day1 --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --reg 
day1-to-day2.lta --init-fsl --t1

mri_vol2vol --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --targ 
day1-f-in-day1-3danat.nii.gz --o day1-f-in-day2-3danat.nii.gz --reg 
day1-to-day2.lta --nearest --inv

mri_vol2vol --regheader --mov day1-f-in-day2-3danat.nii.gz --targ day2-f.nii.gz 
--o day1-f-in-day2-func.nii.gz

but this is a bad solution because I shouldn't have to actually upsample every 
time point to high resolution space and then back down again. I figure there 
must be a way to use the --no-resample flag of mri_vol2vol or something to keep 
the voxel number (relatively) low and just use the transformation matrix 
information to go straight from day 1 functional to day 2 functional.

Let me know if you have any ideas, thanks!
David
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[Freesurfer] FreeSurfer Error Edit Sequence

[David S Lee]

Hello Experts,

Do you suggest FreeSurfer users to *strictly* follow the *error edit
sequence* (Brain Mask --> WM --> GM --> Control Points) listed here (link
below)?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

If not, can users follow this sequence instead: Brain Mask --> Control
Points --> GM --> WM? The justification here is to minimize the time spent
to perform hand edits.

Thank you for your time,

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] FreeSurfer Edit Sequence Inquiry

[David S Lee]

Hello FreeSurfer Group,

I am writing to inquire about Editing Sequence.

The "Troubleshooting your output" page (https://surfer.nmr.mgh.
harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits
sequence as brain mask --> wm volume --> white surface --> control points.

Do you suggest people to absolutely stick to this particular sequence?

Thanks for your time,

David
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[Freesurfer] Jin, David S. wants to share the file alreadyexists_recon-all.log with you

[Jin, David S.]

To view alreadyexists_recon-all.log, sign 
in
 or create an account.
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Re: [Freesurfer] lh.BA_exvivo.annot Already Exists Error

[Jin, David S.]

Jin, David S. has shared a OneDrive for Business file with you. To view it, 
click the link below.


<https://partnershealthcare-my.sharepoint.com/personal/david_jin_mgh_harvard_edu/Documents/Attachments/alreadyexists_recon-all.log>
[https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://partnershealthcare-my.sharepoint.com/personal/david_jin_mgh_harvard_edu/Documents/Attachments/alreadyexists_recon-all.log>

alreadyexists_recon-all.log<https://partnershealthcare-my.sharepoint.com/personal/david_jin_mgh_harvard_edu/Documents/Attachments/alreadyexists_recon-all.log>




Hi,

The command submitted was:


recon-all -autorecon2 -autorecon3 -subjid D31223 -openmp 4


The screen output was:


ERROR: /home/david/Desktop/JSS_FSnew/test_8core/D31223/label/lh.BA_exvivo.annot 
already exists

Linux locke 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux



I have attached recon-all.log as "alreadyexists_recon-all.log"



Many thanks,

David










From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Wednesday, March 7, 2018 2:09:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lh.BA_exvivo.annot Already Exists Error

Hi David

can you send us the full command line, screen output and recon-all.log?

cheers
Bruce
On
Wed, 7 Mar 2018, Jin, David S. wrote:

>
> Hi,
>
> On our machine, with FS6, when we try to run recon-all, FS throws an error of 
> "lh.BA_exvivo.annot
> already exists" . However, upon deleting lh.BA_exvivo.annot, it still gives 
> the same error. Has
> anybody else encountered this?
>
>
>
>
>
> Many thanks,
>
> David
>
>
>
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To see the collection of prior postings to the list, visit the Freesurfer 
Archives. A searchable archive which of messages PRIOR to March 2004 is at ...



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[Freesurfer] lh.BA_exvivo.annot Already Exists Error

[Jin, David S.]

Hi,

On our machine, with FS6, when we try to run recon-all, FS throws an error of 
"lh.BA_exvivo.annot already exists" . However, upon deleting 
lh.BA_exvivo.annot, it still gives the same error. Has anybody else encountered 
this?





Many thanks,

David
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[Freesurfer] functional to anatomical registration

[David Beeler]

Hi freesurfer people,

I'm trying to understand preprocessing a little better, especially registration 
of functional data to anatomical space. I am currently running everything in 
the volume, doing motion correction per-run and then pooling all the runs in 
the session together for the first level analysis.

As far as I can tell, running preproc-sess with -per-run takes the raw 
functional data (f.nii.gz), pulls out the middle timepoint and calls it 
template.nii.gz, bbregisters func to anat and creates a register.dof6.lta file 
in each of the functional run folders, transforms the aparc+aseg from the 
subject's mri folder and binarizes it into a brainmask (brain.nii.gz), and runs 
mc-afni using f.nii.gz as the input vol and template.nii.gz as the template vol 
to create the motion corrected volume (fmcpr.nii.gz). Is this correct?

Then when I run selxavg3-sess it somehow mri_converts an intermediary motion 
corrected volume from the mc-afni command above (eg 
<run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an fmc.nii.gz file in each run 
folder. Are these fmc.nii.gz's supposed to be coregistered between runs? (i.e. 
if the subject moved a bunch between two of the runs, would those two volumes 
be aligned at all?). How do these files work?

At the end I have an analysis directory with my betas, sigmaps, etc. What 
functional volume is everything registered to? Is the transform between this 
functional volume and anatomical space the register.dof6.lta file located in 
the session directory?

Thanks for bearing with me!
-David


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[Freesurfer] ExploreDTI Workshop in March 2018

[Szabolcs David]

ExploreDTI Workshop -  A course on processing, analyzing, and visualizing
diffusion MRI data
When: 12-14 March, 2018
Where: Utrecht, Netherlands
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs
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[Freesurfer] ERROR: must specify input table of b-values

[David Yang]

Hello,


I am trying to run the trac-all -prep command in TRACULA on a participant. 
However, every time I run the command trac-prepoc exits with errors and I get 
the message: 'ERROR:must specify input table of b-values'. I checked over the 
configuration file and everything seems correct: b-value table is specified and 
in the correct 1 column format, and there are the same number of b-values, 
b-vectors and DTI volumes. Does anyone know why I am getting this message?


1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

2) Platform:  OS X Mavericks 10.9.5
3) trac-all -prep -c $VSDEVEL_DATA/VSDevel_outputs/dmric_1089001_06M.txt
4) Attached is the configuration file, b-values, b-vectors

Thanks,
David
setenv SUBJECTS_DIR /Users/student/Desktop/VSDevel_data/VSDevel_recons

set dtroot = /Users/student/Desktop/VSDevel_data/VSDevel_outputs

set subjlist = (1089001_06M)

set dcmroot = /Users/student/Desktop/VSDevel_data/VSDevel_outputs

set dcmlist = (1089001_06M/1089001_06M_bedpostx/data.nii.gz)

set bvecfile = 
/Users/student/Desktop/VSDevel_data/VSDevel_outputs/1089001_06M/1089001_06M_bedpostx/bvecs.txt

