Re: [Freesurfer] Ris: eTIV question

[Harms, Michael]

That is, going back to your earlier post, I personally don’t find it all
that interesting whether a given brain area is atrophic relative to head
size, especially in the situation where many regions are atrophic (i.e.,
global atrophy).  I’m more interested in knowing whether the atrophy in a
given region is greater (or less than) what would be predicted based on
the global atrophy.

cheers,
-MH
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 10:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Harms, Michael"  wrote:

Even assuming one had a true measure of TIV, if you get meaningfully
different results when using TIV vs. brain size as a covariate, isn’t that
a rather important thing to point out?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Angela

yes, although if the eTIV is (incorrectly) correlated with atrophy you
may be removing some of your effect (and slightly reducing your power)

cheers
Bruce
On
Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:

> Hi Bruce,
> this is true, but I noticed that many papers used TIV as a covariate. In
> addition, in my samples (both pathological and healthy) there is a
> moderate positive correlation between gyrification and TIV (and brain
> volume). For the hemispheric overall gyrification index the correlation
>is
> 0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
> I think that in pathological samples with possible brain atrophy, this is
> a way to control for a possible bias effect. Am I wrong?
>
> Thank you
> Angela
>
>> Hi Angela
>>
>> gyrification is the ratio of areas and hence dimensionless, so I would
>> think it wouldn't be much affected by TIV.
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>>
>>> In the case of a gyrification analysis, does correction for total brain
>>> volume make sense?
>>>
>>> Angela
>>>
>>> Inviato dal mio dispositivo Huawei
>>>
>>>  Messaggio originale 
>>> Oggetto: Re: [Freesurfer] eTIV question
>>> Da: Bruce Fischl
>>> A: Freesurfer support list
>>> CC:
>>>
>>>
>>>   yes, it's a somewhat different and more conservative test. I
>>>   guess you
>>>   could check the talairach transforms of some of your subjects
>>>   with eTIVs
>>>   that don't make sense (or change the most over time) to try to
>>>   see why
>>>   this is happening. Or take Mike's suggestion and test a
>>>   different (but
>>>   probably still interesting) hypothesis
>>>
>>>   On Sun, 21 Feb 2016, Angela Favaro wrote:
>>>
>>>  > Hi, thank you
>>>  > I think this would test something different: 'how much a brain
>>>   area is
>>>  > atrophic controlling for the average brain atrophy' and not
>>>   'how much
>>>  > a brain area is atrophic controlling for the individual
>>>   differences in
>>>  > head size'. Doesn't it?
>>>  >
>>>  > Angela
>>>  >
>>>  >
>>>  > "Harms, Michael" ha scritto:
>>>  >
>>>  >> Hi,
>>>  >> Why not use a measurement of brain size rather than “eTIV”?
>>>  >>
>>>  >> cheers,
>>>  >> -MH
>>>  >>
>>>  >> --
>>>  >> Michael Harms, Ph.D.
>>>  >>
>>>  >> ---
>>>  >> Conte Center for the Neuroscience of Mental Disorders
>>>  >> Washington University School of Medicine
>>>  >> Department of Psychiatry, Box 8134
>>>  >> 660 South Euclid Ave.Tel: 314-747-6173
>>>  >> St. Louis, MO 63110Email: mha...@wustl.edu
>>>  >>
>>>  >>
>>>  >>
>>>  >>
>>>  >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
>>>   on behalf of
>>>  >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
>>>  >>
>>>  >> there is a mistake in the graph, hippocampal volume is TIV2
>>>  >> I apologize for that!
>>>  >>
>>>  >> Angela Favaro ha scritto:
>>>  >>
>>>  >>> Hi Bruce,
>>>  >>> please find attached the graph of the correlation between
>>>   the two time
>>>  >>> point. I did not find outliers or failures. However the
>>>   discrepancy
>>>  >>> between TIVs is particularly high in few cases. Obviously
>>>   these data
>>>  >>> are those 

Re: [Freesurfer] Ris: eTIV question

[Harms, Michael]

Even assuming one had a true measure of TIV, if you get meaningfully
different results when using TIV vs. brain size as a covariate, isn’t that
a rather important thing to point out?

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 2/22/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Angela

yes, although if the eTIV is (incorrectly) correlated with atrophy you
may be removing some of your effect (and slightly reducing your power)

cheers
Bruce
On
Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:

> Hi Bruce,
> this is true, but I noticed that many papers used TIV as a covariate. In
> addition, in my samples (both pathological and healthy) there is a
> moderate positive correlation between gyrification and TIV (and brain
> volume). For the hemispheric overall gyrification index the correlation
>is
> 0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
> I think that in pathological samples with possible brain atrophy, this is
> a way to control for a possible bias effect. Am I wrong?
>
> Thank you
> Angela
>
>> Hi Angela
>>
>> gyrification is the ratio of areas and hence dimensionless, so I would
>> think it wouldn't be much affected by TIV.
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>>
>>> In the case of a gyrification analysis, does correction for total brain
>>> volume make sense?
>>>
>>> Angela
>>>
>>> Inviato dal mio dispositivo Huawei
>>>
>>>  Messaggio originale 
>>> Oggetto: Re: [Freesurfer] eTIV question
>>> Da: Bruce Fischl
>>> A: Freesurfer support list
>>> CC:
>>>
>>>
>>>   yes, it's a somewhat different and more conservative test. I
>>>   guess you
>>>   could check the talairach transforms of some of your subjects
>>>   with eTIVs
>>>   that don't make sense (or change the most over time) to try to
>>>   see why
>>>   this is happening. Or take Mike's suggestion and test a
>>>   different (but
>>>   probably still interesting) hypothesis
>>>
>>>   On Sun, 21 Feb 2016, Angela Favaro wrote:
>>>
>>>  > Hi, thank you
>>>  > I think this would test something different: 'how much a brain
>>>   area is
>>>  > atrophic controlling for the average brain atrophy' and not
>>>   'how much
>>>  > a brain area is atrophic controlling for the individual
>>>   differences in
>>>  > head size'. Doesn't it?
>>>  >
>>>  > Angela
>>>  >
>>>  >
>>>  > "Harms, Michael" ha scritto:
>>>  >
>>>  >> Hi,
>>>  >> Why not use a measurement of brain size rather than “eTIV”?
>>>  >>
>>>  >> cheers,
>>>  >> -MH
>>>  >>
>>>  >> --
>>>  >> Michael Harms, Ph.D.
>>>  >>
>>>  >> ---
>>>  >> Conte Center for the Neuroscience of Mental Disorders
>>>  >> Washington University School of Medicine
>>>  >> Department of Psychiatry, Box 8134
>>>  >> 660 South Euclid Ave.Tel: 314-747-6173
>>>  >> St. Louis, MO 63110Email: mha...@wustl.edu
>>>  >>
>>>  >>
>>>  >>
>>>  >>
>>>  >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
>>>   on behalf of
>>>  >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
>>>  >>
>>>  >> there is a mistake in the graph, hippocampal volume is TIV2
>>>  >> I apologize for that!
>>>  >>
>>>  >> Angela Favaro ha scritto:
>>>  >>
>>>  >>> Hi Bruce,
>>>  >>> please find attached the graph of the correlation between
>>>   the two time
>>>  >>> point. I did not find outliers or failures. However the
>>>   discrepancy
>>>  >>> between TIVs is particularly high in few cases. Obviously
>>>   these data
>>>  >>> are those before running longitudinal streaming
>>>  >>> This is a sample of adolescents with low body weight
>>>   (anorexia nervosa).
>>>  >>> In my previous study (on young adults with low weight) I
>>>   found no
>>>  >>> correlation between TIV and body weight and high
>>>   correlations between
>>>  >>> fs estimated TIV and manually segmented TIV (r=0.94 in the
>>>   whole
>>>  >>> sample and r=0.93 in the underweight sample (n=38)).
>>>  >>> Do you think that the young age can be a factor? or patients
>>>   who are
>>>  >>> more acutely underweight?
>>>  >>> Thank you for any suggestion
>>>  >>>
>>>  >>> Angela
>>>  >>>
>>>  >>>
>>>  >>> Bruce Fischl ha scritto:
>>>  >>>
>>>   Hi Angel
>>>  
>>>   the time1/time2 correlation of eTIV is pretty worrisome.
>>>   

[Freesurfer] Read_surf error in reading "lh.seghead" head surface created from "mkheadsurf"

[Maheen Siddiqui]

Dear FreeSurfer users,

I have used the "mkheadsurf" function to create "lh.seghead" in the surf
folder of my subject. Now I am trying to extract the vertices and faces of
"lh.seghead" in the following way:

   *[vertex_coords, faces] = read_surf('lh.seghead')*

but get an error in read_surf which is:

 *Undefined function or variable "faces".*

* Error in read_surf (line 80)*
* faces = faces+1;*

After a bit of investigation I found that the "magic" number of the file
is 16777213 while the triangle magic number is 16777214. Since these are
unequal, it doesn't go into the if statement where faces are defined.

When I try to changed the magic number manually to be the same as the
triangle magic number, I get the following error:

 *Error using reshape*
* To RESHAPE the number of elements must not change.*

* Error in read_surf (line 76)*
* faces = reshape(faces, 3, fnum)' ;*

But I don't think making this change is a good idea as it would affect the
surfaces that I try to read that DO have magic number that is actually
equal to the triangle magic number.

Does anybody know why this might be happening? Any suggestions for me to
try? The read_surf works fine when I use it for the pial surface, just not
the lh.seghead. I am using FreeSurfer version 5.3.0.

I would appreciate any advice!

