Re: [Freesurfer] FS6.0 on 2yo subjects

[Lilla Zollei]

Hi Dimitrios,
Agree with Burce. The youngest we have processed with the standard 
pipeline was about 4.5yrs.

Lilla

On Wed, 18 Sep 2019, Bruce Fischl wrote:


Hi Dimitrios

it's kind of an empirical question. Lilla does have some newer tools you 
might consider instead of things aren't as accurate as you want


cheers
Bruce
On Wed, 18 Sep 2019, Alexopoulos, Dimitrios wrote:



 External Email - Use Caution

 We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old
 subjects.

 Although the output looks good (see below), is it recommended to use FS6.0
 on a young cohort?

  

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Re: [Freesurfer] FS6.0 on 2yo subjects

[Bruce Fischl]

Hi Dimitrios

it's kind of an empirical question. Lilla does have some newer tools you 
might consider instead of things aren't as accurate as you want


cheers
Bruce
On Wed, 18 
Sep 2019, Alexopoulos, Dimitrios wrote:




External Email - Use Caution

We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old subjects.

Although the output looks good (see below), is it recommended to use FS6.0
on a young cohort?

 

[IMAGE][IMAGE]

 

[IMAGE]

 





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Re: [Freesurfer] issue with lesions

[Sam W]

External Email - Use Caution

Thanks Doug. The problem is that for some patients the lesion affects the
segmentation dramatically. For example I have one patient with a large
lesion in the right cerebellum which is partly in GM and partly in WM. If I
load the aseg file I see that a portion of the right cerebellar hemisphere
is assigned to the left cerebellar hemisphere (the right white matter is
also being assigned to the left hemisphere) and the whole cerebellum looks
distorted. I suppose there is no way to inform freesurfer about the lesion
during recon-all?
I followed the steps in the FsTutorials for the cerebral cortex, but how
can I do the same for the cerebellum patient? What is the recommended way
to fix a bad segmentation due to cerebellum lesions? Control points, white
matter edits, or something else?
Sam

On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You can get the volume from the aseg.stats file. Unfortunately, we do not
> separate the lesions into left and right. You could do something like
> mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
> mri_volcluster --i wmlesions.mgz --sum lesions.sum.dat --thmin 0.5
> --regheader subject
> This will output a list of lesions clusters in lesions.sum.dat and their
> coordinates. you can see which ones are left and with ones are right.
>
>
>
> On 9/3/2019 5:17 PM, Sam W wrote:
>
> External Email - Use Caution
> Hello,
> I have run recon-all on T1 scans of patients with WM lesions. I noticed
> however that for some patients the lesion is excluded from
> aparc.a2009s+aseg.mgz but for other patients it is included (and labelled
> as non-lesion).
> Ultimately I'd like to extract a) volume information in WM and b) volume
> information of the WM lesion. I think I can get the the WM volume from the
> wmparc.stats file. For the lesion volume I think I can take the
> WM-hypointensities from the aseg file right? However I noticed that if a
> lesion is on the right hemisphere, the Right-WM-hypointensities shows 0s in
> all columns, which cannot be right.
> I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in
> anatomical space, can I use this mask somehow in FS to inform recon-all
> where the lesion occurs?
> Thanks in advance!
> Sam
>
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>
>
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[Freesurfer] FS6.0 on 2yo subjects

[Alexopoulos, Dimitrios]

External Email - Use Caution

We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old subjects.
Although the output looks good (see below), is it recommended to use FS6.0 on a 
young cohort?

[cid:image005.jpg@01D56E40.7241E0E0][cid:image006.jpg@01D56E40.7241E0E0]

[cid:image007.jpg@01D56E40.7241E0E0]


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[Freesurfer] Research Assistant Position (infant/pediatric MR imaging) Boston Children's Hospital/Harvard Medical School

[Gaab, Nadine]