set bvalfile = 
/Users/student/Desktop/VSDevel_data/VSDevel_outputs/1089001_06M/1089001_06M_bedpostx/bvals.txt0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
0
0
0
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2000
2 0 0
0 0 0
0 0 0
-1 0 0
-0.457 0.89 0
0.265 0.485 0.834
-0.937 -0.284 0.202
-0.063 -0.806 0.588
0.679 -0.094 0.728
-0.687 0.279 0.671
0.233 0.95 0.209
-0.923 0.179 0.342
0.111 -0.98 -0.164
0.132 -0.854 -0.503
-0.367 -0.769 -0.523
0.291 -0.705 0.647
0.676 0.714 0.185
0.599 0.078 -0.797
0.733 -0.679 0.039
-0.8 -0.216 -0.559
-0.558 -0.341 -0.756
0.435 -0.599 -0.672
0.785 0.596 -0.17
-0.496 0.791 0.357
0.66 0.434 -0.614
-0.842 -0.145 0.52
-0.144 0.43 0.891
0.302 0.282 -0.911
-0.229 -0.931 0.284
-0.943 0.012 -0.334
-0.011 -0.025 1
-0.403 0.848 -0.345
-0.922 0.388 -0.01
-0.04 0.487 -0.872
0.297 0.146 0.944
0.374 -0.166 -0.912
0.285 -0.22 0.933
0.856 -0.318 0.408
0.903 0.383 0.195
-0.765 0.531 0.364
0.519 -0.427 0.74
-0.669 0.607 -0.429
0.104 -0.973 0.205
0.66 0.57 0.49
0.035 0.691 0.722
-0.333 -0.606 0.722
0 0 0
0 0 0
0 0 0
-1 0 0
-0.457 0.89 0
0.265 0.485 0.834
-0.937 -0.284 0.202
-0.063 -0.806 0.588
0.679 -0.094 0.728
-0.687 0.279 0.671
0.233 0.95 0.209
-0.923 0.179 0.342
0.111 -0.98 -0.164
0.132 -0.854 -0.503
-0.367 -0.769 -0.523
0.291 -0.705 0.647
0.676 0.714 0.185
0.599 0.078 -0.797
0.733 -0.679 0.039
-0.8 -0.216 -0.559
-0.558 -0.341 -0.756
0.435 -0.599 -0.672
0.785 0.596 -0.17
0.66 0.434 -0.614
-0.842 -0.145 0.52
-0.144 0.43 0.891
0.302 0.282 -0.911
-0.229 -0.931 0.284
-0.943 0.012 -0.334
-0.011 -0.025 1
-0.403 0.848 -0.345
-0.922 0.388 -0.01
-0.04 0.487 -0.872
0.297 0.146 0.944
0.374 -0.166 -0.912
0.285 -0.22 0.933
0.856 -0.318 0.408
0.903 0.383 0.195
-0.539 -0.729 0.422
0.478 0.878 -0.04
-0.765 0.531 0.364
0.519 -0.427 0.74
-0.669 0.607 -0.429
0.104 -0.973 0.205
0.66 0.57 0.49
0.035 0.691 0.722
-0.333 -0.606 0.722___
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[Freesurfer] lme_mass_RgGrow problem

[David Pagliaccio]

Hello,
We have been trying to analyze some longitudinal structural data using the
FreeSurfer Mixed Effects Model toolbox and have been running into some
issues.

We have 2-3 timepoints per individual imaged across adolescence and 3
groups of interest. We set up a design matrix  to examine potential
quadratic effects of age by group including factors for:
1. Intercept
2. time
3. time ^2
4. Group 1 vs. others
5. Group 1 x time
6. Group 1 x time ^2
7. Group 2 vs. others
8. Group 2 x time
9. Group 2 x time ^2
10. age at baseline
11. sex

We started a model to examine thickness, testing out the first model below
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex);

Then, we have been getting stuck at
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);

This starts the segmentation into homogeneous region but seems to get stuck
after displaying "Computing seeds..."

Is there a way to diagnose or fix this problem? Any thoughts would be
great, thanks!
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Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[David Semanek]

Thanks Bruce I’ll prepare something and upload it, hopefully before the 
weekend. I’ll let you know when I’ve got it uploaded.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
 
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recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
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PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM.  Thank you for your cooperation.

On 4/20/17, 11:14 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:

Hi David

I can take a look at a subject of yours as well if you upload it (both 5.3
and 6.0 processed versions if you have them) and point me at voxel coords.
The white surface is by design insensitive to local variations which is
what makes it robust, but also makes it more difficult to modify. I'll take
a look and think about how to make it easier

cheers
Bruce


On Thu, 20 Apr 2017, David Semanek
wrote:

>
> Thank you for looking into the deeper mechanics of this issue. In my case 
I
> am dealing with motion contaminated 1.5T data which require extensive and
> somewhat intricate edits to the white matter bleed into the pial surface, 
as
> well as into dura. In working with a past dataset of similar 
characteristics
> I was consistently impressed with fs 5.3’s ability to properly segment 
white
> matter in most cases and the robustness of the editing response. I was 
left
> with the overall impression that freesurfer handled noisy data quite well
> with a little bit of help. Our results from the analysis of corrected vs
> uncorrected data were very strong in favor of the editing protocol.
>
>  
>
> My experience with 6.0, aside from any issues of information not 
propagating
> through the longitudinal stream, is that there are many more cases in 
which
> the white matter surface will not conform to the edits suggested in the
> white matter volume. A number of tricks to “convince” the software in 
cases
> of non-response used in 5.3, such as making sure to complete edits on
> adjacent slices, are simply not effective. I am left with the overall
> impression that I have very little control over the white matter surfaces
> really, beyond making suggestions which may only slightly change the 
degree
> of error, but does not fundamentally change the structure of the white
> matter surface enough to remove the misclassification entirely in many
> cases.
>
>  
>
> Best,
>
>  
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
>  
>
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended
> recipient.  It may contain confidential information which is legally
> privileged or otherwise protected by law.  If you received this e-mail in
> error or from someone who was not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing or
> copying the e-mail.  PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM.  Thank you for your
> cooperation.
>
>  
>
> From: Antonin Skoch <a...@ikem.cz>
> Date: Thursday, April 20, 2017 at 10:25 AM
> To: David Semanek <seman...@nyspi.columbia.edu>,
> "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
>  
>
> Dear David,
>
> thank you for the feedback; I saw your posts concerning edits and 
responded
> to them, see
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
>
> Just my case is not concerning poor response to the edits (which I believe
> is not systematical

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[David Semanek]

Thank you for looking into the deeper mechanics of this issue. In my case I am 
dealing with motion contaminated 1.5T data which require extensive and somewhat 
intricate edits to the white matter bleed into the pial surface, as well as 
into dura. In working with a past dataset of similar characteristics I was 
consistently impressed with fs 5.3’s ability to properly segment white matter 
in most cases and the robustness of the editing response. I was left with the 
overall impression that freesurfer handled noisy data quite well with a little 
bit of help. Our results from the analysis of corrected vs uncorrected data 
were very strong in favor of the editing protocol.

My experience with 6.0, aside from any issues of information not propagating 
through the longitudinal stream, is that there are many more cases in which the 
white matter surface will not conform to the edits suggested in the white 
matter volume. A number of tricks to “convince” the software in cases of 
non-response used in 5.3, such as making sure to complete edits on adjacent 
slices, are simply not effective. I am left with the overall impression that I 
have very little control over the white matter surfaces really, beyond making 
suggestions which may only slightly change the degree of error, but does not 
fundamentally change the structure of the white matter surface enough to remove 
the misclassification entirely in many cases.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Antonin Skoch <a...@ikem.cz>
Date: Thursday, April 20, 2017 at 10:25 AM
To: David Semanek <seman...@nyspi.columbia.edu>, 
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in 
comparison to v5.3 - worse GM/WM contrast

Dear David,

thank you for the feedback; I saw your posts concerning edits and responded to 
them, see

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html

Just my case is not concerning poor response to the edits (which I believe is 
not systematically different between 5.3 and 6.0), my concern is that the data 
processed by v6.0 need much more wm.mgz edits than data processed by v5.3.

I think that my issue lies in -normalization2 step of recon-all. One of the 
difference between v5.3 and v6.0 is that by default the -mprage flag is passed 
to mri_normalize. This affects several parameters inside mri_normalize. I tried 
to reprocess my subjects using v6.0 with -no-mprage, but unfortunately this did 
not help.