Thanks,

Maheen
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bbregister problems

[Douglas Greve]

If you have spm, you can use --init-spm. Alternatively, you can use 
mri_coreg instead of bbr (bbr is not as effective on blurry data)


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

mri_coreg --s $fs --mov  ${pet_ext}_LIA.nii --lta output.lta

Also, why is the top of the head cut off? That makes it much more 
difficult to register.


doug



On 2/22/16 8:02 PM, Pradeep wrote:

Hello All,

I am trying to map pet scans to MRI  using bbregister and quite a few 
subjects were improperly registered.


Here are my steps:
bbregister --s $fs --mov  ${pet_ext}_LIA.nii --init-fsl --t1 --lta 
output.lta

tkregister2 --mov summed_LIA.nii --reg output.dat --surf


[ mri]$ more output.dat.mincost
0.860663 0.000513 0.000492 -11.863233
The first value is quite close to 1 so its bad

I have attached a screen shot of the image and the log file generated 
after bbregister.
Please let me know if there are any parameters that I could tweak to 
make the registration better.


Thank you for your help,
-Pradeep



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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] control points function

[Kiersten Snyder]

Hello,
I am new to using Freesurfer and am currently using it for a biomedical
image processing class. I am working on a project and would like to know
the image processing technique behind the Control Points function.  Is it
region growing, or what other process?

Thanks for the help!
Kiersten
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Ris: eTIV question

[Bruce Fischl]

Hi Angela

yes, although if the eTIV is (incorrectly) correlated with atrophy you 
may be removing some of your effect (and slightly reducing your power)


cheers
Bruce
On 
Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:



Hi Bruce,
this is true, but I noticed that many papers used TIV as a covariate. In
addition, in my samples (both pathological and healthy) there is a
moderate positive correlation between gyrification and TIV (and brain
volume). For the hemispheric overall gyrification index the correlation is
0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
I think that in pathological samples with possible brain atrophy, this is
a way to control for a possible bias effect. Am I wrong?

Thank you
Angela


Hi Angela

gyrification is the ratio of areas and hence dimensionless, so I would
think it wouldn't be much affected by TIV.

cheers
Bruce


On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:


In the case of a gyrification analysis, does correction for total brain
volume make sense?

Angela

Inviato dal mio dispositivo Huawei

 Messaggio originale 
Oggetto: Re: [Freesurfer] eTIV question
Da: Bruce Fischl
A: Freesurfer support list
CC:


  yes, it's a somewhat different and more conservative test. I
  guess you
  could check the talairach transforms of some of your subjects
  with eTIVs
  that don't make sense (or change the most over time) to try to
  see why
  this is happening. Or take Mike's suggestion and test a
  different (but
  probably still interesting) hypothesis

  On Sun, 21 Feb 2016, Angela Favaro wrote:

 > Hi, thank you
 > I think this would test something different: 'how much a brain
  area is
 > atrophic controlling for the average brain atrophy' and not
  'how much
 > a brain area is atrophic controlling for the individual
  differences in
 > head size'. Doesn't it?
 >
 > Angela
 >
 >
 > "Harms, Michael" ha scritto:
 >
 >> Hi,
 >> Why not use a measurement of brain size rather than “eTIV”?
 >>
 >> cheers,
 >> -MH
 >>
 >> --
 >> Michael Harms, Ph.D.
 >>
 >> ---
 >> Conte Center for the Neuroscience of Mental Disorders
 >> Washington University School of Medicine
 >> Department of Psychiatry, Box 8134
 >> 660 South Euclid Ave.Tel: 314-747-6173
 >> St. Louis, MO 63110Email: mha...@wustl.edu
 >>
 >>
 >>
 >>
 >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of
 >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
 >>
 >> there is a mistake in the graph, hippocampal volume is TIV2
 >> I apologize for that!
 >>
 >> Angela Favaro ha scritto:
 >>
 >>> Hi Bruce,
 >>> please find attached the graph of the correlation between
  the two time
 >>> point. I did not find outliers or failures. However the
  discrepancy
 >>> between TIVs is particularly high in few cases. Obviously
  these data
 >>> are those before running longitudinal streaming
 >>> This is a sample of adolescents with low body weight
  (anorexia nervosa).
 >>> In my previous study (on young adults with low weight) I
  found no
 >>> correlation between TIV and body weight and high
  correlations between
 >>> fs estimated TIV and manually segmented TIV (r=0.94 in the
  whole
 >>> sample and r=0.93 in the underweight sample (n=38)).
 >>> Do you think that the young age can be a factor? or patients
  who are
 >>> more acutely underweight?
 >>> Thank you for any suggestion
 >>>
 >>> Angela
 >>>
 >>>
 >>> Bruce Fischl ha scritto:
 >>>
  Hi Angel
 
  the time1/time2 correlation of eTIV is pretty worrisome.
  Are you sure
  that there aren't outliers/failures in that set?
 
  Bruce
 
 
  On Sun, 14 Feb 2016, angela.fav...@unipd.it wrote:
 
 > Dear Freesurfer experts,
 > I have a question about eTIV (FS 5.3) which I use as a
  covariate where
 > appropriate. Is it in some way influenced by the presence
  of brain
 > atrophy?
 > I have a new sample of subjects in a longitudinal study:
  at time 1 they
 > have some atrophy (due to low body weight) that improves
  in time 2 (4
 > months). I observed that eTIV-time1 is slightly correlated
  with weight
 > (r=0.3) whereas no correlation is present at time 2. The
  correlation
 > between eTIV-time1 and eTIV-time2 is somewhat lower than
  expected
 > (r=0.53)
 > and is lower than correlation between SegBrain_Vol_1 and
  SegBrain_Vol_2
 > (0.65).
 >
 > Do you suggest in these cases to perform manual
  segmentation to obtain
 > TIV? or is there any 

Re: [Freesurfer] Ris: eTIV question

[angela . favaro]

Hi Bruce,
this is true, but I noticed that many papers used TIV as a covariate. In
addition, in my samples (both pathological and healthy) there is a
moderate positive correlation between gyrification and TIV (and brain
volume). For the hemispheric overall gyrification index the correlation is
0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
I think that in pathological samples with possible brain atrophy, this is
a way to control for a possible bias effect. Am I wrong?

Thank you
Angela

> Hi Angela
>
> gyrification is the ratio of areas and hence dimensionless, so I would
> think it wouldn't be much affected by TIV.
>
> cheers
> Bruce
>
>
> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>
>> In the case of a gyrification analysis, does correction for total brain
>> volume make sense?
>>
>> Angela
>>
>> Inviato dal mio dispositivo Huawei
>>
>>  Messaggio originale 
>> Oggetto: Re: [Freesurfer] eTIV question
>> Da: Bruce Fischl
>> A: Freesurfer support list
>> CC:
>>
>>
>>   yes, it's a somewhat different and more conservative test. I
>>   guess you
>>   could check the talairach transforms of some of your subjects
>>   with eTIVs
>>   that don't make sense (or change the most over time) to try to
>>   see why
>>   this is happening. Or take Mike's suggestion and test a
>>   different (but
>>   probably still interesting) hypothesis
>>
>>   On Sun, 21 Feb 2016, Angela Favaro wrote:
>>
>>   > Hi, thank you
>>   > I think this would test something different: 'how much a brain
>>   area is
>>   > atrophic controlling for the average brain atrophy' and not
>>   'how much
>>   > a brain area is atrophic controlling for the individual
>>   differences in
>>   > head size'. Doesn't it?
>>   >
>>   > Angela
>>   >
>>   >
>>   > "Harms, Michael" ha scritto:
>>   >
>>   >> Hi,
>>   >> Why not use a measurement of brain size rather than “eTIV”?
>>   >>
>>   >> cheers,
>>   >> -MH
>>   >>
>>   >> --
>>   >> Michael Harms, Ph.D.
>>   >>
>>   >> ---
>>   >> Conte Center for the Neuroscience of Mental Disorders
>>   >> Washington University School of Medicine
>>   >> Department of Psychiatry, Box 8134
>>   >> 660 South Euclid Ave.Tel: 314-747-6173
>>   >> St. Louis, MO 63110Email: mha...@wustl.edu
>>   >>
>>   >>
>>   >>
>>   >>
>>   >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
>>   on behalf of
>>   >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
>>   >>
>>   >> there is a mistake in the graph, hippocampal volume is TIV2
>>   >> I apologize for that!
>>   >>
>>   >> Angela Favaro ha scritto:
>>   >>
>>   >>> Hi Bruce,
>>   >>> please find attached the graph of the correlation between
>>   the two time
>>   >>> point. I did not find outliers or failures. However the
>>   discrepancy
>>   >>> between TIVs is particularly high in few cases. Obviously
>>   these data
>>   >>> are those before running longitudinal streaming
>>   >>> This is a sample of adolescents with low body weight
>>   (anorexia nervosa).
>>   >>> In my previous study (on young adults with low weight) I
>>   found no
>>   >>> correlation between TIV and body weight and high
>>   correlations between
>>   >>> fs estimated TIV and manually segmented TIV (r=0.94 in the
>>   whole
>>   >>> sample and r=0.93 in the underweight sample (n=38)).
>>   >>> Do you think that the young age can be a factor? or patients
>>   who are
>>   >>> more acutely underweight?
>>   >>> Thank you for any suggestion
>>   >>>
>>   >>> Angela
>>   >>>
>>   >>>
>>   >>> Bruce Fischl ha scritto:
>>   >>>
>>    Hi Angel
>>   
>>    the time1/time2 correlation of eTIV is pretty worrisome.
>>   Are you sure
>>    that there aren't outliers/failures in that set?
>>   
>>    Bruce
>>   
>>   
>>    On Sun, 14 Feb 2016, angela.fav...@unipd.it wrote:
>>   
>>   > Dear Freesurfer experts,
>>   > I have a question about eTIV (FS 5.3) which I use as a
>>   covariate where
>>   > appropriate. Is it in some way influenced by the presence
>>   of brain
>>   > atrophy?
>>   > I have a new sample of subjects in a longitudinal study:
>>   at time 1 they
>>   > have some atrophy (due to low body weight) that improves
>>   in time 2 (4
>>   > months). I observed that eTIV-time1 is slightly correlated
>>   with weight
>>   > (r=0.3) whereas no correlation is present at time 2. The
>>   correlation
>>   > between eTIV-time1 and eTIV-time2 is somewhat lower than
>>   expected
>>   > (r=0.53)
>>   

Re: [Freesurfer] Multiple Frames Error

[Marissa Pifer]

Absolutely, I've contacted them about it, and if it is not the right one, I
can use the other. There are only 2 frames so I can narrow it down at
least.