The Gaab Lab (www.gaablab.com) is looking for a Clinical Research Assistant II 
to assist with all study phases of functional and structural MRI for our 
longitudinal infant MRI study. This position is ideal for anyone considering 
future graduate study in cognitive (developmental) neuroscience, computer 
science, cognitive science or neuroscience. This Clinical Research Assistant II 
will be responsible for: Subject recruitment for pediatric research studies 
which will include close interaction with schools and daycare centers in the 
Boston area. Scheduling of pediatric (infant) research subjects. Maintaining of 
database, implementing and maintaining of analysis software; pediatric testing 
(including MRI/fMRI scanning of young children, infants, and their parents) and 
data analyses (psychometrics, psychophysics and functional magnetic imaging), 
stimuli design and administrative work (e.g., preparation of internal review 
board proposals). Under general supervision coordinating activities of daily 
operations of clinical research studies. Screening, consenting, recruiting, and 
selecting patients for studies. Preparing IRB and/or CCI documentation and 
submissions in conjunction with the Principal Investigator and/or other members 
of the research team. Conducting data collection activities and preparing 
analytical reports regarding results of studies. Assisting in writing articles 
and summary papers for various publications.

To qualify, you must have: A Bachelor's Degree in computer science, psychology, 
cognitive science, neuroscience, math, or related field required and one year 
of relevant work experience. Comfort with a heterogeneous computing environment 
(Linux/Unix, Mac, and Windows) as well as some programming experience 
preferred; knowledge of psychological experiment software (E Prime, 
Presentation, etc.) and/or fMRI analyses software helpful. Demonstrable 
pre-existing interest in cognitive neuroscience desired; knowledge of 
neuroanatomy or statistics helpful. Prior experience working with infants and 
small children (e.g. in a preschool or daycare setting or within a research 
project) will be a plus. Must be self-motivated and able to work in a 
fast-paced, changing environment and must like working with children. Boston 
Children’s Hospital offers competitive compensation and unmatched benefits, 
including a rotating days/evenings and week-end schedule, affordable health, 
vision and dental insurance, generous levels of time off, 403(b) Retirement 
Savings plan, Pension, Tuition Reimbursement, cell phone plan discounts and 
discounted rates on T-passes (50% off). Boston Children’s Hospital is an Equal 
Opportunity / Affirmative Action Employer. Qualified applicants will receive 
consideration for employment without regard to their race, color, religion, 
national origin, sex, sexual orientation, gender identity, protected veteran 
status or disability.

Please apply through the Boston Children’s Hospital job portal. The ReqID is 
52838BR​: http://www.childrenshospital.org/career-opportunities

"Nothing in science has any value to society if it is not communicated." Anne 
Roe (1904-1991)

Nadine Gaab, PhD
Associate Professor of Pediatrics
Boston Children's Hospital/Harvard Medical School
Department of Medicine/Division of Developmental Medicine
Laboratories of Cognitive Neuroscience
Mail stop code: BCH3178
1 Autumn Street (Office 643); Boston, MA 02115
nadine.g...@childrens.harvard.edu
phone: 857-218-3021
www.gaablab.com
www.bostonearlyliteracyscreener.com
Twitter: Nadine Gaab (@GaabLab)


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Re: [Freesurfer] mkcontrast-sess question

[Nasiriavanaki, Zahra]

Thanks a lot Doug!
It was exactly what I needed.

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Monday, September 16, 2019 10:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mkcontrast-sess question

Are you trying to do a parametric analysis? See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation

On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Hi

I have a question about weighting different contrasts using mkcontrast-sess 
commmand.
I have single subject functional data with 18 different contrasts, and I am 
willing to weight the different contrasts as (for example) ascending linear. 
Something like:
 mkcontrast-sess -an $analysis   -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 
6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18
 In which contrast number two weights twice as contrast number one and contrast 
number 3 weights twice as contrast number 2 and so on.  Is there any way I can 
do such a thing with mkcontrast-sess? or do you have any suggestion for such an 
analysis?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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[Freesurfer] GNU R package to read and write FreeSurfer data

[Tim Schäfer]

External Email - Use Caution

Dear list,

I needed some GNU R functions which read and write MGH/MGZ files including all 
the header information, so I wrote them and also put them into a package to 
share them. 

Support for binary 'curv' format morphometry files (like 'surf/lh.area') and 
annotations (like 'labels/lh.aparc.annot') in also included.

The package is on CRAN: https://cran.r-project.org/package=freesurferformats

Docs, examples and vignettes are included. Unit tests can be found (with the 
full source code) on GitHub: https://github.com/dfsp-spirit/freesurferformats

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] qdec contrast and data extraction

[Maximo, Jose Omar]

External Email - Use Caution

Hi,

I tried that and it seemed to work. My averages between the 2 groups look 
different now instead of almost identical. Thanks!

