Re: [Freesurfer] How to compute area of subcortical structures

[anirudh nihalani]

Hi Bruce,

Thank you very much for your quick reply. Sorry I hadn't been able to
reply faster as I was trying to figure out the below mentioned issue from
two days.

 I have computed surface area of left-hippocampus using the commands
mri_tessellate and mris_info. However I found that in freeview by selecting
Tools->show label stats, I am able to display area of any label (PFA a
screenshot) but these area stats do not match with the areas obtained using
mri_tessellate and mris_info. I have two queries regarding this:

1) Surface areas of labels displayed in freeview doesn't match with
subcortical structures' areas obtained by running mri_tesselate and
mris_info. For example the attached screenshot shows that area of
left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info
found the area for left-hippocampus to be 3586 (PFA the output of
mris_tessellate and mris_info). Why is there a mismatch?

2) Based on your reply I thought area stats are not calculated for
subcortical structures during "recon-all". If that is the case, how is
freeview displaying area stats for subcortical areas? Also which file does
freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask
because even cortical structures' areas displayed by freeview are not
matching with what is stored in these files.

Please let me know. Thank you.

Regards,
Anirudh
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[Freesurfer] Advice for FreeSurfer developers

[Gronenschild Ed (NP)]

Dear developers,

Is it possible to check the presence of Matlab runtime right at the start of 
recon-all
in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for
a high-res data processing I got this unexpected error message.
Thanks in advance.

Cheers
Ed
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Re: [Freesurfer] mri_vol2surf Matlab Function

[Fatemeh.Molaei-Vaneghi]

What is saved in Matlab cell arrays is simply volumetric SPM data for different 
subjects, ROIs, and etc. For example I have "data {subject no.,contrast 
no.}{roi, hemisphere}" which is a 2D cell with each cell being a cell too. What 
I want is run mri_vol2surf for each of these subjects, each of these contrasts, 
each of these ROIs, each of these hemispheres, and finally for each of 9 
intermediate surfaces.

I already tried "system","unix", and "!" in order to run unix commands in 
Matlab, not successful either. 
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[Freesurfer] TalX TalY TalZ

[Yang, Daniel]

Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? (with 
—fixmni)

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

[Douglas Greve]

does that file exist? Did you run recon-all -qcache ?

On 11/11/15 7:54 AM, Heidi Foo wrote:
Apologies, the error message should be /Error in analyze: couldn't 
open 
/Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz 
or .mgh file./


On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo > wrote:


Hi Dr Greve,

Thank you for your advice, it is deeply appreciated. I removed the
blank lines of wmh.levels and included a carriage return at the
end of the long.qdec.table.txt.

However, there is still /error in analyze: Couldn't open

/Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file./
/
/
I checked my qdec.table.txt (both cross and long) but I did not
see any fsaverage included in the list of subjects. Am I missing
something?

Thank you.

Regards,
Heidi Foo
/
/

On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Also, try removing the blank line at the end of wmh.levels,
and make sure you have a carriage return at the end of
long.qdec.table.txt. This may fix the 2nd error

On 11/09/2015 10:38 PM, Heidi Foo wrote:

Dear Dr Greve,

Thanks for your reply. I have already linked fsaverage to
my SUBJECTS_DIR but the error still persists.

Attached is my qdec (long and cross) files.

Thanks.

Regards,
Heidi Foo



On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:



On 11/06/2015 09:35 PM, Heidi Foo wrote:

Dear FreeSurfer experts,

I am trying to compare between stable WMH group
and rapid
progressed WMH group in regards to the cortical
thickness as
well as volume changes in the gray matter. The
nuisance
variable in my case is age. I ran my analysis
using QDEC but
encountered a few problems:

1. There is error in analyze: couldn't open file

It looks like it cannot find fsaverage. Link it to your
SUBJECTS_DIR if you have not already.

2. If this error doesn't appear, another one does.
QdecGlmDesign::Create: zero factors!
(Attached the screenshot of the errors for your
perusal)

please send the qdec file


I am hoping that you could give me a solution to
my problems.

Thank you so much.

