Re: [Freesurfer] Hippo-subfiled Need Help

[Iglesias Gonzalez, Eugenio]

Its hard to tell without seeing the pixel intensities under the segmentation, 
but at first glance, it looks fine to me

Sent from my phone, please excuse brevity and typos

From: Ramesh Babu
Sent: Monday, May 1, 06:58
Subject: Re: [Freesurfer] Hippo-subfiled Need Help
To: Freesurfer support list

Dear Eugenio,

Thanks for your suggestion. What about the quality if segmented image which I 
have attached.

Please give your suggestions on the attached hippo-seg.

Thanks

Ramesh

On Mon, May 1, 2017 at 12:23 AM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Dear Ramesh,

The subfield segmentations requires running recon-all -all first. But you can 
greatly speed up the execution with the openmp option. Also, you can try 
running two subjects simultaneously, but only for the recon-all -all part (the 
subfields use more memory and might crash).

Cheers,

/Eugenio

Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>-boun...@nmr.mgh.harvard.edu>
 on behalf of Ramesh Babu 
mailto:mgrameshbabu2...@gmail.com>>
Sent: Saturday, April 29, 2017 9:46:24 AM
To: Freesurfer support list
Subject: [Freesurfer] Hippo-subfiled Need Help



Dear Experts,

I ave done hippocampal subfield segmentation by using 1x1x1 t1 scan. Please see 
the attached image and give your suggestions.

It took nearly 7 hrs 10 min. to complete hippo-subfield segmentation for one 
scan by using the command

recon-all -i grp205_t1.nii -s grp205 -sd grp205 -all

Started at Wed Apr 26 11:03:34 IST 2017
Ended   at Wed Apr 26 17:17:35 IST 2017
#@#%# recon-all-run-time-hours 6.234
recon-all -s grp205 finished without error at Wed Apr 26 17:17:35 IST 2017
done

Then for hipposubfield,

recon-all -s grp205 -sd grp205 -hippocampal-subfields-T1

I want to run for 40 scans grp-1 20 scans and grp-2 20 scans. How to modify in 
the command. Since it is taking long time I want to run 10 scans n give rest 
again 10 scans. Can I do so?

I am15.6 GiB ram, Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor, GeForce GT 
610/PCIe/SSE2 graphic card.It is octa core processor. Can I run 8 analysis 
simultaneously (in 8 separate terminal?).

Your suggestion will be helpful to me to proceed further.

Thanks

RB

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[Freesurfer] Consistent volume increases for some regions when using longitudinal stream

[Melanie Ganz]

Dear list and especially Martin,

we have used Freesurfers crosssectional as well as the longitudinal stream 
and are inspecting the outcomes at the moment. 

We have as quality assurance been inspecting regions where the 
difference between initial CROSS results and the corresponding LONG 
results exceeds 10 %. In this process we found that for certain regions 
it seems that the volume increases in almost every case. Below is an
overview of differences  between cross and long with mean, sd, max and 
min values in percent for different regions.

We also manually checked an example of the Caudate where there was an 
increase of 14 % from CROSS to LONG. This difference can be seen 
between  CROSS to LONG for time point 2. It seems like the longitudinal 
is correct when it covers more of the Caudate. The other time point for 
that subject and their base seems to provide extra information which is a good 
thing. 

However our question is why this seems to be a systematic
thing that all scans for the caudate region increases in volume when 
doing the longitudinal processing?
This is also the case for some other regions as seen below.

Kind regards/

Melanie and Mark

--
Percent volume changes between CROSS and LONG over 110 subjects:
Region
  Mean
  Sd
  Max
  Min
 Estimated brain Volume
  1
  4
  32
  -18
 Total Gray Matter Volume
  1
  1
  5
  -2
 White Matter Volume
  -1
  1
  2
  -5
 Caudate
  5
  2
  14
  0
 Putamen
  8
  3
  22
  1
 Thalamus
  2
  3
  13
  -10
 Amygdala
  -1
  4
  33
  -8
 Hippocampus
  1
  4
  33
  -5
 Ventricles
  0
  2
  5
  -5
 Frontal
  0
  2
  6
  -7
 Parietal
  2
  2
  8
  -6
 Temporal
  1
  2
  5
  -5
 Occipital
  1
  2
  9
  -5
 


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

[Douglas N Greve]

I can't seem to replicate your results locally, even with the recon-all 
you used. The one thing I'm missing is the expert options file. Can you 
send that to me?