I have another similar question. I have a cluster that shows a significant 
difference between the groups when looking at volume. When I look at the 
y.ocn.dat file, the values are in the 0.74188 - 2.16321 range, which are pretty 
low for volume. I found a post where it says that you can multiply those values 
with the cluster size(mm^2) from the summary file to convert them to volume. 
Then, I tried using the formula you provided below (beta, res, yhat), but then 
I get some negative values. Negative volumetric values do not make sense, so I 
was thinking if using the absolute value would correct for that.

Any thoughts?

Thanks for all the help so far.

>If you say y = ocn.dat, then
>beta = (X'*X)*X'*y;
>res = y - X*beta;
>yhat = X(:,1:2)*beta(1:2) + res;
>yhat will be a score for each subject with the nuisance variables removed.
>
>On 9/11/19 2:40 PM, Maximo, Jose Omar wrote:
>
>External Email - Use Caution
>

>Hi,

>

>I plotted the data from the *.y.ocn.dat file and the graph still shows no 
>apparent significant difference between the groups (see attached pic). Then I 
>>found a post with the following:

>

the ocn.dat files have data that is uncorrected in that sense and might need to 
nuisance factors removed before plotting.

There is a design matrix in there (Xg.dat). You can load that into matlab along 
with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn)

to get the betas. You can then compute yhat = X2*beta2 where X2 has nuisance 
columns removed and beta2 has the same nuisance coefficients removed, then 
treat yhat as your data to be plotted.

>

>I tried that since I have 2 nuisance factors (age and TICV) and want to plot 
>my significant cluster w/o any nuisance effects. This is what I get

>

   1.8973

   1.8973

   1.8973

   …

   3.4728

   3.4728

   3.4728

   …

>Are these the mean averages for each group (cortical thickness). If so, is 
>there a way to get a score for each subject?

>

>Best,

>Omar

  >

>Look  in the *.y.ocn.dat file.

>

> From mri_glmfit-sim --help

>

>csdbase.y.ocn.dat - this is a summary of the input (y) over each

>cluster. It has a column for each cluster. Each row is a subject. The

>value is the average of the input (y) in each cluster. This is a

>simple text file.

>

>

>

>On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote:

>  External Email - Use Caution

>

> Hi,

>

> Which specific file should I load? I see cluster.mgh, cluster.summary, 
> sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat.

>

> How can I extract the values from fsaverage space?

>

> Basically, what is the correct way to extract values from these significant 
> clusters?

>

> Many thanks,

> Omar

>

>  Date: Tue, 3 Sep 2019 15:15:02 +

>  From: "Greve, Douglas N.,Ph.D."  mgh.harvard.edu>

>  Subject: Re: [Freesurfer] qdec contrast and data extraction

>  To: "freesurfer at 
> nmr.mgh.harvard.edu"
>   nmr.mgh.harvard.edu>

>  Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a218 at 
> mgh.harvard.edu>

>  Content-Type: text/plain; charset="utf-8"

>

>  You might have done something wrong along the way. When you run the 
> montecarlo correction, it will create a file with the thickness values in it 
> for each cluster. the first thing to do is to load that and see if you see 
> the expected differences. The other thing is to not go back into native space 
> to extract the numbers. There are several operations that happen as it moves 
> into fsaverage space and in preparation for group analysis (interpolation, 
> and smoothing); sometimes these make a big difference. if the ROI is small, 
> it may not map accurately back into the native space (and you should not need 
> to draw it in the first place)

>

>  On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:

>

>  External Email - Use Caution

>  Hi,

>

>  I have a question:

>

>  My design is 2 groups (HC and Patients in that respective order) and 2 
> nuisance factors (age and eTIV). When I look at the average volume difference 
> between the 2 groups, I get blue and red clusters. I presume the color coding 
> is where each group is greater than the other (Blue = Patients > HC and Red = 
> HC > Patients).