Marissa

On Mon, Feb 22, 2016 at 3:46 PM, Douglas N Greve 
wrote:

> But is that the right frame to use? I would check with whoever collected
> the data and get it sorted out before diving into an analysis.
>
> On 02/22/2016 02:34 PM, Marissa Pifer wrote:
> > Bruce,
> >
> > I'm not sure why it has multiple frames. It was a spin echo, T1
> > weighted structural MRI. I input the command you suggested and
> > recon-all is running now.
> >
> > Thank you for your help!
> >
> > Marissa
> >
> > On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl
> > > wrote:
> >
> > Hi Marissa
> >
> > why does it have multiple frames? What kind of acquisition was it?
> > If you know which frame is the correct one you can always extract
> > it, for example
> >
> > cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig
> > mv 001.mgz two_frames.mgz
> > mri_convert -nth 0 two_frames.mgz 001.mgz
> >
> > Bruce
> >
> >
> > On Mon, 22 Feb 2016, Marissa Pifer wrote:
> >
> > Hi freesurfers,
> > I am trying to run the recon-all command on a T1 weighted
> > structural image for one of my subjects and I keep getting
> > this error
> >
> > "Checking for (invalid) multi-frame inputs...
> >
> > ERROR: input(s) cannot have multiple frames!
> >
> >
>  /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz
> > has 2 frames
> >
> > Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version
> > 13.4.0: Sun Aug 17 19:50:11 PDT 2014;
> > root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
> >
> >
> > recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22
> > 11:13:26 EST 2016"
> >
> >
> > I looked through the mailing list and saw that a few other
> > people have had this problem as well, and I tried some of the
> > solutions that were suggested but still have not been able to
> > get past this. I have run the recon-all command on all of the
> > other subjects in our data set, and none of them have this
> > problem. Not sure what is different about this scan.
> >
> >
> > Anyone run into this problem and were able to fix it?
> >
> >
> > Thanks in advance,
> >
> >
> > Marissa
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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.
> >
> >
> >
> >
> > ___
> > 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
>
___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Multiple Frames Error

[Douglas N Greve]

But is that the right frame to use? I would check with whoever collected 
the data and get it sorted out before diving into an analysis.

On 02/22/2016 02:34 PM, Marissa Pifer wrote:
> Bruce,
>
> I'm not sure why it has multiple frames. It was a spin echo, T1 
> weighted structural MRI. I input the command you suggested and 
> recon-all is running now.
>
> Thank you for your help!
>
> Marissa
>
> On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl 
> > wrote:
>
> Hi Marissa
>
> why does it have multiple frames? What kind of acquisition was it?
> If you know which frame is the correct one you can always extract
> it, for example
>
> cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig
> mv 001.mgz two_frames.mgz
> mri_convert -nth 0 two_frames.mgz 001.mgz
>
> Bruce
>
>
> On Mon, 22 Feb 2016, Marissa Pifer wrote:
>
> Hi freesurfers,
> I am trying to run the recon-all command on a T1 weighted
> structural image for one of my subjects and I keep getting
> this error
>
> "Checking for (invalid) multi-frame inputs...
>
> ERROR: input(s) cannot have multiple frames!
>
> 
> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz
> has 2 frames
>
> Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version
> 13.4.0: Sun Aug 17 19:50:11 PDT 2014;
> root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
>
>
> recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22
> 11:13:26 EST 2016"
>
>
> I looked through the mailing list and saw that a few other
> people have had this problem as well, and I tried some of the
> solutions that were suggested but still have not been able to
> get past this. I have run the recon-all command on all of the
> other subjects in our data set, and none of them have this
> problem. Not sure what is different about this scan.
>
>
> Anyone run into this problem and were able to fix it?
>
>
> Thanks in advance,
>
>
> Marissa
>
>
>
> ___
> 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.
>
>
>
>
> ___
> 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
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Re: [Freesurfer] qdec

[Douglas N Greve]

can you send one of them?

On 02/22/2016 03:13 PM, levi solomyak wrote:
> Hi Douglas,
>
> I get the same error for every subject individually. I'm guessing 
> there is a problem with my aseg.stats files but when I look through 
> them they look okay to me. What would be the best way to identify the 
> problem?
>
> Thank you!
> LS
>
> On Mon, Feb 22, 2016 at 11:18 AM, Douglas N Greve 
> > wrote:
>
> Not sure. Can you run it separately for each subject? I suspect that
> there might be a subject with a bad stats file
>
> On 02/19/2016 02:58 PM, levi solomyak wrote:
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the
> command you
> > suggested on the first five subjects. Any help you could provide
> would
> > be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
> 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line 538, in
> > 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
> >
> > On Fri, Feb 19, 2016 at 2:53 PM, levi solomyak
> 
> > >> wrote:
> >
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the
> command
> > you suggested on the first five subjects. Any help you could
> > provide would be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820
> 105115 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line 538,
> > in 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line 115,
> in parse
> >
> > On Fri, Feb 19, 2016 at 2:47 PM, levi solomyak
> > 
> >> wrote:
> >
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the
> > command you suggested on the first five subjects. Any
> help you
> > could provide would be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820
> 105115
> > 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line
> > 538, in 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line
> 115, in
> > parse
> > self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
> > IndexError: list index out of range
> >
> >
> >
> > On Mon, Dec 21, 2015 at 6:13 PM, Douglas N Greve
> >  
> >>
> > wrote:
> >
> > Can you run the command below outside of qdec and
> send us
> > the error it
> > prints to the terminal?
> >
> > asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820
> > 105115 110411
> > 111312 111413 111716 112819 113215 113619 113922 114419
> > 115320 116524
> > 117122 117324 118528 135225 135932 150625 

Re: [Freesurfer] qdec

[levi solomyak]

Hi Douglas,

I get the same error for every subject individually. I'm guessing there is
a problem with my aseg.stats files but when I look through them they look
okay to me. What would be the best way to identify the problem?

Thank you!
LS

On Mon, Feb 22, 2016 at 11:18 AM, Douglas N Greve  wrote:

> Not sure. Can you run it separately for each subject? I suspect that
> there might be a subject with a bad stats file
>
> On 02/19/2016 02:58 PM, levi solomyak wrote:
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the command you
> > suggested on the first five subjects. Any help you could provide would
> > be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line 538, in
> > 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
> >
> > On Fri, Feb 19, 2016 at 2:53 PM, levi solomyak  > > wrote:
> >
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the command
> > you suggested on the first five subjects. Any help you could
> > provide would be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line 538,
> > in 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
> >
> > On Fri, Feb 19, 2016 at 2:47 PM, levi solomyak
> > > wrote:
> >
> > Hi Douglas,
> >
> > Sure! Below is the terminal outputs when I try and run the
> > command you suggested on the first five subjects. Any help you
> > could provide would be much appreciated!
> >
> > Best,
> > LS
> >
> >  $asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115
> > 110411
> > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> > Parsing the .stats files
> > Traceback (most recent call last):
> >   File "/Applications/freesurfer/bin/asegstats2table", line
> > 538, in 
> > id_name_map, measurelist = parsed.parse(options.meas)
> >   File "/Applications/freesurfer/bin/fsutils.py", line 115, in
> > parse
> > self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
> > IndexError: list index out of range
> >
> >
> >
> > On Mon, Dec 21, 2015 at 6:13 PM, Douglas N Greve
> > >
> > wrote:
> >
> > Can you run the command below outside of qdec and send us
> > the error it
> > prints to the terminal?
> >
> > asegstats2table --common-segs --meas volume --tablefile
> >
>  
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> > --statsfile=aseg.stats --subjects 100307 101006 104820
> > 105115 110411
> > 111312 111413 111716 112819 113215 113619 113922 114419
> > 115320 116524
> > 117122 117324 118528 135225 135932 150625 150726 151223
> > 151526 170934
> > 171633 172130 172332 172534 172938 173334 175439 177645
> > 177746 178142
> > 200109 200614 20 201414 201818 203418 204016 204521
> > 304020 307127
> > 308331 310621 316633 329440 365343 366042 377451 380036
> > 385450 386250
> > 412528 433839 436239 480141 486759 497865 499566 500222
> > 510326 530635
> > 531536 540436 561242 562446 565452 566454 567052 567961
> > 568963 571548
> > 580044 580347 581349 583858 586460 594156 598568 599671
> >
> >
> >
> > On 12/14/2015 02:15 PM, levi solomyak wrote:
> > > Dear experts,
> > >
> > > I've 

Re: [Freesurfer] Multiple Frames Error

[Marissa Pifer]

Bruce,

I'm not sure why it has multiple frames. It was a spin echo, T1 weighted
structural MRI. I input the command you suggested and recon-all is running
now.

Thank you for your help!