Regards,
Heidi


-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu

>
Phone Number: 617-724-2358 
>
Fax: 617-726-7422  >

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html

   


Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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the e-mail
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-- 
Douglas N. Greve, Ph.D.

MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  

Re: [Freesurfer] mri_vol2surf Matlab Function

[Douglas Greve]

mri_vol2surrf  operates on volumetric data. If your data is not 
volumetric, then you can't use it. If it is volumetric but not stored on 
disk in a volume format (eg, nii. mgz), then you cannot use it directly. 
If you can write out your data in such a format, then you can use it.


On 11/11/15 6:51 AM, Fatemeh.Molaei-Vaneghi wrote:
> What is saved in Matlab cell arrays is simply volumetric SPM data for 
> different subjects, ROIs, and etc. For example I have "data {subject 
> no.,contrast no.}{roi, hemisphere}" which is a 2D cell with each cell being a 
> cell too. What I want is run mri_vol2surf for each of these subjects, each of 
> these contrasts, each of these ROIs, each of these hemispheres, and finally 
> for each of 9 intermediate surfaces.
>
> I already tried "system","unix", and "!" in order to run unix commands in 
> Matlab, not successful either.
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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[Freesurfer] OS version on Edits/Analysis

[Andrew Schoen]

Hi all,

I know there is good evidence to support analyzing and performing edits on the 
same version of freesurfer, and the same operating system. However, our systems 
are going to be updating to Scientific Linux 7, from Scientific Linux 6 in the 
coming weeks. We are planning to keep a legacy box (Linux 6) box for about a 
year to finish our current processing/edits. However, since many of our studies 
can take a while from processing to final analysis, and we may revisit datasets 
after a year or two, I was wondering if it is okay to finish all edits on a 
given version of Linux (6), and later run all analyses on a different version 
of Linux (7). Namely, we are interested to know how long we would need to keep 
the legacy box around, in case we want to revisit data for additional analyses 
(e.g. all edits/reprocessing would be done on one version, analyses on another).

Thanks!

Andrew Schoen
Center for Investigating Healthy Minds
Waisman Center
University of Wisconsin - Madison
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Re: [Freesurfer] TalX TalY TalZ

[Douglas Greve]

If you use --fixmni, then they are reported in approximate talairach space

On 11/11/15 10:08 AM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? 
(with —fixmni)


Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu


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Re: [Freesurfer] How to compute area of subcortical structures

[Douglas Greve]

Probably Ruopeng will have to weigh in on freeview.

On 11/11/15 5:57 AM, anirudh nihalani wrote:

Hi Bruce,

   Sorry I forgot to attach the files mentioned in my last email. PFA 
the files here. Thank you.


Regards,
Anirudh

On Wed, 11 Nov 2015 at 16:18 anirudh nihalani 
mailto:anirudhnihal...@gmail.com>> wrote:


Hi Bruce,

Thank you very much for your quick reply. Sorry I hadn't been
able to reply faster as I was trying to figure out the below
mentioned issue from two days.

 I have computed surface area of left-hippocampus using the
commands mri_tessellate and mris_info. However I found that in
freeview by selecting Tools->show label stats, I am able to
display area of any label (PFA a screenshot) but these area stats
do not match with the areas obtained using mri_tessellate and
mris_info. I have two queries regarding this:

1) Surface areas of labels displayed in freeview doesn't match
with subcortical structures' areas obtained by running
mri_tesselate and mris_info. For example the attached screenshot
shows that area of left-hippocampus is 71 mm^2 where as
mri_tessellate followed by mris_info found the area for
left-hippocampus to be 3586 (PFA the output of mris_tessellate and
mris_info). Why is there a mismatch?

2) Based on your reply I thought area stats are not calculated for
subcortical structures during "recon-all". If that is the case,
how is freeview displaying area stats for subcortical areas? Also
which file does freeview use to display these stats? Is it
stats/[l/r]h.aparc.stats? I ask because even cortical structures'
areas displayed by freeview are not matching with what is stored
in these files.

Please let me know. Thank you.

