Re: [Freesurfer] how to dilate a mgh binary mask file in fsaverage space. The file is in .mgh format.

[Bruce Fischl]

Hi Ani

the dev version of freeview has some label morphology operations in the 
interface, including dilation. Try downloading the dev version and see if 
it solves your problem


cheers
Bruce

p.s. I think mri_label2label can also do a dilation
On Wed, 5 Sep 2018, Anik 
Dar wrote:




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Hi 
I have created a .mgh file which is a bunch of vertices all with a value of 1. 
Please see pic. 
Screen Shot 2018-09-05 at 7.06.04 PM.png

I want to create a bigger region of interest by dilating this yellow region 
lets say with a radius
of 10 vertices around this region. How to do it ?

Thank you.

Ani

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[Freesurfer] Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018

[Kelvin Mok]

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-- Forwarded message -
*From:* Amir Shmuel, Dr.
*Subject:* Resting-State and Brain Connectivity 2018: Early registration
fee applies until September 14, 2018


*Resting-State and Brain Connectivity 2018: *Early registration fee applies
until September 14, 2018



Educational course: September 24-25

Conference, featuring 45 world-renowned speakers: September 26-28

Satellite workshop on how to incorporate machine and deep learning in your
data analysis: September 29

*http://restingstate.com/2018/ *



*Amir Shmuel*

*Chair of the organizing committee*

*Resting-State and Brain Connectivity 2018*

*Montreal, QC, Canada*



*[image:
http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-2018-650-300x218.jpg]*
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Re: [Freesurfer] Mean FA values for major tracts all greater than 1

[Yendiki, Anastasia]

You should probably be suspicious.

From: Katherine Damme 
mailto:katherine.da...@gmail.com>>
Date: Wednesday, September 5, 2018 at 1:48 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>>
Subject: Mean FA values for major tracts all greater than 1


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Hello Freesurfer Support group,

I have run tracula on hundreds of subjects for a study and their primary tracts 
are all showing that MFA is greater than 1. Typically, I expected that MFA 
should be in the .3 to 1 range. Should I be suspicious that these MFA values 
are over the top of that range or is this common for major tracts like the 
forceps major?

Thank you for your insights on this potential error.

Kate
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[Freesurfer] Mean FA values for major tracts all greater than 1

[Katherine Damme]

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Hello Freesurfer Support group,

I have run tracula on hundreds of subjects for a study and their primary
tracts are all showing that MFA is greater than 1. Typically, I expected
that MFA should be in the .3 to 1 range. Should I be suspicious that these
MFA values are over the top of that range or is this common for major
tracts like the forceps major?

Thank you for your insights on this potential error.

Kate
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Re: [Freesurfer] mris_compute_parc_overlap average minimum distance measurement

[Bruce Fischl]

Hi Jared

I think you description is accurate, but I believe we compute the 
distances both ways then average them, making it symmetric. As to surfae 
area corrections, I guess that kind of depends on what you care about.


cheers
Bruce
On 
Wed, 5 Sep 2018, Zimmerman, Jared wrote:




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Hi Freesurfers,

 

I’m using mris_compute_parc_overlap to compare the similarity between two
parcellations and I’m curious about how the average minimum distance
measurement is calculated.

 

The help text for the function says “… a table of mean minimum distances
between corresponding labels.”  My questions are 1) what set of measurements
is being meaned here, and 2) what exactly is the measurement.  My current
interpretation is that for every vertex in annot1 the minimum distance to a
vertex in annot2 with the same label is calculated such that overlapping
regions have a distance of zero.  The mean is then calculated over these
distance measures for all vertices in a given label.

 

If this is true, do you recommend doing any subject level corrections? 
Seems like subjects with larger cortical surface areas would be biased to
have larger distances.

 

Thanks,

Jared


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[Freesurfer] mris_compute_parc_overlap average minimum distance measurement

[Zimmerman, Jared]

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Hi Freesurfers,

I’m using mris_compute_parc_overlap to compare the similarity between two 
parcellations and I’m curious about how the average minimum distance 
measurement is calculated.

The help text for the function says “… a table of mean minimum distances 
between corresponding labels.”  My questions are 1) what set of measurements is 
being meaned here, and 2) what exactly is the measurement.  My current 
interpretation is that for every vertex in annot1 the minimum distance to a 
vertex in annot2 with the same label is calculated such that overlapping 
regions have a distance of zero.  The mean is then calculated over these 
distance measures for all vertices in a given label.

If this is true, do you recommend doing any subject level corrections?  Seems 
like subjects with larger cortical surface areas would be biased to have larger 
distances.

Thanks,
Jared
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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Martin Reuter]

Hi Anwar, 

I see, you want to convert the mgh file back to some text table. Not
sure how that worked, but I think mri_convert could do it (but maybe
only for a single subject with several structures, not sure about
multiple subjects - this is a stacked file). Another way is to open the
mgh in matlab or python and then you get a vector and output it to a
text file.