On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with 
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice number 
> (coronal) also 100.
>
> I have processed the subjects with v 6.0 (in fact dev version from feb 2017, 
> but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e. 
> the wm.mgz and surfaces are much better, but v5.3 looks still better, at 
> least for subject 1.
> I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site.
>
> The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with 
> -cubic is very minor, but still there is some other thing which renders 
> wm.mgz worse than with v5.3 for subject 1.
> The -cubic has profound effect, the images seem much smooth with lose of 
> contrast without using -cubic.
>
> Regards,
>
> Antonin
>
>
> And what slice number?
> On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> > Anonin, of the three subjects you sent, which one is shown in these
> > pictures?
> >
> >
> > On 04/19/2017 05:23 PM, Antonin Skoch wrote:
> >> 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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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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[Freesurfer] Neuroscience of Language Postdoctoral Position at the University of California, San Francisco (UCSF) in California, USA

[Roeland Hancock]

Neuroscience of Language Postdoctoral Position at the University of California, 
San Francisco (UCSF) in California, USA
 
The Hoeft Neuroscience Lab (http://brainLENS.org PI: Fumiko Hoeft MD PhD) at 
the UCSF Dept of Psychiatry and Weill Institute for Neurosciences is looking 
for a full-time postdoctoral fellow for the ‘Intergenerational Neuroimaging of 
Language and Reading Networks’  project, which uses a ‘natural’ cross-fostering 
family design to partially dissociate the effects of genetics, prenatal, and 
postnatal environment on the human neural systems that underlie language 
processing. Related articles on this approach in different domains can be found 
here: Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy), Ho et al. Trends 
in Neurosci 2016 (http://goo.gl/SyXLcK), and Scientific American 
(http://goo.gl/YTiH6D). 

The successful candidate must have a PhD in Cognitive Psychology, Cognitive 
Neuroscience, Cognitive Science, Linguistics or a closely related field, 
experience in neuroimaging, excellent foundational skills in computation, 
programming and mathematics/statistics, and exceptional organizational skills. 
Candidates with experience in neurolinguistics or behavioral genetics are 
particularly encouraged to apply. Compensation is in accordance with the NIH 
pay scale for postdoctoral fellows. Appointments are made for 1 year terms with 
the possibility of renewal. Postdoctoral fellows are represented by UC Postdoc 
Union and enjoy competitive benefit packages.

The Hoeft Neuroscience Lab is an interdisciplinary research environment that 
applies cutting-edge neuroimaging techniques, genetic analysis, and 
computational approaches to examine language development processes, the 
etiology of neurodevelopmental disorders and the impact of diverse linguistic 
environments (e.g. bilingual education) on development. The successful 
candidate will have the opportunity to be involved in other research projects 
in the Laboratory, outreach and community engagement projects, and access to a 
wealth of archival developmental and longitudinal neuroimaging data on language 
and literacy. 
 
The position can begin immediately.
Applications should be emailed to brainl...@ucsf.edu  with “[Postdoc job]” and 
the applicant's full name in the subject of the email. Applications must 
include:
1. A current CV
2. A one page statement of research interests related to the proposed project
3. A one page cover letter describing qualifications for the position with 
specific examples, career goals and why you feel you are a good fit for the 
lab. 
4. The names of three references. Qualified candidates will be asked to have 
letters of reference forwarded. Do not submit reference letters with the 
application.

The University of California, San Francisco is a premier biomedical research 
institution, ranked second in the world for Neuroscience and Behavior by US 
News. UCSF has outstanding resources for cognitive neuroscience research, 
including a research-dedicated Siemens Prisma 3T MRI scanner in addition to 
shared 3T and 7T GE scanners, MEG and TMS equipment. The laboratory enjoys 
close collaborations with other research groups in the Bay Area, and national 
and international collaborations. 

The San Francisco Bay Area is a vibrant, multi-cultural city, ranked one of the 
most walkable cities in the US. In addition to the area’s outstanding cultural 
attractions and cuisine, the unique beauty of redwood forests, coastal cliffs, 
wine country and natural preserves is less than an hour from the city.___
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Re: [Freesurfer] Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?

[Jared Saletin]

Thanks Bruce!

That’s really good to know. So therefore, no need to have a “compromise” set of 
echo images for dura correction if I’m not feeding both inputs to recon-all? 
Would it make sense to run both days separately and just average thickness 
values between ROIs to reach a single value for each subject?

I guess this question is slightly complicated by having functional data on both 
days as well. I was debating which structural scan (post-freesurfer) to use as 
my registration base for the functional data. It seems I have two options: use 
the scan collected the same day as the functional — or use a single structural 
for both days (hence the impulse to feed both scans to a single recon-all.

I suppose a third option is just pick the scan with best quality and go with 
that for everything.