See the example screenshots processed by v5.3 and v6.0 with -no-mprage:

The brain.mgz is still more aggressively filtered in v6.0 and there is much 
more prominent leak of ?h.white outside brain, which is probably caused by 
extended filtration which affects GM/WM contrast.

Looking at the source code of mri_normalize.c I did not comprehend where the 
basis of the issue lies, but in any case there are big differences in 
mri_normalize.c code between versions.

Antonin
From: David Semanek <seman...@nyspi.columbia.edu>
To: Antonin Skoch <a...@ikem.cz>, "freesurfer@nmr.mgh.harvard.edu" 
<freesurfer@nmr.mgh.harvard.edu>
Sent: 4/20/2017 3:41 PM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in 
comparison to v5.3 - worse GM/WM contrast

Agreed. A validated protocol run on a very large group of subjects in 5.3 was 
attempted with similar data in 6.0 and not only was the longitudinal edit 
stream nearly non-functional for white matter edits, cross edit performance was 
disappointing.



I am currently waiting on a response to these potential issues before pursuing 
further work with 6.0.



Best,



David P. Semanek, HCISPP

Research Technician, Posner Lab

Division of Child and Adolescent Psychiatry

Columbia University Medical Center

New York State Psychiatric Institute

1051 Riverside Drive, Pardes Bldg. Rm. 2424

New York, NY 10032

PH: (646) 774-5885



IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to sen

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[David Semanek]

Agreed. A validated protocol run on a very large group of subjects in 5.3 was 
attempted with similar data in 6.0 and not only was the longitudinal edit 
stream nearly non-functional for white matter edits, cross edit performance was 
disappointing.

I am currently waiting on a response to these potential issues before pursuing 
further work with 6.0.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Antonin Skoch <a...@ikem.cz>
Date: Wednesday, April 19, 2017 at 5:23 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison 
to v5.3 - worse GM/WM contrast

Dear experts,

I am sending just one more example to illustrate issue with white surface 
estimation in v6.0. See the attached screenshots: In v6.0 there seems to be 
insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking 
at three spots dramatically outwards towards pial surface. The white surface in 
v5.3 looks much more anatomically relevant in the same spot.

Could you please comment on how to avoid such issues in v.6.0?

Regards,

Antonin Skoch


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Re: [Freesurfer] ERROR

[David Semanek]

In my experience, OSX has weird issues with things in system and Application 
directories. My guess would be your files have inherited some permission flags 
from the Linux environment and OSX is having trouble making them properly 
available.

The first thing I would try would be to copy them to a location in your User 
directory. I use a folder conveniently called 
~/MRI/FS_Subject_Folders/[study_name] for all my freesurfer work and then just 
edit the SetUpFreeSurfer.sh file to change my SUBJECTS_DIR for my current 
project.

If Freesurfer (and Finder) still can’t see them there, you could try copying 
them again from your Linux box using the cp --no-preserve=mode to copy just the 
files without any inherited permissions and see if that works. I’ve personally 
never needed to do that bringing files over from Linux so I’m not totally sure 
what the outcome would be but that’s my first thought.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Damien MARIE <damien.ma...@unige.ch>
Date: Saturday, April 15, 2017 at 9:21 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] ERROR

Hi,

I ran recon-all on a server where Ubuntu is running.

Recently I installed separately freesurfer on a macbook, it is working (e.g. 
tkmedit bert), I moved my processed subjects to freesurfer/subjects on the 
macbook but I can not work with them. I have the below error. I changed the 
permission to 777, it is still not working. Now what is really strange is that, 
using the finder I do not see the files in freesurfer/subjects but by doing ls 
-l in a terminal, I can see them…

Please note that SUBJECT_DIR is defined.

Any idea is welcome.

Thank you and best,


Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit 
hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz
ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in 
/Applications/freesurfer/subjects or it is not readable by you

Damien
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Re: [Freesurfer] manual edits

[David Semanek]

Hi John,

Yes understanding how freesurfer deals with edits can be a bit confusing. I 
have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross 
sectional data in Freesurfer 5.3 so perhaps I can help.

Recon-all is basically a script which runs a series of about 25 or so 
processing steps in a defined sequence. The software generally will be able to 
recognize when an edit has been done at a particular intervention point and 
will take those edits into account when running that step unless you 
specifically instruct it not to.

The most common types of edits are edits to the wm.mgz to fix white matter 
defects and tissue incorrectly identified as white matter, and edits to the 
brainmask.mgz to fix cases where the skull strip is insufficient to prevent 
dura and other non-cortical tissue from making it into the gray matter/pial 
surfaces. White matter edits need to be done directly on the wm.mgz and gray 
matter/skull strip edits need to be done on the brainmask.mgz. Editing those 
two files and saving them directly in freeview is sufficient to register those 
edits for recon-all.

If you have edited only the brainmask.mgz, it is sufficient to run 
–autorecon-pial since the white matter surfaces will not need to be 
regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or 
–autorecon2-cp  if you used control points as well as white matter edits). If 
you have edited both the brainmask.mgz and the wm.mgz, then you only need to 
run –autorecon2-wm since the pial surfaces will be regenerated taking into 
account the brainmask.mgz edits as part of that workflow. Keep in mind that you 
still need to run –autorecon3 to complete the reprocessing of these data 
(-autorecon-pial includes the steps from –autorecon3) but that can be done when 
you are happy with your final surfaces if you want to save processing time on 
iterative edits.

Here is the wiki page referring to edits: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

I hope this is helpful.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
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PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
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From: John Anderson <john.ande...@protonmail.com>
Reply-To: John Anderson <john.ande...@protonmail.com>
Date: Wednesday, April 12, 2017 at 6:45 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] manual edits

Dear Freesurfer experts,
I am not an expert in manual edits, so I highly appreciate any feedback 
regarding the issues in my questions below. I ran the following command line 
“recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing 
the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached.
Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz"

1.   When I reviewed “wm.mgz” I see interactions between the white matter 
(wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by 
removing the wm voxels from the cortex, and the data was saved in the file 
“wm.seg.mgz”

2.   I found many holes in many slices similar to the (black arrow). I 
filled all these holes. The data saved in “wm.seg.mgz”

3.   I fixed some issues related to dura and bad skullstipping
Then I ran the command:
“recon-all -autorecon2-wm -autorecon3 -subjid ” which output the file 
“brain.finalsurfs.mgz”
and the command
“recon-all -autorecon-pial -subjid ”
Now, I want to understand where Freesurfer implement the new edits? Which files 
will be used as the main files that include the new edits. Logically, the edits 
must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I 
open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original 
non-edited files. I am not sure what I am doing wrong so I highly appreciate 
any help.
John

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

I believe what I am seeing in the long stream is the edits not properly taking 
effect.

I uploaded a subject with two timepoints, and only baseline edits to the wm as 
dsemanek2.zip about a week and a half ago. There doesn’t seem to be any 
significant changes to the surfaces in the base or either of the long runs. I 
will redo this subject on my end with some more extreme edits for testing to 
see if I can “force” something.

Thanks again for looking,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
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MESSAGE FROM YOUR SYSTEM.  Thank you for your cooperation.

From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Date: Wednesday, April 5, 2017 at 2:19 AM
To: David Semanek <seman...@nyspi.columbia.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Hoopes, 
Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Hi David,

so edits are affecting the surfaces in cross, just not as much as you would 
like. We need to check if there is a problem there.