Best, Martin


On Tue, 2018-09-04 at 20:05 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> 
> Hi Martin/Doug:
> 
> Still looking for an answer. Could not find a way to list the
> percentage change values for each subject in a tabular form.
> 
> Thanks,
> 
> Anwar
> 
> On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"  ybrook.ca> wrote:
> 
> External Email - Use Caution
> 
> Hello Martin:
> 
> I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42
> (that came with it by default).
> 
> If I omit --out-pc1 but keep --do-pc1 still do not get any output
> as a .dat or .stats file. I only get .mgh file in surf folder.
> 
> I need percentage change values of tp2 from tp1 for each subject
> in a tabular form.
> 
> Best,
> 
> Anwar
> 
> On 2018-08-30, 3:22 AM, "Martin Reuter"  .edu> wrote:
> 
> Hi Anwar,
> 
> what FS version are you using?
> 
> Also what happens if you omit the --out-pc1 but keep the --
> do-pc1 ?
> Also no output with that ending? It should write it to the
> default
> location.
> 
> Best, Martin
> 
> 
> 
> 
> 
> On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat
> wrote:
> > External Email - Use Caution
> > Dear Doug:
> >
> > I am trying to get a table containing pc1 values for each
> subject in
> > a longitudinal study and failed to extract this. I use the
> code
> > below:
> >
> > long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas 
> thickness
> > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
> --do-label
> > --time years --qcache fsaverage --sd
> > /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-
> pc1.dat
> >
> > It says
> > long_mris_slopes: error: no such option: --out-pc1
> >
> >
> > However in the --help file it says:
> >
> > Within-Subject Output:
> > Pass these to overwrite the default names:
> >
> > --out-avg=OUT_AVG   filename to store temporal average
> in
> > /stats/
> (default:
> > long..-avg.dat)
> > --out-rate=OUT_RATE
> > filename to store rate in
> > /stats/
> > (default: long..-
> rate.dat)
> > --out-pc1fit=OUT_PC1FIT
> > filename to store pct. change (to
> tp1fit) in
> > /stats/
> (default:
> > long..-pc1fit.dat)
> > --out-pc1=OUT_PC1   filename to store pct. change (to
> tp1) in
> > /stats/
> (default:
> > long..-pc1.dat)
> > --out-spc=OUT_SPC   filename to store sym. pct. change
> in
> > /stats/
> (default:
> > long..-spc.dat)
> > --out-resid=OUT_RESID
> > filename to store residual in
> > /stats/
> (default:
> > long..-
> resid.dat),
> > requires
> > --resid 
> > --out-stack=OUT_STACK
> > filename to store stacked measure
> file
> > /stats/
> (default:
> > long..-stack.dat)
> >
> >   Stacked Tables:
> > To output tables with results from all subjects
> >
> > --stack-avg=STACK_AVG
> > full filename to stack temporal
> average
> > tables
> > (default no stacking)
> > --stack-rate=STACK_RATE
> > full filename to stack rate tables
> (default
> > no
> > stacking)
> > --stack-pc1fit=STACK_PC1FIT
> > full filename to stack pct. change
> to tp1fit
> > tables
> > (default no stacking)
> > --stack-pc1=STACK_PC1
> > full filename to stack pct. change
> to tp1
> > tables
> > (default no stacking)
> > --stack-spc=STACK_SPC
> > full filename to stack sym. pct.
> tables
> > (default no
>   

[Freesurfer] Get corresponding vertex of another subject

[Michael .]

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Hi,

i want to create a lookup table for the vertex correspondence between the
subjects A & B (pial files). e.g verticesA(100) corresponds to
verticesB(122)

Of course the number of vertices is different between the subjects, e.g one
vertex of A can correspond to several vertices from B.

Currently, I am reading in the pial files of subject A using 'read_surf'
and create two label files (lh/rh) containing all vertices. In order to get
the corresponding vertices of Subject B, i use "label2label".

label file A:
#!ascii label, from subject
142350
0 -7.814680 -88.725967 9.598738 1.00
1 -8.505306 -88.835274 9.457685 2.00
2 -9.234029 -89.900490 9.420641 3.00

resulting label file:
#!ascii label  , from subject cvs_avg35_inMNI152/Segmentation vox2ras=TkReg
137427
888  -7.179  -84.047  -28.333 1.00
642  -7.533  -84.272  -28.382 2.00
637  -7.717  -84.612  -28.118 3.00

But how can I interpret the result?
Can I assume that verticesA(0) corresponds to verticesB(888)?
Or verticesA(0) corresponds to verticesB(888)?

Or is there another way to create such a lookup table?