Do you have a gut feeling on which is the better strategy?

Best,
Jared


> Hi Jared
> 
> it's really an empirical question. With high quality data we have found 
> that adding scans doesn't help CNR very much (it reduced the N but the 
> blurring induced by differential distortion also reduces the C). If your 
> scans are noisy it might be worth it, but it really depends on the 
> acquisition
> 
> cheers
> Bruce
> 
> 
> On Fri, 28 Apr 2017, Jared 
> Saletin wrote:
> 
> > Hi Freesurfer Experts!
> >
> > I have two scans for each subject in a new experiment—taken on subsequent 
> > days, each using the MEMPRAGE protocol.
> >
> > I’ve successfully implemented DURA correction using the 4 echos when I’ve 
> > reconstructed each scan separately.
> >
> > However, since I have 2 scans for each subject, I was thinking rather than 
> > reconstruct the brain twice and average the thickness measurements, it 
> > would be better to feed both MEMPRAGE scans to recon-all.
> >
> > My question is if I do this, which echos should I use for Dura correction: 
> > day 1 or day 2 or is there a way to combine them into an average?
> >
> > Is this (feeding both days’ scans to recon-all) a reasonable strategy, or 
> > am I better to reconstruct the data separately?
> >
> > Thanks so much!
> > Jared
> > ___
> > Freesurfer mailing list
> > Freesurfer at nmr.mgh.harvard.edu 
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > 
> >


—

Jared M. Saletin, PhD

Assistant Professor of Psychiatry and Human Behavior
Alpert Medical School of Brown University

E.P. Bradley Sleep Research Lab
300 Duncan Drive
Providence, RI 02906

Email: jared_sale...@brown.edu
Phone: 401-421-9440 
Fax: 401-453-3578



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Re: [Freesurfer] Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?

[Bruce Fischl]

Hi Jared

again it depends on data quality. If it is good enough you are probably 
better off just picking the best scan and reconning it.


cheers
Bruce


On Mon, 1 May 2017, Jared Saletin wrote:



Thanks Bruce!
That’s really good to know. So therefore, no need to have a “compromise” set
of echo images for dura correction if I’m not feeding both inputs to
recon-all? Would it make sense to run both days separately and just average
thickness values between ROIs to reach a single value for each subject?

I guess this question is slightly complicated by having functional data on
both days as well. I was debating which structural scan (post-freesurfer) to
use as my registration base for the functional data. It seems I have two
options: use the scan collected the same day as the functional — or use a
single structural for both days (hence the impulse to feed both scans to a
single recon-all.

I suppose a third option is just pick the scan with best quality and go with
that for everything.

Do you have a gut feeling on which is the better strategy?

Best,
Jared


Hi Jared

it's really an empirical question. With high quality data we have found 
that adding scans doesn't help CNR very much (it reduced the N but the 
blurring induced by differential distortion also reduces the C). If your 
scans are noisy it might be worth it, but it really depends on the 
acquisition


cheers
Bruce


On Fri, 28 Apr 2017, Jared 
Saletin wrote:


> Hi Freesurfer Experts!
>
> I have two scans for each subject in a new experiment—taken on subsequent 
days, each using the MEMPRAGE protocol.

>
> I’ve successfully implemented DURA correction using the 4 echos when I’ve 
reconstructed each scan separately.

>
> However, since I have 2 scans for each subject, I was thinking rather than
 reconstruct the brain twice and average the thickness measurements, it woul
d be better to feed both MEMPRAGE scans to recon-all.
>
> My question is if I do this, which echos should I use for Dura correction:
 day 1 or day 2 or is there a way to combine them into an average?
>
> Is this (feeding both days’ scans to recon-all) a reasonable strategy, or 
am I better to reconstruct the data separately?

>
> Thanks so much!
> Jared
> ___
> Freesurfer mailing list
> Freesurfer at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>



—

Jared M. Saletin, PhD

Assistant Professor of Psychiatry and Human Behavior
Alpert Medical School of Brown University

E.P. Bradley Sleep Research Lab
300 Duncan Drive
Providence, RI 02906

Email: jared_sale...@brown.edu
Phone: 401-421-9440 
Fax: 401-453-3578




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[Freesurfer] R: R: R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt

[stdp82]

Dear list and Eugenio, 

I have run for each subject
mri_label2vol --label SUBJ/label/rh.perirhinal_exvivo.thresh.label --regheader 
SUBJ/mri/norm.mgz --fill-ribbon --subject SUBJ --hemi rh --o 
SUBJ/mri/rh.perirhinal.nii.gz

next, to use FS-FAST on perihrinal.nii.gz, I have run
fcseed-config -seg SUBJ/mri/lh.perirhinal.nii.gz -fcname L_Perirhinal.dat -fsd 
rest -mean -cfg mean.L_Perirhinal.config