Regards,
Anirudh



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Re: [Freesurfer] Advice for FreeSurfer developers

[Douglas Greve]

Hi Ed, generally recon-all does not need matlab. Are you running the 
gyrification analysis? That should be the only thing that needs matlab.
doug

On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote:
> Dear developers,
>
> Is it possible to check the presence of Matlab runtime right at the start of 
> recon-all
> in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours 
> for
> a high-res data processing I got this unexpected error message.
> Thanks in advance.
>
> Cheers
> Ed
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>
>

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Re: [Freesurfer] mri_vol2surf Matlab Function

[Fatemeh.Molaei-Vaneghi]

Thank you for taking the time and responding. I managed to correct my shell 
script, and now it works! I would guess running shell scripts from Matlab is 
generally not a good idea.

Best,
Fatemeh 
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Re: [Freesurfer] How to compute area of subcortical structures

[Lee Tirrell]

Hi Anirudh,

Label Stats just shows the area of the label in that slice, not surface area 
of the entire label (17, Left Hippocampus in your case).  So for your slice in 
the screenshot, there were 71 voxels labeled 17, so the area is 71.  The 
mri_tessellate then mris_info commands give the surface area of the entire left 
hippocampus (not just the area of the 2D slice).


Best,
Lee

On Wed, 11 Nov 2015, Douglas Greve wrote:


Probably Ruopeng will have to weigh in on freeview.

On 11/11/15 5:57 AM, anirudh nihalani wrote:
  Hi Bruce,
   Sorry I forgot to attach the files mentioned in my last email. PFA the files 
here. Thank you.

Regards,
Anirudh

On Wed, 11 Nov 2015 at 16:18 anirudh nihalani  wrote:
  Hi Bruce,
    Thank you very much for your quick reply. Sorry I hadn't been able to reply 
faster as I was trying to figure out the below mentioned issue from two days.

 I have computed surface area of left-hippocampus using the commands 
mri_tessellate and mris_info. However I found that in freeview by selecting 
Tools->show label stats, I am able to display area of any label (PFA a
screenshot) but these area stats do not match with the areas obtained using 
mri_tessellate and mris_info. I have two queries regarding this:

1) Surface areas of labels displayed in freeview doesn't match with subcortical 
structures' areas obtained by running mri_tesselate and mris_info. For example 
the attached screenshot shows that area of left-hippocampus is
71 mm^2 where as mri_tessellate followed by mris_info found the area for 
left-hippocampus to be 3586 (PFA the output of mris_tessellate and mris_info). 
Why is there a mismatch?

2) Based on your reply I thought area stats are not calculated for subcortical structures 
during "recon-all". If that is the case, how is freeview displaying area stats 
for subcortical areas? Also which file does freeview
use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask because even 
cortical structures' areas displayed by freeview are not matching with what is 
stored in these files.

Please let me know. Thank you.

Regards,
Anirudh



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Re: [Freesurfer] TalX TalY TalZ

[Yang, Daniel]

Thanks, Doug! Got it. So FreeSurfer registers the individual scans to the 
MNI305 atlas but mri_surfcluster reports approx. Talairach coordinates with the 
default option: —fixmni

I was a little bit confused because this website 
(https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) says that the 
following: "Note on Talairach: 
FreeSurfer does not 
report true "Talairach" coordinates. The coordinates listed unter "Talairach" 
are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 
space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). 
FreeSurfer also reports 
"Talairach MNI" coordinates. These are MNI305 space.”

If my understanding is correct, by default, the “Talairach” coordinates 
reported by mri_surfcluster (with —fixmni) are non-linear transformation from 
the MNI305 space; they are approx. Talairach coord as you suggested. And If I 
ever use —nofixmni, then it is what is internally used by FreeSurfer, the 
MNI305 space, or the "Talairach MNI” coordinates.

Is the understanding above correct?

Thanks!

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, November 11, 2015 at 11:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TalX TalY TalZ

If you use --fixmni, then they are reported in approximate talairach space

On 11/11/15 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? (with 
—fixmni)

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu



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[Freesurfer] group mean greater than X

[Dace Apshvalka]

Hi,

How would I make a one sided t-test to see whether group mean is greater than X 
(any other number than 0)?