For the longitudinal stream, edits in the base should affect surfaces in the 
base, which in turn will affect surfaces in the long. In long, surfaces would 
start from a better starting position. Furthermore, wm edits from cross should 
be propagated to long, to make sure that surfaces don’t move back to the wrong 
position. So far the theory.
If you don’t see any effect of WM edits (in the base) on surfaces (in the base) 
then there is a problem. This step should be basically identical to how we 
treat edits in cross.

Best, Martin


On 04 Apr 2017, at 23:13, David Semanek 
<seman...@nyspi.columbia.edu<mailto:seman...@nyspi.columbia.edu>> wrote:

Thanks for looking into this. I have uploaded another two subject folders as 
dsemanek3.zip, this time from a single time point for the same subject having 
been run through the cross stream of recon-all, the one with “test” appended at 
the end has had white matter edits on sagittal slices 126-142.

So, I have been able to get the surfaces to change in a single cross run as 
demonstrated in this upload. For this test, I did some edits that are typical 
on this dataset. Although the surfaces did change to reflect the edits, in a 
couple of places the surfaces did not change enough, and still encompassed 
space in the wm volume which had the white matter voxels removed.

For the first pass through these data before I realized there was a potential 
problem, I had initially edited the cross folders for the subjects and then ran 
the base, expecting the edits to be transferred over, but they did not seem to 
be. So I am still left with two issues: 1) incomplete incorporation of cross 
edits on the cross folders, 2) so far being unable to find an intervention 
point which will change the surfaces in the long stream, I have edited the base 
and then ran the long folders and these were not carried over as demonstrated 
in my previous uploads.

Thanks again,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
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PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
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From: Martin Reuter 
<mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>>
Date: Tuesday, April 4, 2017 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

So the way to debug this is to test if we can replicate th

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Thanks for looking into this. I have uploaded another two subject folders as 
dsemanek3.zip, this time from a single time point for the same subject having 
been run through the cross stream of recon-all, the one with “test” appended at 
the end has had white matter edits on sagittal slices 126-142.

So, I have been able to get the surfaces to change in a single cross run as 
demonstrated in this upload. For this test, I did some edits that are typical 
on this dataset. Although the surfaces did change to reflect the edits, in a 
couple of places the surfaces did not change enough, and still encompassed 
space in the wm volume which had the white matter voxels removed.

For the first pass through these data before I realized there was a potential 
problem, I had initially edited the cross folders for the subjects and then ran 
the base, expecting the edits to be transferred over, but they did not seem to 
be. So I am still left with two issues: 1) incomplete incorporation of cross 
edits on the cross folders, 2) so far being unable to find an intervention 
point which will change the surfaces in the long stream, I have edited the base 
and then ran the long folders and these were not carried over as demonstrated 
in my previous uploads.

Thanks again,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
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or otherwise protected by law.  If you received this e-mail in error or from 
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From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Date: Tuesday, April 4, 2017 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


So the way to debug this is to test if we can replicate the problem of WM edits 
not taking effect in a regular cross sectional stream.

If true this means that there is a bug to the way WM edits are considered in 
FS6.0. It is unlikely that we missed that, but can happen. Probably something 
else is going on here.



For that it would be good to have a single time point (cross sectional step) 
with WM edits send over, so that Andrew can take a look at that.



Best, Martin



On 04/04/2017 05:03 PM, David Semanek wrote:
I used –uselongbasewmedits only as a test to see if I could get some condition 
under which the wm edits would be taken into account when the surfaces were 
generated.

I did not use that flag for the data I uploaded. The wm edits to base did not 
influence the base wm surfaces or the cross wm surfaces. The cross wm edits 
(not uploaded) did not influence cross, base, or long wm surfaces.

I’ve found no condition under which wm edits have influenced the white matter 
surface in any of my data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Martin Reuter 
<mreu...@nmr.mgh.harvard.edu><mailto:mreu...@nmr.mgh.harvard.edu>
Date: Tuesday, March 28, 2017 at 1:27 PM
To: <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


This is how it should work:

WM edits in the base should affect surfaces in the base, these surfaces should 
be used as initialization for the long processing and fix most of the things 
there. If not , you need to edit the cross, because WM edits are copied into 
long from cross.



Using the -uselongbasewmedits flag is usually not recommended. It copies WM 
edits from base to the long and that is only meaningful if there is very little 
longitudinal change.



Best, Martin

On 03/23/2017 04:12 PM, 

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

I used –uselongbasewmedits only as a test to see if I could get some condition 
under which the wm edits would be taken into account when the surfaces were 
generated.

I did not use that flag for the data I uploaded. The wm edits to base did not 
influence the base wm surfaces or the cross wm surfaces. The cross wm edits 
(not uploaded) did not influence cross, base, or long wm surfaces.

I’ve found no condition under which wm edits have influenced the white matter 
surface in any of my data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Date: Tuesday, March 28, 2017 at 1:27 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


This is how it should work:

WM edits in the base should affect surfaces in the base, these surfaces should 
be used as initialization for the long processing and fix most of the things 
there. If not , you need to edit the cross, because WM edits are copied into 
long from cross.



Using the -uselongbasewmedits flag is usually not recommended. It copies WM 
edits from base to the long and that is only meaningful if there is very little 
longitudinal change.



Best, Martin

On 03/23/2017 04:12 PM, David Semanek wrote:
Thanks for taking another look at our data.

I have uploaded another subject in the archive dsemanek2.zip . For this subject 
I have:

1) run the cross processing stream on both timepoints
2) created the base
3) edited the wm.mgz on the base
4) rerun –base –autorecon2-wm –autorecon3
5) run the long stream to create the long folders for the two time points

It doesn’t look like the white matter edits were factored into any of the 
surfaces at any point in the process. NB: some edits have been exaggerated over 
protocol for the purpose of testing the software.

These folders were processed on OSX 10.11. I am running the same subject on 
Linux and I will let you know if I get a qualitatively different outcome.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu>
Date: Monday, March 20, 2017 at 4:54 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David 
Semanek <seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Hi David,



That is interesting. Sorry to ask you to upload data again, but if you could 
upload this subject (with only base wm.mgz edits), I could try to replicate 
this and see why no wm changes are showing up in the longs.



best,

Andrew


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of David Semanek 
<seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Sent: Monday, March 20, 2017 1:59 PM
To: Hoopes, Andrew; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Andrew, thanks for your response. I am still not seeing the white matter edit 
performance that I am expecting, or that I have seen from using the cross 
stream on 5.3 in the past with a differe

Re: [Freesurfer] wm edits not incorporated

[David Semanek]

Yes, I have this exact same problem. I have uploaded two rounds of data for 
review to the ftp service a week or so ago and I believe they are being 
reviewed.

After several days of testing on my end with various permutations of flags and 
cross and long runs and intervention points I didn’t see a single white matter 
surface change to reflect any edits.

I used this exact same protocol on a very large dataset (N>300) using only 
cross runs on Freesurfer 5.3 on Linux about 1.5 years back and didn’t have this 
problem. I have tested this latest dataset on both Mac and Linux, 5.3 and 6.0, 
cross and long, and nothing has changed the white matter surfaces.

I’m really baffled.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: Octavian Lie <octavian@gmail.com>
Date: Monday, April 3, 2017 at 11:26 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, Bruce 
Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm edits not incorporated



Dear Bruce,

I just transferred subject r02.tar.gz.
Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on 
reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

For example, the complete command line for  a rerun on this particular subject 
is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 
-parallel > output.txt &

Here are some of the edited voxels which are not excluded from the wm on rerun:

-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147

I mention this is not the only subject where I have this problem.
Thank you for your help.
Octavian



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Re: [Freesurfer] ExploreDTI Workshop!