Marissa

On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl 
wrote:

> Hi Marissa
>
> why does it have multiple frames? What kind of acquisition was it? If you
> know which frame is the correct one you can always extract it, for example
>
> cd  /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig
> mv 001.mgz two_frames.mgz
> mri_convert -nth 0 two_frames.mgz 001.mgz
>
> Bruce
>
>
> On Mon, 22 Feb 2016, Marissa Pifer wrote:
>
> Hi freesurfers,
>> I am trying to run the recon-all command on a T1 weighted structural
>> image for one of my subjects and I keep getting this error
>>
>> "Checking for (invalid) multi-frame inputs...
>>
>> ERROR: input(s) cannot have multiple frames!
>>
>> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz
>> has 2 frames
>>
>> Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun
>> Aug 17 19:50:11 PDT 2014;
>> root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
>>
>>
>> recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
>>
>>
>> I looked through the mailing list and saw that a few other people have
>> had this problem as well, and I tried some of the
>> solutions that were suggested but still have not been able to get past
>> this. I have run the recon-all command on all of the
>> other subjects in our data set, and none of them have this problem. Not
>> sure what is different about this scan.
>>
>>
>> Anyone run into this problem and were able to fix it?
>>
>>
>> Thanks in advance,
>>
>>
>> Marissa
>>
>>
>>
> ___
> 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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

[Afzal, Afsana]

Hi, 

Sorry about the lack of clarification. 

Yes, it's a functional study. Each of the classes is a subject. I basically 
want to compute the main effect of risk at the group level (i.e. High Risk 
minus Low Risk) but there are multiple observations per risk level since there 
are three different reward levels within each risk level (low Reward, med 
Reward, high Reward). 
I was thinking of setting up all the risk-reward conditions as active (=1s) in 
the fsgd file and then subtracting the conditions using the contrast matrices 
below to get the main effect of Risk. 

Please let me know if that makes a bit more sense. 

Thanks for your help, 
Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 22, 2016 12:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

I'm having a hard time deciphering what you are doing. Is this a
functional study? What are the 5 classes? Why are there all 1s
regardless of risk or reward level?

On 02/19/2016 10:52 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm analyzing a decision making task with a 3x3 condition matrix:
> pairings of low, medium, high levels of risk with low, medium, high
> levels of reward.
>
> I've set up the following FSGD file to do a repeated
> measures/within-subject ANOVA:
>
> GroupDescriptorFile 1
> Class hc001
> Class hc002
> Class hc003
> Class hc004
> Class hc005
> Variables   lRsk_lRwd lRsk_mRwd   lRsk_hRwd   mRsk_lRwd
> mRsk_mRwd   mRsk_hRwd   hRsk_lRwd hRsk_mRwd   hRsk_hRwd
> Input hc001 hc0011 1   1   1 1   1
>   1 1   1
> Input hc002 hc002 1 1   1   1   1   1
>   1 1   1
> Input hc003 hc003 1   1 1   1   1   1
> 1 1   1
> Input hc004 hc004 1   1 1   1   1   1
> 1 1   1
> Input hc005 hc005 1 1   1   1   1   1
> 1 1   1
>
> I've also created the following contrast matrices:
>
> Con1: Does difference between highRisk andLowRisk differ from 0?
> 0 0 0 0 0 -1 -1 -1 0  0  0 1  1  1
>
> Con2: Does difference between highRisk andMedRisk differ from 0?
> 0 0 0 0 0  0  0  0 -1 -1 -1 1  1  1
>
> Is this an appropriate way of setting up the ANOVA?
>
> Thanks for your help,
>
> Afsana
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> 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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] eTIV question

[Jared Tanner]

My experience with eTIV is that it's great with a perfect Talairach
transform but otherwise is less accurate than other measures. Manually
fixing the transforms and reprocessing as necessary will result in great
eTIVs but requires quite a bit of manual work.

What we do instead is just use the brainmask volume (but our data are MRIs
of non-demented older adults so there's not typically extensive atrophy).
We've found that brainmask has a Dice Similarity Coefficient of 0.95 and an
ICC of 0.92 with manually traced intracranial masks (inferior termination
on a straight line between the lowest portion of the clivus and occipital
bone). eTIV had an ICC of 0.67 with our manual masks (but we didn't fix the
transformations).

Jared


Jared Tanner, Ph.D.
Research Assistant Professor
Clinical and Health Psychology
University of Florida



> -- Forwarded message --
> From: "Harms, Michael" 
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Cc:
> Date: Sun, 21 Feb 2016 18:10:12 +
> Subject: Re: [Freesurfer] eTIV question
>
> Hi,
> Why not use a measurement of brain size rather than “eTIV”?
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
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Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)

[Z K]

I suspect its failing because the data file is zipped. Try unzipping it 
first, then run the recon:

   $> gunzip myscan.nii.gz
   $> /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz

If that does not work please upload the data and I will take a look.

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

-Zeke


On 02/22/2016 12:43 PM, Veronica.Popescu wrote:
> Dear Zeke,
> This is the output:
>
> "Mon Feb 22 18:27:05 CET 2016
> /usr/local/freesurfer/subjects/myscan
> /usr/local/freesurfer/bin/recon-all
> -s myscan -i myscan.nii.gz
> subjid myscan
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> FREESURFER_HOME /usr/local/freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
> Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 64 kbytes
> maxproc  15308
> maxlocks unlimited
> maxsignal15308
> maxmessage   819200
> maxnice  0
> maxrtprio0
> maxrttimeunlimited
>
>   total   used   free sharedbuffers cached
> Mem:   39403923452568 487824 223760 2629882343920
> -/+ buffers/cache: 8456603094732
> Swap:  2023420  772881946132
>
> 
> program versions used
> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 
> 2010-02-20 at 20:19:13
> ###
> GCADIR /usr/local/freesurfer/average
> GCA RB_all_2008-03-26.gca
> GCASkull RB_all_withskull_2008-03-26.gca
> AvgCurvTif average.curvature.filled.buckner40.tif
> GCSDIR /usr/local/freesurfer/average
> GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> ###
> /usr/local/freesurfer/subjects/myscan
>
>   mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz 
> /usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz
>
> Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016
>
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting;
> It creates the directory myscan but the folders myscan/mri/orig and 
> myscan/mri/transforms are empty. Before running I changed the rights -R a+w 
> for  /usr/local/freesurfer/subjects.
>
> I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do 
> anything, no error message it just skips to a new line.
> mri_convert -h or mri_convert --help also don't have any output.
> And recon-all -s bert -autorecon1 gives:
>
> "Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rwxrwxrwx 1 root root 472994 Feb  8 16:54 
> /usr/local/freesurfer/subjects/bert/scripts/recon-all.log
> Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> INFO: current FREESURFER_HOME does not match that of previous processing.
>  Current: /usr/local/freesurfer
>  Previous: /space/freesurfer/centos4.0/stable
> #
> #@# MotionCor Mon Feb 22 18:24:35 CET 2016
> Found 3 runs
> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
> /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has  frames
> Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"
>
>
>
>
> I tried to use
>
> If I try to run:
>
> "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v 
> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f 
> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f 
> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f 
> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red"
> as indicated on the website nothing happens, no error message.
>
>
>
>
>
> -Origineel Bericht-
>> Van: freesurfer-requ...@nmr.mgh.harvard.edu
>> Aan: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)

[Veronica.Popescu]

Dear Zeke,
This is the output: 

"Mon Feb 22 18:27:05 CET 2016
/usr/local/freesurfer/subjects/myscan
/usr/local/freesurfer/bin/recon-all
-s myscan -i myscan.nii.gz
subjid myscan
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  15308 
maxlocks unlimited
maxsignal    15308 
maxmessage   819200 
maxnice  0 
maxrtprio    0 
maxrttime    unlimited

 total   used   free shared    buffers cached
Mem:   3940392    3452568 487824 223760 262988    2343920
-/+ buffers/cache: 845660    3094732
Swap:  2023420  77288    1946132


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 
2010-02-20 at 20:19:13
###
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/usr/local/freesurfer/subjects/myscan

 mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz 
/usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz 

Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting;
It creates the directory myscan but the folders myscan/mri/orig and 
myscan/mri/transforms are empty. Before running I changed the rights -R a+w for 
 /usr/local/freesurfer/subjects. 

I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, 
no error message it just skips to a new line.
mri_convert -h or mri_convert --help also don't have any output. 
And recon-all -s bert -autorecon1 gives:

"Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 root root 472994 Feb  8 16:54 
/usr/local/freesurfer/subjects/bert/scripts/recon-all.log
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /space/freesurfer/centos4.0/stable
#
#@# MotionCor Mon Feb 22 18:24:35 CET 2016
Found 3 runs
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has  frames
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"




I tried to use

If I try to run:

"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v 
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f 
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" 
as indicated on the website nothing happens, no error message. 





-Origineel Bericht- 
> Van: freesurfer-requ...@nmr.mgh.harvard.edu 
> Aan: freesurfer@nmr.mgh.harvard.edu 
> Datum: 10-02-2016 17:28 
> Onderwerp: Freesurfer Digest, Vol 144, Issue 14 
> 
> Send Freesurfer mailing list submissions to
>  freesurfer@nmr.mgh.harvard.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>  freesurfer-requ...@nmr.mgh.harvard.edu
> 
> You can reach the person managing the list at
>  freesurfer-ow...@nmr.mgh.harvard.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents 

Re: [Freesurfer] mris_make_surfaces dimensions error

[Bruce Fischl]

can you send the full screen output also?
On Mon, 22 Feb 2016, Corinna Bauer 
wrote:



Hi Bruce, I checked and it is indeed a volume file with 256x256x256 size.