Thanks,
Dace

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Re: [Freesurfer] OS version on Edits/Analysis

[Martin Reuter]

Hi Andrew,

that should be OK, as long as there is a clear line between
image processing/editing
vs
post-processing (glm fit, other type of analysis).

Best, Martin


On 11/11/2015 11:00 AM, Andrew Schoen wrote:
> Hi all,
>
> I know there is good evidence to support analyzing and performing edits on 
> the same version of freesurfer, and the same operating system. However, our 
> systems are going to be updating to Scientific Linux 7, from Scientific Linux 
> 6 in the coming weeks. We are planning to keep a legacy box (Linux 6) box for 
> about a year to finish our current processing/edits. However, since many of 
> our studies can take a while from processing to final analysis, and we may 
> revisit datasets after a year or two, I was wondering if it is okay to finish 
> all edits on a given version of Linux (6), and later run all analyses on a 
> different version of Linux (7). Namely, we are interested to know how long we 
> would need to keep the legacy box around, in case we want to revisit data for 
> additional analyses (e.g. all edits/reprocessing would be done on one 
> version, analyses on another).
>
> Thanks!
>
> Andrew Schoen
> Center for Investigating Healthy Minds
> Waisman Center
> University of Wisconsin - Madison
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>

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

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Re: [Freesurfer] group mean greater than X

[Douglas Greve]

Just look for positive activation. The p-values were computed assuming 
two-sided, so if one-sided is really what you want, divide the p-values 
by 2. Note that the correction for multiple comparisons (mri_glmfit-sim) 
will do this for you automatically when you specify a signed test
doug

On 11/11/15 2:58 PM, Dace Apshvalka wrote:
> Hi,
>
> How would I make a one sided t-test to see whether group mean is greater than 
> X (any other number than 0)?
>
> Thanks,
> Dace
>
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[Freesurfer] group mean greater than X

[Dace Apshvalka]

Sorry, I was not very clear.

I meant, how do I test whether the group mean is greater than 5, for
example.

The default is 0, but can I change it somehow?


Dace
-- 

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Re: [Freesurfer] group mean greater than X

[Douglas Greve]

I guess you could subtract 5 from the gamma.mgh, then recompute the t = 
gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p 
or sig given the dof.
doug

ps. Please remember to include previous correspondences so we know the 
context of the question

On 11/11/15 4:10 PM, Dace Apshvalka wrote:
> Sorry, I was not very clear.
>
> I meant, how do I test whether the group mean is greater than 5, for
> example.
>
> The default is 0, but can I change it somehow?
>
>
> Dace

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Re: [Freesurfer] group mean greater than X

[Kirstie Whitaker]

Could you also just subtract 5 from all your input data? Then when you test
against zero (and only look at positive p values) you'll really be testing
whether the values are greater than 5?

Kx

On 11 November 2015 at 21:35, Douglas Greve 
wrote:

> I guess you could subtract 5 from the gamma.mgh, then recompute the t =
> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p
> or sig given the dof.
> doug
>
> ps. Please remember to include previous correspondences so we know the
> context of the question
>
> On 11/11/15 4:10 PM, Dace Apshvalka wrote:
> > Sorry, I was not very clear.
> >
> > I meant, how do I test whether the group mean is greater than 5, for
> > example.
> >
> > The default is 0, but can I change it somehow?
> >
> >
> > Dace
>
> ___
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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
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-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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Re: [Freesurfer] group mean greater than X

[Dace Apshvalka]

That's what I will do. Just wanted to enquire whether there is an
option to specify the value directly for the one-sample ttest.

Thank you!