This error occurs:
ERROR: no segmentations IDs (-segid) or ROI (-roi) specified
What's should I do?
Thanks

Stefano

On Mon, 06 Feb 2017 13:59:38 -0800
Do you mean to use them as seeds in FSFAST? You'll need to map them into 
the conformed space using mri_label2vol with the --regheader option (see 
the --help); view the volume to make sure it looks ok. Then run 
fcseed-config specifying the volume with -seg and the code with segid




Messaggio originale

Da: std...@virgilio.it

Data: 6-feb-2017 22.27

A: "Freesurfer support list"

Ogg: [Freesurfer] R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt



Thank you very much.Could you provide me any suggestion to extract CA1 left or 
CA1 right?And how can I use them in FAST? By codes?Regards,Stefano



Messaggio originale

Da: "Iglesias Gonzalez, Eugenio" 

Data: 6-feb-2017 17.42

A: "std...@virgilio.it", "Freesurfer support 
list"

Ogg: Re: [Freesurfer] R: Re:  Hipposubfields in FreeSuerferColorLUT.txt






You would extract CA1 left from lh.hippoSfLabels-T1.v10.mgz and CA1 right from 
rh.hippoSfLabels-T1.v10.mgz (assuming you’ve used T1s to segment the subfields).
Cheers,
/E





Juan Eugenio Iglesias

ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/








On 6 Feb 2017, at 16:17, 
std...@virgilio.it wrote:



Thanks Eugenio for your response.
My apologies but this matter is unclear to me.
If I would use results for FS-FAST how I can identify for example CA1 right 
from CA1 left?
Additionally, for enthorinal which is the correct code in FAST?
Stefano

Messaggio originale
Da: "Iglesias Gonzalez, Eugenio" 
Data: 6-feb-2017 15.54
A: "std...@virgilio.it", "Freesurfer support 
list"
Ogg: Re: [Freesurfer] Hipposubfields in FreeSuerferColorLUT.txt

Ciao Stefano,
The results for the left and right hippocampi are in different files, so 
there’s no ambiguity despite the fact that they indeed share the same label 
codes.
Cheers,
/Eugenio





Juan Eugenio Iglesias

ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/








On 6 Feb 2017, at 13:18, 
std...@virgilio.it wrote:



Hi list,
within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the 
hippo-subfield outputs?
Additionally, how can I obtain separate right and left masks?

Thanks

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

[Antonin Skoch]

Dear Doug,

that is strange. What precisely you cannot replicate? The results with v5.3 or 
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in 
many subjects and the difference between -cubic and no cubic seems profound and 
systematic in favor of v5.3 in the aspect of wm.mgz leak ouside brain and GM/WM 
contrast.

Concerning the expert options file: Despite using flag -xopts-use in recon-all 
in v5.3, I did not use any expert option file in 
the subject I have uploaded. The reason of using -xopts-use was that I was 
processing the subjects in batch where some of them had expert-options file 
with entry bbregister -init-header due to the fact that init-fsl failed in 
these subjects.
I wanted to make my life easier by processing all of them by identical 
recon-all command line parameters and added -xopts-use to all subjects (even in 
the subjects without expert option file). I supposed that this could not do any 
harm.

Antonin


I can't seem to replicate your results locally, even with the recon-all 
you used. The one thing I'm missing is the expert options file. Can you 
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with 
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice number 
> (coronal) also 100.
>
> I have processed the subjects with v 6.0 (in fact dev version from feb 2017, 
> but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e. 
> the wm.mgz and surfaces are much better, but v5.3 looks still better, at 
> least for subject 1.
> I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site.
>
> The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with 
> -cubic is very minor, but still there is some other thing which renders 
> wm.mgz worse than with v5.3 for subject 1.
> The -cubic has profound effect, the images seem much smooth with lose of 
> contrast without using -cubic.
>
> Regards,
>
> Antonin
>
>
> And what slice number?
> On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> > Anonin, of the three subjects you sent, which one is shown in these
> > pictures?
> >
> >
> > On 04/19/2017 05:23 PM, Antonin Skoch wrote:
> >> 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] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[Douglas Greve]

It is subject #1, trying to replicate in our version of 5.3 using the 
scripts/recon-all.local-copy


./recon-all.local-copy -all -FLAIRpial -s 1.dng.v53.local-cubic -cubic

The results were close, but they were not exact



On 5/1/17 4:13 PM, Antonin Skoch wrote:

Dear Doug,

that is strange. What precisely you cannot replicate? The results with v5.3 or 
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in 
many subjects and the difference between -cubic and no cubic seems profound and 
systematic in favor of v5.3 in the aspect of wm.mgz leak ouside brain and GM/WM 
contrast.