The full command line was: mris_make_surfaces -cover_seg edited_ribbon.mgz 
subject_id lh

Thanks

Corinna

On Sat, Feb 20, 2016 at 1:38 PM, Bruce Fischl  
wrote:
  Hi Corinna

  can you send us your full command line? Sounds like you are using a
  surface overlay as the cover_seg parameter instead of a volume one. Try
  running mri_info on it to make sure it is a volume (i.e. 256x256x256). If
  not, you will need to sample it into the volume with mri_surf2vol

  thanks
  Bruce

  On Thu, 18 Feb 2016, Corinna Bauer
  wrote:

  > Hello all,
  > I am attempting to reshape the pial surfaces to fill the new boundaries 
in
  > my edited ribbon.mgz file. I am using mris_make_surfaces with the 
-cover_seg
  > flag but keep getting this error:
  > ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2
  > height=1.
  >
  > Any suggestions?
  >
  > Thanks!
  > Corinna
  >
  > FYI: I am trying to reshape the pial boundary based off this previous
  > thread.
  > 
https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/04134
  > 8.html
  >
  >
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Re: [Freesurfer] Multiple Frames Error

[Bruce Fischl]

Hi Marissa

why does it have multiple frames? What kind of acquisition was it? If you 
know which frame is the correct one you can always extract it, for example


cd  /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig
mv 001.mgz two_frames.mgz
mri_convert -nth 0 two_frames.mgz 001.mgz

Bruce

On Mon, 
22 Feb 2016, Marissa Pifer wrote:



Hi freesurfers,
I am trying to run the recon-all command on a T1 weighted structural image for 
one of my subjects and I keep getting this error

"Checking for (invalid) multi-frame inputs...

ERROR: input(s) cannot have multiple frames!

/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 
frames

Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 
19:50:11 PDT 2014;
root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64


recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"


I looked through the mailing list and saw that a few other people have had this 
problem as well, and I tried some of the
solutions that were suggested but still have not been able to get past this. I 
have run the recon-all command on all of the
other subjects in our data set, and none of them have this problem. Not sure 
what is different about this scan.


Anyone run into this problem and were able to fix it? 


Thanks in advance,


Marissa 


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Re: [Freesurfer] Variations in results between qdec GUI and Command Line

[Douglas N Greve]

Hi Vikas, I can't quite understand what the problem is. Is it that the 
direction of the effect is not what you expect? That would have nothing 
to do with the correction for multiple comparisons. If you were not able 
to run in QDEC, what does the subject line of the email mean?
doug

On 02/22/2016 06:07 AM, Vikas Bandalli wrote:
> Dear Freesurfer Team,
>
> I am facing a discrepancy in the result when I run a Monte Carlo Z 
> simulation. I have a group with 3 levels(normal,Non-psychotic and 
> psychotic).I tried running an analysis to c the variation in cortical 
> thickness between the same groups in the QDEC GUI,but since iit was 
> impossible to do so and reading a few similar instances on the 
> Freesurfer mailing list,I decided to run the analysis in Command line 
> using mri_glmfit after mris_preproc.The detailed instructions I 
> followed was from the below mentioned page
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> However,Published literature with similar cases has ran the simulation 
> using pairing method i.e, lets say in this case between 
> normal-psychotic,normal-non-psychotic and psychotic-non-psychotic.
> I have done both the methods to compare,However,I have the opposite 
> results and discrepancy in results. (If there was a negative 
> correlation between normal-psychotic in GUI, there was a positive 
> correlation between normal-psychotic in the Command line analysis).
> Kindly note that the simulation was run for MC-z 1.3(0.05) in both GUI 
> and Command line.
> Please help me with this issue and which is the TRUE result.
>
> -- 
> Vikas B. R.
> Medical student
> Bangalore Medical College and Research Institute (BMCRI),
> Bangalore,India,
> Ph : +918904286825
>
>
> ___
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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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

[Douglas N Greve]

I'm having a hard time deciphering what you are doing. Is this a 
functional study? What are the 5 classes? Why are there all 1s 
regardless of risk or reward level?

On 02/19/2016 10:52 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm analyzing a decision making task with a 3x3 condition matrix: 
> pairings of low, medium, high levels of risk with low, medium, high 
> levels of reward.
>
> I've set up the following FSGD file to do a repeated 
> measures/within-subject ANOVA:
>
> GroupDescriptorFile 1
> Class hc001
> Class hc002
> Class hc003
> Class hc004
> Class hc005
> Variables   lRsk_lRwd lRsk_mRwd   lRsk_hRwd   mRsk_lRwd 
> mRsk_mRwd   mRsk_hRwd   hRsk_lRwd hRsk_mRwd   hRsk_hRwd
> Input hc001 hc0011 1   1   1 1   1 
>   1 1   1
> Input hc002 hc002 1 1   1   1   1   1 
>   1 1   1
> Input hc003 hc003 1   1 1   1   1   1 
> 1 1   1
> Input hc004 hc004 1   1 1   1   1   1 
> 1 1   1
> Input hc005 hc005 1 1   1   1   1   1 
> 1 1   1
>
> I've also created the following contrast matrices:
>
> Con1: Does difference between highRisk andLowRisk differ from 0?
> 0 0 0 0 0 -1 -1 -1 0  0  0 1  1  1
>
> Con2: Does difference between highRisk andMedRisk differ from 0?
> 0 0 0 0 0  0  0  0 -1 -1 -1 1  1  1
>
> Is this an appropriate way of setting up the ANOVA?
>
> Thanks for your help,
>
> Afsana
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
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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
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Re: [Freesurfer] mris_make_surfaces dimensions error

[Corinna Bauer]

Hi Bruce,
I checked and it is indeed a volume file with 256x256x256 size.

The full command line was: mris_make_surfaces -cover_seg edited_ribbon.mgz
subject_id lh

Thanks

Corinna

On Sat, Feb 20, 2016 at 1:38 PM, Bruce Fischl 
wrote:

> Hi Corinna
>
> can you send us your full command line? Sounds like you are using a
> surface overlay as the cover_seg parameter instead of a volume one. Try
> running mri_info on it to make sure it is a volume (i.e. 256x256x256). If
> not, you will need to sample it into the volume with mri_surf2vol
>
> thanks
> Bruce
>
> On Thu, 18 Feb 2016, Corinna Bauer
> wrote:
>
> > Hello all,
> > I am attempting to reshape the pial surfaces to fill the new boundaries
> in
> > my edited ribbon.mgz file. I am using mris_make_surfaces with the
> -cover_seg
> > flag but keep getting this error:
> > ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2
> > height=1.
> >
> > Any suggestions?
> >
> > Thanks!
> > Corinna
> >
> > FYI: I am trying to reshape the pial boundary based off this previous
> > thread.
> >
> https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/04134
> > 8.html
> >
> >
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[Freesurfer] nu correct crash

[Martin Reuter]

Hi Angela,

this does not seem to be related to longitudinal processing, your 
commands are OK. For some reason the nu_correct crashes (I changed the 
subject line). I don't know what causes that, maybe someone else has an 
idea. You have enough disk space?


I copy the part from the log here:

Iteration 1 Thu Feb 18 14:07:56 CET 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.56783/nu0.mnc 
./tmp.mri_nu_correct.mni.56783/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.56783/0/
Can't locate MNI/Startup.pm in @INC (@INC contains: 
/Applications/freesurfer/mni 
/Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 
/Network/Library/Perl/5.12/darwin-thread-multi-2level 
/Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 
/System/Library/Perl/5.12/darwin-thread-multi-2level 
/System/Library/Perl/5.12 
/System/Library/Perl/Extras/5.12/darwin-thread-multi-2level 
/System/Library/Perl/Extras/5.12 .) at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at 
/Applications/freesurfer/mni/bin/nu_correct line 37.

ERROR: nu_correct
Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 
23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj025.long.template100 exited with ERRORS at Thu Feb 18 
14:07:56 CET 2016


Best, Martin


On 02/18/2016 08:11 AM, angela.fav...@unipd.it wrote:

Hi all,
I would be very grateful of any advice for the problem below with e-TIV.

I have another problem with the longitudinal streaming (it is the first
time I use it). I am running the .base and .long procedure in subjects
with only one measure to include them in a mixed liner model analysis (as
suggested in the wiki).
I run the following commands:

recon-all -base template100 -tp subj025 -all

recon-all -long subj025 template100 -all

However at the second command line an error occur (attached is the log):

BEGIN failed--compilation aborted at
/Applications/freesurfer/mni/bin/nu_correct line 37.
ERROR: nu_correct
Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug
23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64

recon-all -s subj025.long.template100 exited with ERRORS

Which is my mistake? I looked for a solution in the mailing list, but I
did not find an answer.
Thank you for any help!

Angela




Dear Freesurfer experts,
I have a question about eTIV (FS 5.3) which I use as a covariate where
appropriate. Is it in some way influenced by the presence of brain
atrophy?
I have a new sample of subjects in a longitudinal study: at time 1 they
have some atrophy (due to low body weight) that improves in time 2 (4
months). I observed that eTIV-time1 is slightly correlated with weight
(r=0.3) whereas no correlation is present at time 2. The correlation
between eTIV-time1 and eTIV-time2 is somewhat lower than expected (r=0.53)
and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2
(0.65).

Do you suggest in these cases to perform manual segmentation to obtain
TIV? or is there any other method (in freesurfer) to obtain an estimate of
TIV not influenced by brain atrophy? What about using BrainMask_to_TIV?