[Szabolcs David]

FYI - *ExploreDTI* Workshop!
When: 10-12 July, 2017
Where: Utrecht, Netherlands
Details: http://www.exploredti.com/workshop

Hope to see you in the Dutch summer ;)

Cheers,
Szabolcs
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Thanks for taking another look at our data.

I have uploaded another subject in the archive dsemanek2.zip . For this subject 
I have:

1) run the cross processing stream on both timepoints
2) created the base
3) edited the wm.mgz on the base
4) rerun –base –autorecon2-wm –autorecon3
5) run the long stream to create the long folders for the two time points

It doesn’t look like the white matter edits were factored into any of the 
surfaces at any point in the process. NB: some edits have been exaggerated over 
protocol for the purpose of testing the software.

These folders were processed on OSX 10.11. I am running the same subject on 
Linux and I will let you know if I get a qualitatively different outcome.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Date: Monday, March 20, 2017 at 4:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, David Semanek 
<seman...@nyspi.columbia.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Hi David,



That is interesting. Sorry to ask you to upload data again, but if you could 
upload this subject (with only base wm.mgz edits), I could try to replicate 
this and see why no wm changes are showing up in the longs.



best,

Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek 
<seman...@nyspi.columbia.edu>
Sent: Monday, March 20, 2017 1:59 PM
To: Hoopes, Andrew; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Andrew, thanks for your response. I am still not seeing the white matter edit 
performance that I am expecting, or that I have seen from using the cross 
stream on 5.3 in the past with a different dataset.



I started with a new subject with two timepoints. I ran recon-all on both for 
the cross stream with no edits, and then ran the base. I edited the wm.mgz for 
the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp 
xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but 
I went ahead and ran the two long runs using “recon-all –all –long xx_tx 
xx_base” and although there are minor differences in the base and time point 
surfaces, the white matter edits I did on the base were largely ignored, and 
none of them were included in the time point long run wm.mgz files.



I am tempted to try these same analyses using Linux (I am running this on OSX 
10.11 currently), as I experienced a completely different response from the 
surface generation modules to my edits in the past when using Linux. I’m 
thinking this is a real long shot, but I cannot otherwise figure out why the 
software would be behaving so differently from my past experiences.



Any thoughts? Thanks!

Best,



David P. Semanek, HCISPP

Research Technician, Posner Lab

Division of Child and Adolescent Psychiatry

Columbia University Medical Center

New York State Psychiatric Institute

1051 Riverside Drive, Pardes Bldg. Rm. 2424

New York, NY 10032

PH: (646) 774-5885



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



From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, David Semanek 
<seman...@nyspi.columbia.edu>
Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams



Hi David



Try editing the base wm.mgz first instead of editing the long and cross wm 
files. Rerun autorecon2-wm and autor

[Freesurfer] Custom brain segmentation to equal sized regions

[david . kamson]

Freesurfers,

Is there a way to segment each hemisphere to an identical number of equal
sized regions which are as close in size and location as possible to their
contralateral homotopic regions.
Eg. I’d like to segment the left hemisphere to regions with a 2 cm2
surface and do the same for the right in order to compare asymmetries in
these small regions. Anybody had done this before?

David

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Andrew, thanks for your response. I am still not seeing the white matter edit 
performance that I am expecting, or that I have seen from using the cross 
stream on 5.3 in the past with a different dataset.

I started with a new subject with two timepoints. I ran recon-all on both for 
the cross stream with no edits, and then ran the base. I edited the wm.mgz for 
the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp 
xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but 
I went ahead and ran the two long runs using “recon-all –all –long xx_tx 
xx_base” and although there are minor differences in the base and time point 
surfaces, the white matter edits I did on the base were largely ignored, and 
none of them were included in the time point long run wm.mgz files.

I am tempted to try these same analyses using Linux (I am running this on OSX 
10.11 currently), as I experienced a completely different response from the 
surface generation modules to my edits in the past when using Linux. I’m 
thinking this is a real long shot, but I cannot otherwise figure out why the 
software would be behaving so differently from my past experiences.

Any thoughts? Thanks!

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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

From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, David Semanek 
<seman...@nyspi.columbia.edu>
Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Hi David



Try editing the base wm.mgz first instead of editing the long and cross wm 
files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely 
rerun the longitudinals. The long surfaces are initialized from the base 
surfaces, so this could be why your wm fixes seem to have no effect.

You can find more info here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet<https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits>

If editing the base doesn't solve the problem, you can send me the commands you 
ran in order and I can look into this further.

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek 
<seman...@nyspi.columbia.edu>
Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Thanks, I have uploaded the cross and long stream processing from one subject 
which requires numerous white matter edits to correct defects in the white 
matter surfaces; the file is on the ftp server as dsemanek.zip.

Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to 
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 
have been run on them, as well as the long folder for the first time point, 
s02_t1.long.s02_base.

It was in working with the rerun results of s02_t1.long.s02_base that I noticed 
the white matter surfaces after being regenerated with the edited wm.mgz did 
not reflect any of the edits. The easiest way to see this is to load the wm.mgz 
with the white matter surfaces and scroll through the slices, there are 
numerous areas where the contours of the white matter surfaces do not follow 
the voxels of the wm.mgz volume, mostly near what should be identified as 
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t 
change at all after running autorecon2-wm with the wm.mgz edits.

Thanks for taking a look at our data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in e

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Thanks, I have uploaded the cross and long stream processing from one subject 
which requires numerous white matter edits to correct defects in the white 
matter surfaces; the file is on the ftp server as dsemanek.zip.

Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to 
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 
have been run on them, as well as the long folder for the first time point, 
s02_t1.long.s02_base.

It was in working with the rerun results of s02_t1.long.s02_base that I noticed 
the white matter surfaces after being regenerated with the edited wm.mgz did 
not reflect any of the edits. The easiest way to see this is to load the wm.mgz 
with the white matter surfaces and scroll through the slices, there are 
numerous areas where the contours of the white matter surfaces do not follow 
the voxels of the wm.mgz volume, mostly near what should be identified as 
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t 
change at all after running autorecon2-wm with the wm.mgz edits.

Thanks for taking a look at our data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
 
IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
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On 3/12/17, 4:13 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:

Hi David

if you upload a subject to our ftp site and give us enough detail to
replicate what you tried we will take a look

cheers
Bruce
On Fri, 10 Mar 2017, David
Semanek wrote:

>
> Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
> required a fair number of manual edits to the white matter volume in order
> to correct defects in the white matter surface. Typically, these edits 
take
> the form of removing voxels in the wm.mgz volume that have been 
incorrectly
> identified as white matter, usually near the pial surface caused by
> intensity artifacts resulting from motion. My experience in the past is 
that
> generating the white matter surface after edits to the wm.mgz volume will
> reliably change the geometry of the resulting surfaces.
>
>  
>
> However, on my current dataset, 1.5T adolescent brains with pervasive 
motion
> artifacts that do not meet the threshold for unusable data, absolutely no
> intervention I have done on the wm.mgz volume has any impact at all on the
> generation of the white matter surfaces. I am really very puzzled by this.
> All of the files that result from wm.mgz reflect the edits, however the 
aseg
> does not.
>
>  
>
> The resulting white matter surfaces always follow the aseg white matter
> definitions and never the wm.mgz edits. I feel as if there might be
> something I am missing but this protocol has reliably been used to do 
white
> matter edits in the past. I thought it may be an issue with fs 6 or the 
long
> stream, but I have tried the same edits in 5.3, 6, long and cross streams
> and nothing at all has worked.
>
>  
>
> Does anyone have any suggestions, or perhaps a hint that I am overlooking
> something common?
>
>  
>
> Thanks,
>
>  
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
>  
>
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended
> recipient.  It may contain confidential information which is legally
> privileged or otherwise protected by law.  If you received this e-mail in
> error or from someone who was not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing or
> copying the e-mail.  PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
> E-MAIL AND DELETE THIS

[Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Hello, I have worked quite a bit in the past with fs 5.3 on datasets which 
required a fair number of manual edits to the white matter volume in order to 
correct defects in the white matter surface. Typically, these edits take the 
form of removing voxels in the wm.mgz volume that have been incorrectly 
identified as white matter, usually near the pial surface caused by intensity 
artifacts resulting from motion. My experience in the past is that generating 
the white matter surface after edits to the wm.mgz volume will reliably change 
the geometry of the resulting surfaces.