Concerning the expert options file: Despite using flag -xopts-use in recon-all 
in v5.3, I did not use any expert option file in
the subject I have uploaded. The reason of using -xopts-use was that I was 
processing the subjects in batch where some of them had expert-options file 
with entry bbregister -init-header due to the fact that init-fsl failed in 
these subjects.
I wanted to make my life easier by processing all of them by identical 
recon-all command line parameters and added -xopts-use to all subjects (even in 
the subjects without expert option file). I supposed that this could not do any 
harm.

Antonin


I can't seem to replicate your results locally, even with the recon-all
you used. The one thing I'm missing is the expert options file. Can you
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice number
> (coronal) also 100.
>
> I have processed the subjects with v 6.0 (in fact dev version from feb 2017,
> but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e.
> the wm.mgz and surfaces are much better, but v5.3 looks still better, at
> least for subject 1.
> I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site.
>
> The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with
> -cubic is very minor, but still there is some other thing which renders
> wm.mgz worse than with v5.3 for subject 1.
> The -cubic has profound effect, the images seem much smooth with lose of
> contrast without using -cubic.
>
> Regards,
>
> Antonin
>
>
> And what slice number?
> On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> > Anonin, of the three subjects you sent, which one is shown in these
> > pictures?
> >
> >
> > On 04/19/2017 05:23 PM, Antonin Skoch wrote:
> >> 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] [FreeSurfer] cortical parcellation

[VA Research]

thanks guys!

On Fri, Apr 28, 2017 at 4:16 PM, Douglas N Greve 
wrote:

> No, you can do it with
>
> mri_binarize --i aparc+aseg.mgz --match ID --o roi.ID.nii.gz
>
> where ID is the parc id from the FreeSurferColorLUT.txt
>
>
> On 04/28/2017 06:58 PM, VA Research wrote:
> > Does freesurfer output individual roi volume masks for each of the
> > cortical parcellations in aparc+aseg?
> >
> > thanks
> >
> > Joseph Veliz
> > VA Hospital West LA
> >
> >
> > ___
> > 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[Antonin Skoch]

Doug,

did you process from scratch or did you retain edits to brainmask.mgz and 
wm.mgz?

The -cubic should not be necessary, since recon-all (which I primarily obtained 
from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ has 
UseCubic=1 ).

I could try to replicate v5.3 again on my side.

Antonin



It is subject #1, trying to replicate in our version of 5.3 using the  
scripts/recon-all.local-copy ./recon-all.local-copy -all -FLAIRpial -s 
1.dng.v53.local-cubic -cubicThe results were close, but they were not exact



On 5/1/17 4:13 PM, Antonin Skoch wrote:
Dear Doug,

that is strange. What precisely you cannot replicate? The results with v5.3 or 
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in 
many subjects and the difference between -cubic and no cubic seems profound and 
systematic in favor of v5.3 in the aspect of wm.mgz leak ouside brain and GM/WM 
contrast.

Concerning the expert options file: Despite using flag -xopts-use in recon-all 
in v5.3, I did not use any expert option file in
the subject I have uploaded. The reason of using -xopts-use was that I was 
processing the subjects in batch where some of them had expert-options file 
with entry bbregister -init-header due to the fact that init-fsl failed in 
these subjects.
I wanted to make my life easier by processing all of them by identical 
recon-all command line parameters and added -xopts-use to all subjects (even in 
the subjects without expert option file). I supposed that this could not do any 
harm.

Antonin


I can't seem to replicate your results locally, even with the recon-all
you used. The one thing I'm missing is the expert options file. Can you
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice number
> (coronal) also 100.
>
> I have processed the subjects with v 6.0 (in fact dev version from feb 2017,
> but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e.
> the wm.mgz and surfaces are much better, but v5.3 looks still better, at
> least for subject 1.
> I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site.
>
> The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with
> -cubic is very minor, but still there is some other thing which renders
> wm.mgz worse than with v5.3 for subject 1.
> The -cubic has profound effect, the images seem much smooth with lose of
> contrast without using -cubic.
>
> Regards,
>
> Antonin
>
>
> And what slice number?
> On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> > Anonin, of the three subjects you sent, which one is shown in these
> > pictures?
> >
> >
> > On 04/19/2017 05:23 PM, Antonin Skoch wrote:
> >> 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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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