Thank you for any suggestion

Angela


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Re: [Freesurfer] Longitudinal results questions

[Martin Reuter]

Hi Seth,

I assume the image you send shows the surfaces of the two time point 
taken from the *.long.baseid directories (and not from the cross 
sectionally processed directories)? There are many reasons why surfaces 
are different across time points. Some include
- motion artifacts in one time point, not (or less) in the other, or 
other acquisition problems and non-linearities

- real atrophy
- misalignment in the base step (this is pretty rare, but you can check 
the registration by switching/blending between the time points after 
registration, from the .long. directories). If there is a visible global 
shift or rotation, it may make sense to play around with the 
robust_template command in the base to see if a better alignment is 
possible, or if there are non-linearities causing the problems.


You say that when looking at individual images with surfaces, they look 
spot on. That means that surfaces are created correctly, but for some 
reason your images are different.


Images in the longitudinal stream should not be much more blurry as in 
the cross stream. They do get interpolated to the base space, but this 
is done in a single step together with the conforming. So in most cases, 
there is no additional interpolation (unless images are already 
conformed before, then there is a second interpolation step that could 
introduce some blurring - although I think I use cubic interpolation for 
that, so it should be minimal). Take a look at the surfaces in the base 
(subject template) they need to be accurate there. If they include dura, 
edit the base.


Best, Martin




On 02/16/2016 09:29 AM, Hutton, Seth wrote:


Hello FreeSurfers,

My lab has been using the longitudinal processing stream for our 
data set and seem to be getting some potentially troublesome results. 
The attached images present a snap shot of the issues we are 
encountering.


As you can see in the left image, there seems to be some kind of 
shifting going on. However, when you view each individual T1 with 
their corresponding boundary maps they look spot on. My question is 
whether or not this will have any major implication when we are trying 
to do a longitudinal analysis of cortical thickness?


The more troublesome issue which is shown on the right is an overall 
"messiness" that seems to occur in some scans. When looking back at 
the template and the original FreeSurfer images there doesn't appear 
to be any issue. It's only when the longitudinal image is constructed 
that there seems to be some exaggerated blur as well as some over 
inclusions of dura (this isn't shown in the image but has happened in 
a handful of our subjects).


Has anyone else experienced these kinds of issues? Only a quarter of 
our subjects that look as good "quality wise" as the examples posted 
on your wiki.


Thanks,

Seth Hutton

**
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Re: [Freesurfer] Use of gcs altlas with freesurfer on T1 image

[Douglas N Greve]

you can use mri_aparc2aseg. Look in the recon-all.log file for an 
example command line.

On 02/22/2016 07:33 AM, Thomas Jacquemont wrote:
> Dear,
>
> Thank you for all your advice. I have a last question, at the end of the
> process I have two different volumes containing the right and the left
> hemisphere parcellation.
> How can I combine these two parcellation to get one whole brain parcellation?
> Thank you, have a nice day.
>
> Yours faithfully,
>
> Thomas
>
>
>
>> On 2/19/16 11:00 AM, Thomas Jacquemont wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I would like to use the P. Hagmann atlas (Lausanne 2008 available here
>>> https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on
>>> my
>>> subjects. I ran Recon all on their T1 images and then these two commands
>>> to get the Hagmann parcellation for my subject:
>>>
>>> mris_ca_label -dir ../subject_dir/003_S_2374 rh sphere.reg
>>> /aramis/home/jacquemont/DataAramis/Atlas/Hagmann/myatlas_250_rh.gcs
>>> ./test_sub_003_S_2374.rh.Hagmann500.annot
>>>
>>> mri_label2vol --subject 003_S_2374 --hemi rh --annot
>>> ./test_sub_003_S_2374.rh.Hagmann500.annot  --temp
>>> ../subject_dir/003_S_2374/mri/orig/001.mgz --o
>>> annoted_volume_Hagmann500_003_S_2374.mgz --identity
>>>
>>> I have two questions. First, looking at the recon all log file I saw
>>> that
>>> the command is used this way:
>>>
>>> #@# Cortical Parc lh mardi 19 janvier 2016, 23:32:45 (UTC+0100)
>>>  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz
>>> -seed
>>> 1234 NameSubject_M0 lh ../surf/lh.sphere.reg
>>> /path/to/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>>> ../label/lh.aparc.annot
>>>
>>> I would like to know what is the "seed" option? Do I need it?
>> There is some  randomness built into mris_ca_label, and the seed is the
>> seed for the random generator. We want the results to be dterministic
>> (ie, gives the same answer when re-run in the same way) so we always
>> seed with the same number. Probably you will want this too, so use the
>> seed option.
>>> Secondly, By surperimposed the resulting parcellation file (output of
>>> the
>>> mri_label2vol command) to the repective T1 image it seems that they are
>>> not in the same space. How could I have the pacellated file in the same
>>> space as the T1 image? Is the way I am using these two command good?
>>> What
>>> inputs should I change? The sphere file (for mris_ca_label), the --temp
>>> (for mri_label2vol), etc...
>> Use --regheader orig.mgz instead of --identity
>> doug
>>
>>> Thank you for your help,
>>>
>>> Yours faithfully,
>>>
>>> Thomas
>>>
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Re: [Freesurfer] Multiple Frames Error

[Douglas N Greve]

Each input file should have one frame. What sequence did you run on the 
scanner? This usually happens when someone collected a multiecho mprage. 
If so, then compute the rms of the multiple echoes and run recon-all on that


On 02/22/2016 11:29 AM, Marissa Pifer wrote:
> Hi freesurfers,
>
> I am trying to run the recon-all command on a T1 weighted structural 
> image for one of my subjects and I keep getting this error
>
> "Checking for (invalid) multi-frame inputs...
>
> ERROR: input(s) cannot have multiple frames!
>
> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz 
> has 2 frames
>
> Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: 
> Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
>
>
> recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
>
>
> I looked through the mailing list and saw that a few other people have 
> had this problem as well, and I tried some of the solutions that were 
> suggested but still have not been able to get past this. I have run 
> the recon-all command on all of the other subjects in our data set, 
> and none of them have this problem. Not sure what is different about 
> this scan.
>
>
> Anyone run into this problem and were able to fix it?
>
>
> Thanks in advance,
>
>
> Marissa
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Multiple Frames Error

[Marissa Pifer]

Hi freesurfers,

I am trying to run the recon-all command on a T1 weighted structural image
for one of my subjects and I keep getting this error

"Checking for (invalid) multi-frame inputs...

ERROR: input(s) cannot have multiple frames!

/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz
has 2 frames

Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug
17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64


recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"


I looked through the mailing list and saw that a few other people have had
this problem as well, and I tried some of the solutions that were suggested
but still have not been able to get past this. I have run the recon-all
command on all of the other subjects in our data set, and none of them have
this problem. Not sure what is different about this scan.


Anyone run into this problem and were able to fix it?


Thanks in advance,


Marissa
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Re: [Freesurfer] comparison between two hemisphere in single

[Douglas N Greve]

On 02/20/2016 05:47 AM, Ashkan Faghiri wrote:
> Thank you doug for you answer.
>
> So now I have two other question.
> 1- how can I check the inter hemisphere registration quality? e.g. can 
> I check if the parcellation for the two hemisphere are matched well? 
> or there is other ways?
You can map the curvature (--meas curv) and see how well they align. You 
can so this with mris_preproc with --meas curv. The output will have two 
frames, one for each hemi. Load it up in tksurfer or freeview as an 
overlay and switch between the two.
>
> 2- how can I correct for multiple correction for single subject? 
> calculate the p vale for each vertex (to find significant difference 
> between the two hemisphere) and correct these for multiple correction.
I am not aware of a way to do this. You'd have to have a measure of 
variability. I guess if you had a bunch of "normal" subjects, you could 
run them through the process and generate a map of means and stddevs, 
then use that to compute a z-score, then use that to compute a 
-log10(p), then correct that.
>
> Regards,
> Ashkan
>
> What is your mris_preproc command line? If you run mris_preproc with
> --xhemi, it should give you two frames (left hemi and right hemi). If
> you want to compute left-right, then add --paired-diff to the command
> line. The output will be on the lh of fsaverage_sym. This can be
> displayed on the white, pial, or inflated of fsaverage_sym. You
> can use
> mris_apply_reg to map this back to the subject's native surface if you
> want to display it there.
> doug
>
> On 2/19/16 9:18 AM, Ashkan Faghiri wrote:
> > Hello,
> >
> > sorry for asking this again
> >
> > I want to calculate the difference between the thickness of one
> > subjects different hemispheres and show this on pial (left or right or
> > even fsaverage_sys). so I have ran :
> >
> > surfreg --s $subject --t fsaverage_sym --lh
> > surfreg --s $subject --t fsaverage_sym --lh --xhemi
> >
> > for my one subject. now I have two .reg files:
> > shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg
> > shahi/surf/lh.fsaverage_sym.sphere.reg
> >
> > If I am understanding this right, these two are the transform matrix
> > for both hemisphere of my one subject to fsaverage_sym (*right?*)
> >
> > if I run mris_preproc with xhemi option I will get a vector which have
> > the length equal to number of vertexes. it's values are left-right
> > (*or right-left?*). how can I convert this vector to pial or inflated
> > surface? and how can I use lh.fsaverage_sym.sphere.reg to register my
> > pial directly to fsaverage_sym?
> >
> > Regards,
> > Ashkan
> > --
> > --
> > Ashkan Faghiri
> > MSc student of Bioelectrical Engineering
> > Department of Electrical Engineering
> > Sharif University of Technology
> >
> >
> > ___
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> -- 
>
> -- 
> Ashkan Faghiri
> MSc student of Bioelectrical Engineering
> Department of Electrical Engineering
> Sharif University of Technology
>
>
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Re: [Freesurfer] qdec

[Douglas N Greve]