Dace

> Could you also just subtract 5 from all your input data? Then when you test
> against zero (and only look at positive p values) you'll really be testing
> whether the values are greater than 5?
>
> Kx
>
> On 11 November 2015 at 21:35, Douglas Greve 
> wrote:
>
>> I guess you could subtract 5 from the gamma.mgh, then recompute the t =
>> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p
>> or sig given the dof.
>> doug
>>
>> ps. Please remember to include previous correspondences so we know the
>> context of the question
>>
>> On 11/11/15 4:10 PM, Dace Apshvalka wrote:
>> > Sorry, I was not very clear.
>> >
>> > I meant, how do I test whether the group mean is greater than 5, for
>> > example.
>> >
>> > The default is 0, but can I change it somehow?
>> >
>> >
>> > Dace
>>
>> ___
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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
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>>
>
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[Freesurfer] Computing Statistics with Custom ROI Masks

[Shady El Damaty]

Hi FS-ers,

I'm a bit stuck trying to compute cortical and subcortical statistics using
the Buckner 2011 Cerebellum mask.  I tried using mri_segstats to generate
the .stats file for the provided image:

mri_segstats --seg
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum
> test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum
> test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty
> sysname  Darwin
> hostname Apricot.local
> machine  x86_64
> user shady
> UseRobust  0
> Loading
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Segmentation fault: 11


Clearly I am doing something wrong.  Can someone throw a pointer my way
about how I can go about computing statistics on my subjects (or any
arbitrary volume) using this mask?

In the end I would like to be able to generate a .stats file for every
subject in my SUBJECTS_DIR using any custom mask.. how can I make this
possible?

Your help would be very greatly appreciated!
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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22

[Gonzalo Rojas Costa]

Hi Martin:

  But, between version 5.3 and 6.0 there are any differences in the
algorithms for subcortical volume, cortical thickness, etc., or only
additions to that, such as the hippocampus or brainstem subfields ?...
and in general, if I segment for example the same healthy control in
freesurfer 5.3 and 6.0 in the same operating system, there will be any
difference in subcortical volumes and/or cortical thickness ?...

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl



On Wed, Nov 11, 2015 at 7:57 AM,
 wrote:

> --
>
> Message: 24
> Date: Tue, 10 Nov 2015 16:57:43 -0500
> From: Martin Reuter 
> Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences...
> To: Freesurfer support list 
> Message-ID: <56426857.3030...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi Gonzalo,
>
> of course.
>
> There is even a difference when running the same FS version with a
> different operating system (due to differences in the numerical
> libraries, optimizations etc).
>
> Are changes big or small?
> In a single case they can be very big (it could be a case that failed in
> 5.3 and works with 6.0 - or the other way)
>
> Are changes directional (significantly larger or smaller volumes/thickness)?
> Hard to say and hard to detect if small, but it can happen due to a new
> algorithm that measurements are consistently larger (/smaller) than in
> another version. We try to avoid this, but it can theoretically happen.
>
> That is why it is so important to stick with the same version and
> operating system when processing data.
>
> Best, Martin
>
> On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote:
>> Hi:
>>
>>There are any difference between subcortical structures volume,
>> cortical thickness, supratentorial volume, gray matter volume, etc.
>> computed with freesurfer 5.3 and 6.0 ?...
>>
>>Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu

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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22

[Martin Reuter]

Hi Gonzalo,

yes there are changes to many of the algorithms (sometimes bug fixes or 
improvements, sometimes parameter changes etc) which will generate different 
results. It can happen in individual cases that subcortical volume or cortical 
thickness differs a lot between 5.3 and 6.0, even when running on the same 
operating system. It is unlikely that this will change results of a study with 
sufficient power (group comparison). 