However, on my current dataset, 1.5T adolescent brains with pervasive motion 
artifacts that do not meet the threshold for unusable data, absolutely no 
intervention I have done on the wm.mgz volume has any impact at all on the 
generation of the white matter surfaces. I am really very puzzled by this. All 
of the files that result from wm.mgz reflect the edits, however the aseg does 
not.

The resulting white matter surfaces always follow the aseg white matter 
definitions and never the wm.mgz edits. I feel as if there might be something I 
am missing but this protocol has reliably been used to do white matter edits in 
the past. I thought it may be an issue with fs 6 or the long stream, but I have 
tried the same edits in 5.3, 6, long and cross streams and nothing at all has 
worked.

Does anyone have any suggestions, or perhaps a hint that I am overlooking 
something common?

Thanks,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail.  
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Saltzman, David]

We adjusted the offset and that was clearly the problem. Looks like it worked 
great. Thank you so much for clearing this up!


David Saltzman


Lab Manager

Language and Brain Laboratory

Department of Speech, Language, & Hearing Sciences

University of Connecticut



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Monday, January 30, 2017 12:01:15 PM
To: Freesurfer support list
Cc: Rothermich, Kathrin
Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor 
surface registration?

Hi David

I'm not sure that there is anything actually wrong, I think what you are
seeing is just a visualization issue. The inflated surfaces
will overlap when viewed together in freeview, since they are
centered on each hemi and inflated. You can use the :offset=x,y,z modifier
for the -f ?h.inflated to move them left/right so they don't overlap if you
want.

cheers
Bruce


On Mon, 30 Jan 2017, Saltzman, David wrote:

>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple MRI
> datasets, and seem to be encountering the same error. While the recon-all
> log does not indicate there are any errors (so far as we can tell as
> novices), when we look at the inflated surfaces, there is clearly some
> problem creating the inflated surface, in that the hemispheres appeared to
> be mirrored. For the purpose of simplicity, we will include the log and scan
> information for the most recent anatomical scan we have to run the recon-all
> pipeline on. I believe the attached screenshot (anterior coronal view) will
> make the issue more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
> Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information:
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm [176
> voxels]
> A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm [248
> voxels]
> I-to-S extent:  -186.650 [I] -to-68.350 [S] -step- 1.000 mm [256
> voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> Lab Manager
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>
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Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?

[Saltzman, David]

Hopefully I did this correctly: 
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w


Thanks!


David Saltzman


Lab Manager

Language and Brain Laboratory

Department of Speech, Language, & Hearing Sciences

University of Connecticut



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: Monday, January 30, 2017 11:55:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor 
surface registration?

Can you upload that subject to our filedrop? See below for link


On 01/30/2017 11:19 AM, Saltzman, David wrote:
>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple
> MRI datasets, and seem to be encountering the same error. While the
> recon-all log does not indicate there are any errors (so far as we can
> tell as novices), when we look at the inflated surfaces, there is
> clearly some problem creating the inflated surface, in that the
> hemispheres appeared to be mirrored. For the purpose of simplicity, we
> will include the log and scan information for the most recent
> anatomical scan we have to run the recon-all pipeline on. I believe
> the attached screenshot (anterior coronal view) will make the issue
> more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
> 2) Platform: Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information:
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-94.282 [L] -step- 1.000 mm
> [176 voxels]
> A-to-P extent:  -188.767 [A] -to-58.233 [P] -step- 1.000 mm
> [248 voxels]
> I-to-S extent:  -186.650 [I] -to-    68.350 [S] -step- 1.000 mm
> [256 voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> /Lab Manager/
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Surface space ICA

[David Baric Parker]

Hello!
  I tried to look through the history but couldn't seem to find exactly
what I was looking for.
Is there a recommended way to run ICA on vertex data?  For example, I've
transformed my raw fMRI data to surface space using fsfast, and would like
to extract group level IC's from this data.  Thanks!
-David
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Re: [Freesurfer] Fwd: localGI bug

[David Groppe]

Thanks very much, Yasser.
I've also fixed the bug by using my own, now-outdated copies of
FreeSurfer's MATLAB functions (
https://github.com/epiSurg/EpiSurg/tree/master/FSURF_MATLAB), but I'm
hoping the FreeSurfer developers can fix it in the current releases.
 much appreciated,
  -David


On Tue, Dec 27, 2016 at 11:19 AM, Yasser Alemán <yale...@hggm.es> wrote:

> Hi David,
>
> I had the same problem 3 days ago. I have fix it by changing some matlab
> scripts located inside freesurfer_root_directory/matlab
>
> I am sending to you the modified scripts. Please take care and save the
> original versions before copying the new ones.
>
> *Save inside /matlab*
> getFacesArea.m
> mesh_adjacency.m
> SearchProjectionOnPial.m.
>
> I have also found another bug related to matlab startup.m file. If you
> have modified your startup.m file to select by default a working directory
> then the lgi computation will fail. When matlab starts it changes the
> current directory (*<$SUBJECTS_DIR>//surf*) to the directory
> specified in the startup.m file and the scripts are looking for a specified
> filename (ie. lh.pial) inside the specified working directory.
>
> I am sending to you also the modified versions of the scripts with this
> bug  solved. I have tested in our VMs and everything goes ok.
>
> *Save inside /bin*
> mris_compute_lgi
>
> *Save inside /matlab*
> compute_lgi.m
> find_corresponding_center_FSformat.m
> make_roi_paths.m
>
> We have to wait for freesurfer developers to see their opinion. Maybe they
> have fixed this already. The original code and changes are commented.
>
> I hope this can be helpful.
> Best regards
> Yasser
>
>
>
>
>
> 2016-12-23 16:11 GMT+01:00 David Groppe <david.m.gro...@gmail.com>:
>
>>
>> Dear FreeSurfer Developers,
>>  I think there is a bug in FreeSurfer's MATLAB code that is used to
>> compute the local gyrification index. Specifically, when I run this command:
>>
>> *recon-all -s PT001 -localGI*
>>
>>
>> I get the following error:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *face 115000 / 118360mesh_outer =  vertices: [59182x3
>> double]faces: [118360x3 double]facesOfVertex: [59182x1
>> struct]preparing pial mesh structure ..searching for mesh edges...done
>> (171.44 sec) creating path file for vertex 1 / 59182area file for outer
>> ROIs saved at 1In an assignment  A(:) = B, the number of elements in A and
>> B must be the same.Error in dsearchn (line 79)[d(i),t(i)] =
>> min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex =
>> dsearchn(vertices,points);Error in reorganize_verticeslist (line 28)
>> [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
>> Error in make_roi_paths (line 93)reorglist = reorganize_verticeslist
>> (mesh_total, A, mesh_outer, perim,verticeslist, step);*
>>
>>
>>
>>
>> *>> ERROR:  make_roi_paths did not complete successfully!*
>> I ran the command in debugging mode and *x* and *yi *are both empty
>> variables.
>>
>> I am using a freshly installed version of the Lion OS X 10.7 (64b Intel)
>> version of FreeSurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg;
>> freesurfer-Darwin-lion-stable-pub-v5.3.0) and am running on OS 10.11.6
>> using MATLAB version R2015b (8.6.0.267246). The recon-all.log is attached.
>>
>> Let me know if there is any further information I can provide and thanks
>> for producing such a fantastic piece of freeware.
>>  -David Groppe
>>
>>
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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Re: [Freesurfer] ExploreDTI Workshop!