Not sure. Can you run it separately for each subject? I suspect that 
there might be a subject with a bad stats file

On 02/19/2016 02:58 PM, levi solomyak wrote:
> Hi Douglas,
>
> Sure! Below is the terminal outputs when I try and run the command you 
> suggested on the first five subjects. Any help you could provide would 
> be much appreciated!
>
> Best,
> LS
>
>  $asegstats2table --common-segs --meas volume --tablefile 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>  
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/asegstats2table", line 538, in 
> 
> id_name_map, measurelist = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
>
> On Fri, Feb 19, 2016 at 2:53 PM, levi solomyak  > wrote:
>
> Hi Douglas,
>
> Sure! Below is the terminal outputs when I try and run the command
> you suggested on the first five subjects. Any help you could
> provide would be much appreciated!
>
> Best,
> LS
>
>  $asegstats2table --common-segs --meas volume --tablefile
> 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/asegstats2table", line 538,
> in 
> id_name_map, measurelist = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
>
> On Fri, Feb 19, 2016 at 2:47 PM, levi solomyak
> > wrote:
>
> Hi Douglas,
>
> Sure! Below is the terminal outputs when I try and run the
> command you suggested on the first five subjects. Any help you
> could provide would be much appreciated!
>
> Best,
> LS
>
>  $asegstats2table --common-segs --meas volume --tablefile
> 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115
> 110411
> SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/asegstats2table", line
> 538, in 
> id_name_map, measurelist = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 115, in
> parse
> self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
> IndexError: list index out of range
>
>
>
> On Mon, Dec 21, 2015 at 6:13 PM, Douglas N Greve
> >
> wrote:
>
> Can you run the command below outside of qdec and send us
> the error it
> prints to the terminal?
>
> asegstats2table --common-segs --meas volume --tablefile
> 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects 100307 101006 104820
> 105115 110411
> 111312 111413 111716 112819 113215 113619 113922 114419
> 115320 116524
> 117122 117324 118528 135225 135932 150625 150726 151223
> 151526 170934
> 171633 172130 172332 172534 172938 173334 175439 177645
> 177746 178142
> 200109 200614 20 201414 201818 203418 204016 204521
> 304020 307127
> 308331 310621 316633 329440 365343 366042 377451 380036
> 385450 386250
> 412528 433839 436239 480141 486759 497865 499566 500222
> 510326 530635
> 531536 540436 561242 562446 565452 566454 567052 567961
> 568963 571548
> 580044 580347 581349 583858 586460 594156 598568 599671
>
>
>
> On 12/14/2015 02:15 PM, levi solomyak wrote:
> > Dear experts,
> >
> > I've been attempting to generate a stats data table in
> qdec, but each
> > time I get a "Index Error: list index is out of range"
> error. This is
> > occurring when it is trying to parse the .stats file.
> >
> >  I've made sure that the files all line up exactly with
> the qdec table
> > and that SUBJECTS_DIR  is properly sourced so I'm not
> sure how to fix
> > this problem. Any help would be greatly 

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

[María Díez Cirarda]

Dear FS Experts,


I have followed the steps for doing a Repeated Measures ANOVA 2x2 in
Freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
also following the previous post:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026287.html
.


I have already created the FSGD File (2 groups: experimental and control
group) and 2 times (pre-treatment and post-treatment) (I send it attached),
and specified the contrasts of the model:

Tp1vsTp2Gr.Exp  > 0 0 1 0
Tp1vsTp2Gr.Control > 0 0 0 -1
Interaction Effect > 0 0 1 -1

Are these contrasts correct?

I have runned the mri_preproc command, and the "lh.thickness.mgh" file has
been created.
However, when I run the next step, the smoothing, an error message appears
"ERROR: Option lh.thickness.mgh unknown". Am I doing something wrong?
The smoothing is an optional step, therefore, I run the mri_glmfit, (I send
attached the mri_glmfit.log file), and what appears in the terminal is the
file "Results_ANOVA2x2".
I this file "Results_ANOVA 2x2" two lines appear:
0 Tp1vsTp2.GrExp 0 0.740532
1 Tp1vsTp2.GrControl 0 0.672022
The first one is telling us that the cortical thickness in the experimental
group was Tp1>Tp2, and the same for the control group?
Where can I find the interaction results?

Thank you for the help,

Maria.


ANOVA2X2.fsgd
Description: Binary data

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/pd_naroa/subjects/qdec
cmdline mri_glmfit --glmdir lh.anova2x2 --y lh.thickness.mgh --fsgd ANOVA2X2.fsgd doss --C Tp1vsTp2GrExp.mtx --C Tp1vsTp2GrControl.mtx --C Interaction.mtx 
sysname  Linux
hostname neuroimagen1
machine  x86_64
user pd_naroa
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/pd_naroa/subjects/qdec/lh.thickness.mgh
logyflag 0
usedti  0
FSGD ANOVA2X2.fsgd
glmdir lh.anova2x2
IllCondOK 0
ReScaleX 1
DoFFx 0


Results_ANOVA2x2
Description: Binary data
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Re: [Freesurfer] FLAIR registration

[Bruce Fischl]

not sure. Doug?
On Mon, 22 Feb 2016, K. Wagstyl wrote:

> Hi Bruce,
>
> --init-spm works much better thanks. Is there a way to rerun autorecon3
> using --init-spm rather than --init-fsl?
>
> Or do we need to run the commands line by line.
>
> Cheers,
> Konrad
>
> On 2016-02-22 13:45, Bruce Fischl wrote:
>> can you try --init-spm instead of --init-fsl and see if it does better?
>> On
>> Mon, 22 Feb 2016, K. Wagstyl wrote:
>>
>>> Hi all,
>>>
>>> We're trying to use FLAIR images in our recon-all pipeline. For half
>>> of
>>> the participants there are no problems using:
>>> recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
>>>
>>> However for the other half the FLAIR registrations are either a bit
>>> off
>>> or completely flipped, including swapping axes. This then affects the
>>> generate surfaces.
>>>
>>> The problem line seems to be:
>>> bbregister --s  --mov mri/orig/FLAIRraw.mgz --lta
>>> mri/transforms/FLAIRraw.lta --init-fsl --T2
>>>
>>> as the output registration of these files is incorrect.
>>>
>>> We've tried using mri_convert instead of dcm2nii. This does not solve
>>> the problem. Loading the FLAIR.nii in fslview, the image is upside
>>> down,
>>> but the letters indicating orientation are correct.
>>>
>>> Do you have any suggestions about how to solve this problem?
>>>
>>> Thanks,
>>> Konrad
>>> ___
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>>> Freesurfer@nmr.mgh.harvard.edu
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>>>
>>>
>>>
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>>
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>> it is
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>> e-mail
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Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

[Afzal, Afsana]

Hi, Just wanted to check and see if the following is an appropriate set-up for 
a repeated measures ANOVA. Thanks,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana 
[aaf...@mgh.harvard.edu]
Sent: Friday, February 19, 2016 10:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

Hi,

I'm analyzing a decision making task with a 3x3 condition matrix: pairings of 
low, medium, high levels of risk with low, medium, high levels of reward.

I've set up the following FSGD file to do a repeated measures/within-subject 
ANOVA:

GroupDescriptorFile 1
Class hc001
Class hc002
Class hc003
Class hc004
Class hc005
Variables   lRsk_lRwd   lRsk_mRwd   lRsk_hRwd   mRsk_lRwd   
mRsk_mRwd   mRsk_hRwd   hRsk_lRwd   hRsk_mRwd   hRsk_hRwd
Input hc001 hc0011   1   1   1   1  
 1   1   1   1
Input hc002 hc0021   1   1   1   1  
 1   1   1   1
Input hc003 hc0031   1   1   1   1  
 1   1   1   1
Input hc004 hc0041   1   1   1   1  
 1   1   1   1
Input hc005 hc0051   1   1   1   1  
 1   1   1   1

I've also created the following contrast matrices:

Con1: Does difference between highRisk and LowRisk differ from 0?
0 0 0 0 0 -1 -1 -1 0  0  0 1  1  1

Con2: Does difference between highRisk and MedRisk differ from 0?
0 0 0 0 0  0  0  0-1 -1 -1 1  1  1

Is this an appropriate way of setting up the ANOVA?

Thanks for your help,

Afsana
__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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Re: [Freesurfer] FLAIR registration

[K. Wagstyl]

Hi Bruce,

--init-spm works much better thanks. Is there a way to rerun autorecon3 
using --init-spm rather than --init-fsl?

Or do we need to run the commands line by line.