>

>  Then, I processed to extract individual values from each cluster in 
> order to plot them. When I extract data from the blue clusters and plot them, 
> the two groups show no difference in thickness at all, whereas when I look at 
> volume, HC show more than patients in blue clusters (see at

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

[Bruce Fischl]

Hi Vasudev

-openmp N is the best way at the moment. Do you actually have 3 cores to 
dedicate? Usually due to memory access speeds and such we don't see much 
gain after N=4, but I'm surprised there is no effect

cheers
Bruce
On Wed, 18 Sep 2019, 
Dev vasu wrote:




External Email - Use Caution

Dear all,

I am using - openmp 30 to run recon-all, i see now change in the execution
time period.

Could you please highlight me a method to reduce the execution time for
recon-all, if possible some parallel script to do that same.


Thanks
Vasudev

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Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

[Tim Schäfer]

External Email - Use Caution

I would recommend GNU parallel. I have 2 scripts here:

   
https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall_minimal

and an explanation of what they do and how to use them at 
https://www.xsmd.org/brain/2019/03/13/using-gnu-parallel-to-speedup-neuroimaging

You need to adjust some stuff, but they should get you going. You need the Bash 
shell and GNU parallel installed.

Best,

Tim

> On September 18, 2019 at 3:07 PM Dev vasu 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear all,
> 
> I am using - openmp 30 to run recon-all, i see now change in the execution
> time period.
> 
> Could you please highlight me a method to reduce the execution time for
> recon-all, if possible some parallel script to do that same.
> 
> 
> Thanks
> Vasudev
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Hi Vasudev,

in case you use v6, you can use the -parallel flag to process the hemispheres 
(and a few other things if I remember correctly) in parallel. Note that doing 
so will parse the -openmp flag to all instances. E.g.

recon-all -all -openmp 4 -parallel -s subjID -i inputFile

Also the reduction in processing time using openmp is limited – I don’t recall 
exactly if it was bound to the number of physical cores your CPU has or if it 
was an upper limit to due the way the parallelization works (I have something 
like in mind like not much of an increase beyond openmp 8).

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Dev vasu
Gesendet: Mittwoch, 18. September 2019 15:08
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] How to fasten recon-all execution time without using CUDA


External Email - Use Caution
Dear all,

I am using - openmp 30 to run recon-all, i see now change in the execution time 
period.

Could you please highlight me a method to reduce the execution time for 
recon-all, if possible some parallel script to do that same.


Thanks
Vasudev
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[Freesurfer] How to fasten recon-all execution time without using CUDA

[Dev vasu]

External Email - Use Caution

Dear all,

I am using - openmp 30 to run recon-all, i see now change in the execution
time period.

Could you please highlight me a method to reduce the execution time for
recon-all, if possible some parallel script to do that same.


Thanks
Vasudev
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Re: [Freesurfer] negative values of hippocampal subfields volumes

[Iglesias Gonzalez, Juan E.]

Dear Chris,
Can you please send us the output txt file?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Krzysztof Gbyl 

Reply-To: Freesurfer support list 
Date: Wednesday, 18 September 2019 at 08:41
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] negative values of hippocampal subfields volumes


External Email - Use Caution
Hi all,

I am currently running a longitudinal hippocampal subfields analysis using 
version 6.0.
Based on the visual inspection of images, I see that Freesurfer is doing a 
great job.

The problem is that I get negative values of the subfields volumes
e.g.
Hippocamap_tail -420.400366
subiculum -368.134590

The values seems to be reasonable, but why they are negative, i.e. why they 
have a '-' sign.
Could the minus sign be a hyphen?

Has anybody encounther this problem? I hope you can help

BW,
Chris


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[Freesurfer] Names of the segmentation volumes in lh.hippoSfLabels-T1.v10.mgz

[Kai Liu]

External Email - Use Caution

Hi FS experts,

I am using the module of segmentation of hippocampal subfields.

About the output of lh.hippoSfLabels-T1.v10.mgz, could you pls provide the 
correspondence between the values of segmentation volumes in the image file and 
the anatomical names in the file of lh.hippoSfVolumes-T1.v10.txt?

I am pretty confused because there are totally 12 regions as described in the 
.txt file, and I was anticipating 12 values corresponding to 12 segmentation 
volumes in the .mgz file (like aseg). However, I found 14 discontinuous values 
in the .mgz ranging from 203 to 226.

Looking forward to your kind reply.

Kai
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