[Szabolcs David]

And here comes the 3rd ExploreDTI Workshop!
When: 27-29 March, 2017
Where: Utrecht, the Netherlands
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs

On Wed, Jul 20, 2016 at 4:02 PM, Szabolcs David <davidszabolc...@gmail.com>
wrote:

> FYI - we're holding the next ExploreDTI Workshop!
> When: 28-30 November, 2016
> Where: Utrecht
> Details: http://www.exploredti.com/workshop
>
> Cheers,
> Szabolcs
>
> On Sat, Feb 27, 2016 at 8:00 PM, Szabolcs David <davidszabolc...@gmail.com
> > wrote:
>
>> Thrilled to announce that we are going to hold an ExploreDTI workshop in
>> Utrecht (July 4-6)! More details can be found here:
>> http://www.exploredti.com/workshop.
>>
>> We hope to see you there!
>>
>> Cheers,
>> Szabolcs
>>
>
>
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Re: [Freesurfer] ExploreDTI Workshop!

[Szabolcs David]

FYI - we're holding the next ExploreDTI Workshop!
When: 28-30 November, 2016
Where: Utrecht
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs

On Sat, Feb 27, 2016 at 8:00 PM, Szabolcs David <davidszabolc...@gmail.com>
wrote:

> Thrilled to announce that we are going to hold an ExploreDTI workshop in
> Utrecht (July 4-6)! More details can be found here:
> http://www.exploredti.com/workshop.
>
> We hope to see you there!
>
> Cheers,
> Szabolcs
>
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[Freesurfer] converting Tracula outputs to Wavefront OBJ files

[David Allan Ziegler]

Dear Freesurfer/Tracula team,

I would like to convert some of the outputs from Tracula into wavefront
objects in order to render them in Unity.  Does anyone have any advice
on how to do so?

Based on previous threads and looking into Brainder.org's aseg2surf, I
assume I need to use a combination of mri_pretess and mri_tess to
generate tesselated surfaces that can then be converted into ascii files
and then into .obj files using Brainder's surf2obj.  My problem is in
figuring out how to generate the surface meshes from the Tracula
outputs. If anyone can point me to documentation on how to do this or
provide any advice, I'd appreciate it.

Cheers,
David


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[Freesurfer] Nonlinear CVS registration into average brain for coordinates

[Zhou, David Wei]

Hi all,

I have a data set of 14 subjects with intracranial (both cortical and 
subcortical) electrode implants, already recon'ed in Freesurfer, with an 
average brain + surface computed of these subjects. I would like to map each 
subject's electrode coordinates (a set of RAS points) into the average brain 
using a nonlinear transformation to account for individual deviations in 
surface topology.

I'm trying to figure out the steps that must be taken to achieve this. With my 
average brain as a template, it seems like I would use mri_cvs_register to 
produce each subject warped onto the template. After generating those warps, 
how does one apply the same warp to a set of coordinates, for example to find 
out where my electrodes end up in the template brain? Which output file in 
.../cvs contains the data necessary to compute the coordinates in the template?

I'd appreciate any instruction, thanks!

David
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[Freesurfer] getting started

[david sandeman]

Hi 
I am a neurosurgeon working with robotics
I have recently purchased a new macbook pro, running version 10.11.3 of OS X El 
capitan, speficially to run free surfer and other sofrtware designed to enhance 
my 3D segmentation capability
The downloads I have tried only allow me to load freeview automatically. can 
you advise me how to set free surfer up on my mac or refer me to a download 
that will load the software automatically
kindest
david sandeman
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Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels

[Slater David]

Hi Bruce,



I wrote to the HCP user group to ask about this. I received an answer but it’s 
still unclear to me.



As far as I can tell their are tools which can translate Freesurfer surfaces to 
the HCP/Caret format, but there isn’t a tool to convert in the opposite 
direction.



I simply would like to take a surface parcellation in HCP (32k or 164k) format 
and resample it to a standard Freesurfer subject (e.g fsaverage).



Here is my question and the reply from the HCP user group:







Great thanks for your helpful reply.



Unfortunately I'm not working with the HCP data exclusively. In addition we 
have our own data which has been pre-processed with the standard FreeSurfer 
-recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, 
instead they have typical output surfaces from FreeSurfer...



So if I understand correctly I could do the following:



* Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh surfaces 
for each subject

* The Gordon parcellation would then have a direct correspondence with these 
meshes (no resampling required)

* The FreeSurfer "mri_label2vol" tool could then be used to create subject 
specific parcellation maps



Is this correct? Am I missing something?



Thanks,

David





-Message d'origine-

De : Donna Dierker [mailto:do...@brainvis.wustl.edu] Envoyé : 08 March 2016 
18:05 À : Slater David Objet : Re: [HCP-Users] Cortical parcellations in 
Connectome Workbench and FreeSurfer



I hope someone who has actually done something like this answers, but this page 
might be helpful:



https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol



I'm less familiar with Freesurfer tools, but conceptually:



* The Gordon parcellation is available on 32k mesh (or 164k at least).

* The subject's individual surface is available in both of those meshes.

* The parcellation could be projected to the ribbon between the white and pial 
surfaces (possibly via mri_label2vol).

* It would not be necessary to resample the parcellation onto the native mesh 
to do this.

* The subject's native mesh is also available in one of the HCP-downloadable 
packages.

* There is a way, using -surface-project-unproject, to convert stuff back to 
native mesh, but it's tough to get your head around it, and I'm not sure it's 
the shortest path in this case.



Again, hopefully someone who has done this will reply. :)





On Mar 8, 2016, at 4:14 AM, Slater David 
<david.sla...@chuv.ch<mailto:david.sla...@chuv.ch>> wrote:



> Hi,

>

> I have a parcellation I would like to work with from the following paper:

>

> Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., 
> Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area 
> Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.

>

>

> The cortical parcellations are saved in .gii format for both the fs_LR 32k 
> and 164k meshes. My aim is to create a parcellated volume image for each of 
> my subjects in their native space. I know how to do this with Freesurfer 
> tools but I am a little lost with the fs_LR 32k and 164k mesh formats.

>

> If I had the parcellation in a standard Freesurfer subject space (e.g. 
> fsaverage) I would transform the parcalletion to the subject native space and 
> convert the surface labels to a volume parcellation. This is similar to how 
> the aparc niftii files are generated.

>

> How can I get a parcellation of the fs_LR 32k or 164k meshes into a subject's 
> native space parcellation? Or alternatively, how can I convert fs_LR 32k or 
> 164k vertex values to the fsaverage surface?

>

> Thanks,

> David

> ___









-Message d'origine-
De : freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl
Envoyé : 08 March 2016 14:32
À : Freesurfer support list
Objet : Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels



Hi David



I'm pretty sure that the Wash U HCP group has sorted this out. Have you asked 
them?



cheers

Bruce





On Tue, 8 Mar 2016, Slater David wrote:



>

> Hi,

>

>

>

> I have some mesh and label files I would like to use with my

> Freesurfer data however they are in an alternative format (connectome 
> workbench).

>

>

>

> I would like to get the labels into the space of a typical Freesurfer

> subject (e.g. fsaverage), followed by pushing the labels to subject

> native space and creating volume label files (similar to the aparc

> native space parcellations).

>

>

>

> Is it possible to register an isolated mesh file to the fsaverage subject?