Cheers,
Konrad

On 2016-02-22 13:45, Bruce Fischl wrote:
> can you try --init-spm instead of --init-fsl and see if it does better?
> On
> Mon, 22 Feb 2016, K. Wagstyl wrote:
> 
>> Hi all,
>> 
>> We're trying to use FLAIR images in our recon-all pipeline. For half 
>> of
>> the participants there are no problems using:
>> recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
>> 
>> However for the other half the FLAIR registrations are either a bit 
>> off
>> or completely flipped, including swapping axes. This then affects the
>> generate surfaces.
>> 
>> The problem line seems to be:
>> bbregister --s  --mov mri/orig/FLAIRraw.mgz --lta
>> mri/transforms/FLAIRraw.lta --init-fsl --T2
>> 
>> as the output registration of these files is incorrect.
>> 
>> We've tried using mri_convert instead of dcm2nii. This does not solve
>> the problem. Loading the FLAIR.nii in fslview, the image is upside 
>> down,
>> but the letters indicating orientation are correct.
>> 
>> Do you have any suggestions about how to solve this problem?
>> 
>> Thanks,
>> Konrad
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
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Re: [Freesurfer] FLAIR registration

[Bruce Fischl]

can you try --init-spm instead of --init-fsl and see if it does better?
On 
Mon, 22 Feb 2016, K. Wagstyl wrote:

> Hi all,
>
> We're trying to use FLAIR images in our recon-all pipeline. For half of
> the participants there are no problems using:
> recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
>
> However for the other half the FLAIR registrations are either a bit off
> or completely flipped, including swapping axes. This then affects the
> generate surfaces.
>
> The problem line seems to be:
> bbregister --s  --mov mri/orig/FLAIRraw.mgz --lta
> mri/transforms/FLAIRraw.lta --init-fsl --T2
>
> as the output registration of these files is incorrect.
>
> We've tried using mri_convert instead of dcm2nii. This does not solve
> the problem. Loading the FLAIR.nii in fslview, the image is upside down,
> but the letters indicating orientation are correct.
>
> Do you have any suggestions about how to solve this problem?
>
> Thanks,
> Konrad
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>
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Re: [Freesurfer] Ris: eTIV question

[Bruce Fischl]

Hi Angela

gyrification is the ratio of areas and hence dimensionless, so I would 
think it wouldn't be much affected by TIV.


cheers
Bruce


On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:


In the case of a gyrification analysis, does correction for total brain
volume make sense?

Angela

Inviato dal mio dispositivo Huawei

 Messaggio originale 
Oggetto: Re: [Freesurfer] eTIV question
Da: Bruce Fischl
A: Freesurfer support list
CC:


  yes, it's a somewhat different and more conservative test. I
  guess you
  could check the talairach transforms of some of your subjects
  with eTIVs
  that don't make sense (or change the most over time) to try to
  see why
  this is happening. Or take Mike's suggestion and test a
  different (but
  probably still interesting) hypothesis

  On Sun, 21 Feb 2016, Angela Favaro wrote:

  > Hi, thank you
  > I think this would test something different: 'how much a brain
  area is
  > atrophic controlling for the average brain atrophy' and not
  'how much
  > a brain area is atrophic controlling for the individual
  differences in
  > head size'. Doesn't it?
  >
  > Angela
  >
  >
  > "Harms, Michael" ha scritto:
  >
  >> Hi,
  >> Why not use a measurement of brain size rather than “eTIV”?
  >>
  >> cheers,
  >> -MH
  >>
  >> --
  >> Michael Harms, Ph.D.
  >>
  >> ---
  >> Conte Center for the Neuroscience of Mental Disorders
  >> Washington University School of Medicine
  >> Department of Psychiatry, Box 8134
  >> 660 South Euclid Ave.Tel: 314-747-6173
  >> St. Louis, MO 63110Email: mha...@wustl.edu
  >>
  >>
  >>
  >>
  >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of
  >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
  >>
  >> there is a mistake in the graph, hippocampal volume is TIV2
  >> I apologize for that!
  >>
  >> Angela Favaro ha scritto:
  >>
  >>> Hi Bruce,
  >>> please find attached the graph of the correlation between
  the two time
  >>> point. I did not find outliers or failures. However the
  discrepancy
  >>> between TIVs is particularly high in few cases. Obviously
  these data
  >>> are those before running longitudinal streaming
  >>> This is a sample of adolescents with low body weight
  (anorexia nervosa).
  >>> In my previous study (on young adults with low weight) I
  found no
  >>> correlation between TIV and body weight and high
  correlations between
  >>> fs estimated TIV and manually segmented TIV (r=0.94 in the
  whole
  >>> sample and r=0.93 in the underweight sample (n=38)).
  >>> Do you think that the young age can be a factor? or patients
  who are
  >>> more acutely underweight?
  >>> Thank you for any suggestion
  >>>
  >>> Angela
  >>>
  >>>
  >>> Bruce Fischl ha scritto:
  >>>
   Hi Angel
  
   the time1/time2 correlation of eTIV is pretty worrisome.
  Are you sure
   that there aren't outliers/failures in that set?
  
   Bruce
  
  
   On Sun, 14 Feb 2016, angela.fav...@unipd.it wrote:
  
  > Dear Freesurfer experts,
  > I have a question about eTIV (FS 5.3) which I use as a
  covariate where
  > appropriate. Is it in some way influenced by the presence
  of brain
  > atrophy?
  > I have a new sample of subjects in a longitudinal study:
  at time 1 they
  > have some atrophy (due to low body weight) that improves
  in time 2 (4
  > months). I observed that eTIV-time1 is slightly correlated
  with weight
  > (r=0.3) whereas no correlation is present at time 2. The
  correlation
  > between eTIV-time1 and eTIV-time2 is somewhat lower than
  expected
  > (r=0.53)
  > and is lower than correlation between SegBrain_Vol_1 and
  SegBrain_Vol_2
  > (0.65).
  >
  > Do you suggest in these cases to perform manual
  segmentation to obtain
  > TIV? or is there any other method (in freesurfer) to
  obtain an
  > estimate of
  > TIV not influenced by brain atrophy? What about using
  BrainMask_to_TIV?
  >
  > Thank you for any suggestion
  >
  > Angela
  >
  >
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Re: [Freesurfer] Use of gcs altlas with freesurfer on T1 image

[Thomas Jacquemont]

Dear,

Thank you for all your advice. I have a last question, at the end of the
process I have two different volumes containing the right and the left
hemisphere parcellation.
How can I combine these two parcellation to get one whole brain parcellation?
Thank you, have a nice day.

Yours faithfully,

Thomas



>
> On 2/19/16 11:00 AM, Thomas Jacquemont wrote:
>> Dear FreeSurfer experts,
>>
>> I would like to use the P. Hagmann atlas (Lausanne 2008 available here
>> https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on
>> my
>> subjects. I ran Recon all on their T1 images and then these two commands
>> to get the Hagmann parcellation for my subject:
>>
>> mris_ca_label -dir ../subject_dir/003_S_2374 rh sphere.reg
>> /aramis/home/jacquemont/DataAramis/Atlas/Hagmann/myatlas_250_rh.gcs
>> ./test_sub_003_S_2374.rh.Hagmann500.annot
>>
>> mri_label2vol --subject 003_S_2374 --hemi rh --annot
>> ./test_sub_003_S_2374.rh.Hagmann500.annot  --temp
>> ../subject_dir/003_S_2374/mri/orig/001.mgz --o
>> annoted_volume_Hagmann500_003_S_2374.mgz --identity
>>
>> I have two questions. First, looking at the recon all log file I saw
>> that
>> the command is used this way:
>>
>> #@# Cortical Parc lh mardi 19 janvier 2016, 23:32:45 (UTC+0100)
>> mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz
>> -seed
>> 1234 NameSubject_M0 lh ../surf/lh.sphere.reg
>> /path/to/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>> ../label/lh.aparc.annot
>>
>> I would like to know what is the "seed" option? Do I need it?
> There is some  randomness built into mris_ca_label, and the seed is the
> seed for the random generator. We want the results to be dterministic
> (ie, gives the same answer when re-run in the same way) so we always
> seed with the same number. Probably you will want this too, so use the
> seed option.
>>
>> Secondly, By surperimposed the resulting parcellation file (output of
>> the
>> mri_label2vol command) to the repective T1 image it seems that they are
>> not in the same space. How could I have the pacellated file in the same
>> space as the T1 image? Is the way I am using these two command good?
>> What
>> inputs should I change? The sphere file (for mris_ca_label), the --temp
>> (for mri_label2vol), etc...
> Use --regheader orig.mgz instead of --identity
> doug
>
>>
>> Thank you for your help,
>>
>> Yours faithfully,
>>
>> Thomas
>>
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[Freesurfer] Variations in results between qdec GUI and Command Line

[Vikas Bandalli]

Dear Freesurfer Team,

I am facing a discrepancy in the result when I run a Monte Carlo Z
simulation. I have a group with 3 levels(normal,Non-psychotic and
psychotic).I tried running an analysis to c the variation in cortical
thickness between the same groups in the QDEC GUI,but since iit was
impossible to do so and reading a few similar instances on the Freesurfer
mailing list,I decided to run the analysis in Command line using mri_glmfit
after mris_preproc.The detailed instructions I followed was from the below
mentioned page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
However,Published literature with similar cases has ran the simulation
using pairing method i.e, lets say in this case between
normal-psychotic,normal-non-psychotic and psychotic-non-psychotic.
I have done both the methods to compare,However,I have the opposite results
and discrepancy in results. (If there was a negative correlation between
normal-psychotic in GUI, there was a positive correlation between
normal-psychotic in the Command line analysis).
Kindly note that the simulation was run for MC-z 1.3(0.05) in both GUI and
Command line.
Please help me with this issue and which is the TRUE result.

-- 
Vikas B. R.
Medical student
Bangalore Medical College and Research Institute (BMCRI),
Bangalore,India,
Ph : +918904286825
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[Freesurfer] FLAIR registration

[K. Wagstyl]

Hi all,

We're trying to use FLAIR images in our recon-all pipeline. For half of 
the participants there are no problems using:
recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial

However for the other half the FLAIR registrations are either a bit off 
or completely flipped, including swapping axes. This then affects the 
generate surfaces.

The problem line seems to be:
bbregister --s  --mov mri/orig/FLAIRraw.mgz --lta 
mri/transforms/FLAIRraw.lta --init-fsl --T2

as the output registration of these files is incorrect.

We've tried using mri_convert instead of dcm2nii. This does not solve 
the problem. Loading the FLAIR.nii in fslview, the image is upside down, 
but the letters indicating orientation are correct.

Do you have any suggestions about how to solve this problem?

Thanks,
Konrad
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