Best, Martin

> On Nov 11, 2015, at 10:08 PM, Gonzalo Rojas Costa 
>  wrote:
> 
> Hi Martin:
> 
>  But, between version 5.3 and 6.0 there are any differences in the
> algorithms for subcortical volume, cortical thickness, etc., or only
> additions to that, such as the hippocampus or brainstem subfields ?...
> and in general, if I segment for example the same healthy control in
> freesurfer 5.3 and 6.0 in the same operating system, there will be any
> difference in subcortical volumes and/or cortical thickness ?...
> 
>  Sincerely,
> 
> 
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
> 
> 
> 
> On Wed, Nov 11, 2015 at 7:57 AM,
>  wrote:
> 
>> --
>> 
>> Message: 24
>> Date: Tue, 10 Nov 2015 16:57:43 -0500
>> From: Martin Reuter 
>> Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences...
>> To: Freesurfer support list 
>> Message-ID: <56426857.3030...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>> 
>> Hi Gonzalo,
>> 
>> of course.
>> 
>> There is even a difference when running the same FS version with a
>> different operating system (due to differences in the numerical
>> libraries, optimizations etc).
>> 
>> Are changes big or small?
>> In a single case they can be very big (it could be a case that failed in
>> 5.3 and works with 6.0 - or the other way)
>> 
>> Are changes directional (significantly larger or smaller volumes/thickness)?
>> Hard to say and hard to detect if small, but it can happen due to a new
>> algorithm that measurements are consistently larger (/smaller) than in
>> another version. We try to avoid this, but it can theoretically happen.
>> 
>> That is why it is so important to stick with the same version and
>> operating system when processing data.
>> 
>> Best, Martin
>> 
>> On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote:
>>> Hi:
>>> 
>>>   There are any difference between subcortical structures volume,
>>> cortical thickness, supratentorial volume, gray matter volume, etc.
>>> computed with freesurfer 5.3 and 6.0 ?...
>>> 
>>>   Sincerely,
>>> 
>>> 
>>> Gonzalo Rojas Costa
>>> 
>> 
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  : http://reuter.mit.edu
> 
> 


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Re: [Freesurfer] How to compute area of subcortical structures

[Bruce Fischl]

Hi Anirudh

sorry, I'm not sure what/how freeview computes things. Maybe Ruopeng 
can answer?


Bruce



On 
Wed, 11 Nov 2015, anirudh nihalani wrote:



Hi Bruce,
    Thank you very much for your quick reply. Sorry I hadn't been able to reply 
faster as I was trying to
figure out the below mentioned issue from two days.

 I have computed surface area of left-hippocampus using the commands 
mri_tessellate and mris_info. However
I found that in freeview by selecting Tools->show label stats, I am able to 
display area of any label (PFA
a screenshot) but these area stats do not match with the areas obtained using 
mri_tessellate and
mris_info. I have two queries regarding this:

1) Surface areas of labels displayed in freeview doesn't match with subcortical 
structures' areas obtained
by running mri_tesselate and mris_info. For example the attached screenshot 
shows that area of
left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info found 
the area for
left-hippocampus to be 3586 (PFA the output of mris_tessellate and mris_info). 
Why is there a mismatch?

2) Based on your reply I thought area stats are not calculated for subcortical 
structures during
"recon-all". If that is the case, how is freeview displaying area stats for 
subcortical areas? Also which
file does freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? 
I ask because even cortical
structures' areas displayed by freeview are not matching with what is stored in 
these files.

Please let me know. Thank you.

Regards,
Anirudh

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[Freesurfer] dilating labels within a parcellation

[David Grayson]

Hi all,

Is there a tool to surface-dilate all the labels contained within an annotation 
file simultaneously, while preserving the non-overlapping nature of the labels? 
I saw there is a development version of mri_label2label that works for 
individual label files separately, but that gets me into the problem of overlap 
and arbitrary starting points.

Thanks very much,

David
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Re: [Freesurfer] Advice for FreeSurfer developers

[Gronenschild Ed (NP)]

Hi Doug,

I used mostly the default options, nothing special:

recon-all -autorecon1 -clean-tal -expert my_options.txt -hires

where the file my_options.txt contains some options for nu_correct.
Then I entered

recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires

The error occurred with the last recon-all command.
BTW, I really don't know if the -clean-tal option is needed with FS v6.

Cheers
Ed


On 11 Nov 2015, at 18:00, 
mailto:freesurfer-requ...@nmr.mgh.harvard.edu>>
 wrote:

Message: 9
Date: Wed, 11 Nov 2015 11:08:46 -0500
From: Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Advice for FreeSurfer developers
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
<5643680e.1030...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Ed, generally recon-all does not need matlab. Are you running the
gyrification analysis? That should be the only thing that needs matlab.
doug

On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote:
Dear developers,

Is it possible to check the presence of Matlab runtime right at the start of 
recon-all
in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for
a high-res data processing I got this unexpected error message.
Thanks in advance.

Cheers
Ed
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