Thank you in advance!
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Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

[Daniel Ferreira]

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Hi Martin,

Thank you very much for your answer.

Best regards

Dani

2018-09-04 16:38 GMT+02:00 Martin Reuter :

> Hi Dani,
>
> the regular FreeSurfer stream samples everything to 1mm isotropic. This is
> of course problematic, if you have one group scanned at 1mm and the other
> at a different resolution (as group differences could be affected by the
> different resolutions). You would never know how much of what you get is
> group and how much is resolution.
>
> Similarly this is problematic if you switch scanner, software, head-coil,
> resolution in a longitudinal study. Effects cannot be separated any longer
> and all you can report in a paper is that what you find is longitudinal
> effect plus resolution effects and you don’t know how much is which.
>
> FreeSurfers longitudinal stream therefore requires inputs to be the same
> resolution. This safety feature (to prevent potentially meaningless
> analysis) can be circumvented by manually sampling images first - at your
> own risk. If you go that way, you should at least also interpolate the 1mm
> images to a new position (at least then both images will have interpolation
> artefacts, so that differences are only the acquisition resolution and not
> additionally interpolation artefacts in one of the time points).
>
> As an example, taking the same image twice, mapping one to a different
> location and back again produces interpolation artefacts that are
> significant and at orders comparable with 1 year of neurodegenerative
> disease.
>
> Best, Martin
>
>
>
>
>
> On 30. Aug 2018, at 18:22, Daniel Ferreira  wrote:
>
>
>
> Dear colleagues,
>
> I was wondering if resampling voxel size is done during recon-all.
>
> Also, I have data with voxel resolution of 1x1x1 mm at baseline and
> 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation
> by default (or can be performed by any way) that minimizes these
> differences in somehow.
>
> Thank you very much
>
> Dani
>
> --
>
> *Daniel Ferreira, PhD, Assistant Professor*
>
> Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
> and Society
>
> Karolinska Institutet (Sweden)
>
> *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
> email: daniel.ferreira.padi...@ki.se *
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> dispose of the e-mail.
>
>


-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se *
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[Freesurfer] error in selxavg3-sess - mismatch TE

[stdp82]

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Hi list,


I have run the FS-FAST analysis in line with the standard procedures that I use 
routinely.

With new data, selxavg3-sess produces an errror: there is a mis-matched between 
the TE in the analysis (=3) and the TE in the data (=0). I have cheched the 
data information by fslinfo as well as MELODIC and both the operations confirm 
the data have a TE=3 that matches with TE reported in mkanalysis-sess .

How is it possible? Please, could you help me?

Thanks


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[Freesurfer] amygdala segmentation using additional scan error

[오진영]

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Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of
amygdala with additional scan.
I already ran segmentation of hippocampal subfields and nuclei of amygdala
with only T1 image, using segmentHA_T1.sh command and succeeded.
After success of segmentation of amygdala with T1 image, I tried to run
segmentation again with additional scan(T2 image) to get more reliable
results.
However, when I use command segmentHA_T2.sh, I got the following error:

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)


And the last few lines before the error are below:

*Fitting mesh to image data mask took 264.2808 seconds*

*Transforming points*

*Transforming points*

*Wrote image to file image1.mgz*

*Wrote image to file image2.mgz*

*INFO: dst volume info differs from the one stored in lta.  gets modified
now.*

*volume geometry:*

*extent  : (232, 469, 208)*

*voxel   : ( 0.,  0.,  0.)*

*x_(ras) : ( 0., -1.,  0.)*

*y_(ras) : ( 0.,  0., -1.)*

*z_(ras) : ( 1.,  0.,  0.)*

*c_(ras) : (-21.1788, -1.8961,  3.8447)*

*file: T2isotropic.mgz*

*volume geometry:*

*extent  : (256, 256, 256)*

*voxel   : ( 1.,  1.,  1.)*

*x_(ras) : ( 0., -1.,  0.)*

*y_(ras) : ( 0.,  0., -1.)*

*z_(ras) : ( 1.,  0.,  0.)*

*c_(ras) : ( 2.3212,  8.6039, -21.1553)*

*file: /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii*

*Constructing image-to-world transform from header information (asmr1.mgz)*

*Constructing image-to-world transform from header information
(/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)*

*Wrote image to file asmr2.mgz*

*This file does not contain MRI parameters*

*This file does not contain MRI parameters*

*This file does not contain MRI parameters*

*In an assignment  A(:) = B, the number of elements in A and B must be the
same.*


*Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)*




*MATLAB:subsassignnumelmismatch*

*Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun
21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64*

and I have no idea how to solve this problem out.

I use the dev version of freesurfer.
T1 scan image and T2 scan image of participant were taken on the same day.

If you have any recommendations, please send me the email back.

Thanks!

Jinyoung
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