> How can I convert labels on a .gii mesh file to a standard Freesurfer

> subject?

>

>

>

> Thanks,

[Freesurfer] Working with non-FreeSurfer derived meshes and labels

[Slater David]

Hi,

I have some mesh and label files I would like to use with my Freesurfer data 
however they are in an alternative format (connectome workbench).

I would like to get the labels into the space of a typical Freesurfer subject 
(e.g. fsaverage), followed by pushing the labels to subject native space and 
creating volume label files (similar to the aparc native space parcellations).

Is it possible to register an isolated mesh file to the fsaverage subject? How 
can I convert labels on a .gii mesh file to a standard Freesurfer subject?

Thanks,
David

p.s. The goal of this would be to use the following parcellation scheme with my 
freesurfer data:

Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., 
Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation 
from Resting-State Correlations. Cereb. Cortex bhu239-.

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[Freesurfer] ExploreDTI Workshop!

[Szabolcs David]

Thrilled to announce that we are going to hold an ExploreDTI workshop in
Utrecht (July 4-6)! More details can be found here:
http://www.exploredti.com/workshop.

We hope to see you there!

Cheers,
Szabolcs
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[Freesurfer] Planum temporale measurement

[Adam David Felton]

Hello,

I checked the listserv history, but couldn't find an answer to my question:

With the 2009 parcellation scheme, 1) does the planum temporale
parcellation include the posterior ascending ramus (which Destrieux et al.
2010 seems to imply) and 2) does the planum temporale include the posterior
descending ramus?



Thank you!




Adam
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[Freesurfer] recon_checker error

[LIEWALD David]

Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1


I am trying to generate QC data from data generated using Freesurfer ver 5.3 
and I'm getting the following error


"   Checking if all files exist...PASSED

 Checking actual file order...FAILED
 (read ../1006454_20216_2_0/scripts/recon_checker.log)
 ERROR: Actual file order disagrees with common file order for subject 
1006454_20216_2_0"



On checking the recon_checker.log it states


 This subject may have been
 processed with a different version of FreeSurfer other than the version
 used to create the common file order file (based on v5.1 by default if not
 specified by the user).  Consider generating an output file order file for
 your specific dataset using the 'genoutputorderfile' flag.

 See the '-help' flag for details.


I cannot find any details of this flag in any help file or any online help as 
to how to correct his problem


Dave Liewald







The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs

[Slater David]

Hi,

I have the same problem with tksurfer in Ubuntu.

The keyboard entry doesn't work for the tksurfer input boxes - I can't set any 
values in the overlay configuration window, edit label info, configure phase 
encoded data display etc. All of the text / numeric entry boxes have this issue.

Any suggestions on how to fix this?

My freesurfer verion is freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 
but I had the same problem before updating to v6-beta.

Thanks,
David


-Message d'origine-
De : freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl
Envoyé : 15 August 2015 21:12
À : Freesurfer support list
Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard 
inputs

Hi Lars

can you give more details? What prevents you from entering values? Do you get 
any errors when tksurfer loads?

cheers
Bruce

On Sat,
15 Aug 2015, Lars M. Rimol wrote:

> 
> Hi all,
> 
> I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am 
> unable to set threshold values in the edit boxes in the "configure 
> overlay" display in tksurfer. Does anybody know how to fix this (without 
> specifying the threshold on the command line each time)?
> 
> Thank you!
> 
> 
> 
> 
> 
> yours,
> Lars M. Rimol, PhD
> Department of Medicine
> John A. Burns School of Medicine
> University of Hawai'i
> 1356 Lusitana Street, University Tower Honolulu, HI 96813
> 
>
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Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs

[Slater David]

I use freeview a lot and have never had any problems with it. However I want to 
work on occipital patches to do retinotopy.

Can freeview load flat patches? Is there a way to display complex data overlays 
to produce phase maps as was possible in tksurfer?

Thanks,
David


-Message d'origine-
De : freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl
Envoyé : 12 December 2015 16:45
À : Freesurfer support list
Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard 
inputs

Hi David

tksurfer has been deprecated - can you try using freeview instead?
Bruce
On Sat,
12 Dec 2015, Slater David wrote:

> Hi,
>
> I have the same problem with tksurfer in Ubuntu.
>
> The keyboard entry doesn't work for the tksurfer input boxes - I can't set 
> any values in the overlay configuration window, edit label info, configure 
> phase encoded data display etc. All of the text / numeric entry boxes have 
> this issue.
>
> Any suggestions on how to fix this?
>
> My freesurfer verion is 
> freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same 
> problem before updating to v6-beta.
>
> Thanks,
> David
>
>
> -Message d'origine-
> De : freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce 
> Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet 
> : Re: [Freesurfer] configure overlay display in tksurfer by keyboard 
> inputs
>
> Hi Lars
>
> can you give more details? What prevents you from entering values? Do you get 
> any errors when tksurfer loads?
>
> cheers
> Bruce
>
> On Sat,
> 15 Aug 2015, Lars M. Rimol wrote:
>
>>
>> Hi all,
>>
>> I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am 
>> unable to set threshold values in the edit boxes in the "configure 
>> overlay" display in tksurfer. Does anybody know how to fix this (without 
>> specifying the threshold on the command line each time)?
>>
>> Thank you!
>>
>>
>>
>>
>>
>> yours,
>> Lars M. Rimol, PhD
>> Department of Medicine
>> John A. Burns School of Medicine
>> University of Hawai'i
>> 1356 Lusitana Street, University Tower Honolulu, HI 96813
>>
>>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is addressed. If you believe this e-mail was sent to you in error 
> and the e-mail contains patient information, please contact the 
> Partners Compliance HelpLine at http://www.partners.org/complianceline 
> . If the e-mail was sent to you in error but does not contain patient 
> information, please contact the sender and properly dispose of the e-mail.
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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[Freesurfer] file error

[LIEWALD David]

OS Opensuse 13.2

Freesurfer 6 Dev

Logfile Attached


I have had no luck trying to get freesurfer to run. It is failing at the same 
point each time ( Please see log). I have tried with multiple datasets in 
multiple locations both on the local machine and across the network. I have 
also verified that the permissions of the dir are correct and I can manually 
read and write to the. I'm at a loss?



Dave Liewald


Wed Dec  9 11:37:57 GMT 2015
/UK_Biobank_MRI/FS_Output/1006924_20216_2_0
/UK_Biobank_MRI/freesurfer/bin/recon-all
-i 
/UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm
 -s 1006924_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all
subjid 1006924_20216_2_0
setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output
FREESURFER_HOME /UK_Biobank_MRI/freesurfer
Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151207
Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  193285 
maxlocks unlimited
maxsignal193285 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  49495560   435314525964108 119680 242188   41644952
-/+ buffers/cache:1644312   47851248
Swap:314567668   1376  314566292


program versions used
$Id: recon-all,v 1.555 2015/11/17 14:18:41 mreuter Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2015/12/09-11:37:57-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $
mri_convert --version 
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $  User: root 
 Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name:  $  
TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  CVS: 
$Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: root  Machine: 
CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  

[Freesurfer] Path Problem

[LIEWALD David]

Environment : Opensuse 13.2 Freesurver Version 6 (Beta)


Hi I hope you can help with this problem


I'm using the version 6 Beta due to problems with license authentication. 
Freesurfer runs but bails out with a file not found error :



Iteration 1 Fri Dec  4 09:38:57 GMT 2015
nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 
-shrink 2



ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64 x86_64 x86_64 GNU/Linux



on examination of the file structure a directory named 
"tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and 
nothing has been created under the "tmp" directory  in the subject root. I am 
guessing that this is the cause of the error.


any advice on correcting this would be extremely useful


Dave Liewald

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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