date:20160726

Re: [Freesurfer] flipping TRACULA tracts

2016-07-26 Thread Anastasia Yendiki

Hi Barbara - Your hack sounds like the right idea. One option would be to 
switch the FA values between the pathstats.byvoxel.txt files in the lh.* 
and rh.* output directories, by editing the text files without renaming 
the directories.

Hope this helps,

a.y

On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:

> Dear Freesurfers,
>
> I've got data pertaining to patients with left and right-sided temporal
> lobe epilepsy (TLE).
> My aim is to group those tracts according to side of epilepsy for
> waypoint comparisons.
>
> Basically for patients with right TLE I'd like to look at right tracts
> and at the same time for patients with left TLE I'd like to look at left
> tracts (ipsilateral tracts), I need to do the same for the contralateral
> tracts.
> Is there a straightforward way of doing this?
>
> I've already copied the tracts to respective ipsi and contralateral
> byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt;
> do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in
> R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i
> ${i/byvoxel./byvoxel_contraRTLE.}; done
> Now I have to flip the x-coordinates in the patients with right TLE (to
> make them more comparable to the tracts of the patients with left TLE).
> That will not be a problem, but I wonder if I am missing something?
> Can I then just go ahead and run trac-all -stats -c dmrircfile to
> generate the mean waypoint tracts etc.?
>
> Thank you very much,
> Best wishes,
>
> Barbara
>
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>
>
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Re: [Freesurfer] TRACULA fornix tractography

2016-07-26 Thread Anastasia Yendiki

Hi Barbara - We're working on a new atlas for TRACULA that will include 
the fornix. We've already done the manual labeling for it.

Best,

a.y

On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
> 
> As we are analyzing DTI data acquired in patients with epilepsy we are
> especially interested in the fornix.
> I've come across the mri_cc -f option for fornix segmentation (native space)
> but I've also read that manual tracing/labeling of the tracts would be
> needed in the 33 controls for TRACULA (training set - trctrain).
> In Wakana et al. 2011 I see that the fornix was not included due to low
> reproducibility and it further states:
> 
> "the reason for the poor reproducibility is most likely due to not enough
> spatial resolution with respect to the diameter"
> 
> I wonder if you could please guide us in how to best add this tract to
> TRACULA so that it would be consistent in the methods compared with the
> other tract ROI definitions or perhaps state what were the difficulties in
> adding this particular tract to TRACULA.
> 
> Thank you very much,
> Best wishes,
> Barbara
> 
>
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Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

2016-07-26 Thread Anastasia Yendiki



Hi Michael - Which build of freesurfer do you use? I can send you the new 
version of dmri_paths so you can try it out.


Best,

a.y

On Wed, 20 Jul 2016, Harms, Michael wrote:



Hi Anastasia,

I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html

It sounds like a new version of dmri_paths was deemed necessary to
appropriately process single time points in the longitudinal TRACULA stream,
but Janosch’s last post seemed to indicate that her issue wasn’t resolved
even with the new build of dmri_paths that you generated.

thanks,
-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  63110 Email: mha...@wustl.edu

 





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Re: [Freesurfer] TRACULA group stats visualization

2016-07-26 Thread Anastasia Yendiki


Hi Derek - Good to know things worked out!

a.y

On Tue, 19 Jul 2016, Derek Pisner wrote:

> Hi Anastasia,
>
> I thought I should let you know that this issue has now been resolved. We 
> specified the base ID's/ subject ID's incorrectly in the config file! Sorry 
> for the confusion. Now our group output looks correct.
>
> Thanks for your help,
> Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner 
> [dpis...@psychiatry.arizona.edu]
> Sent: Tuesday, July 12, 2016 5:06 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Anastasia,
>
> All subjects had both time-points (for DWI and T1-weighted recons). The 
> recons were run following the standard longitudinal pipeline for FS.
>
> Would it matter that I ran the pipeline piecemeal (i.e. separate 
> configuration files for each subject--see attached example)? In case you are 
> wondering, I did it this way in order to run the pipeline in parallel (i.e. 
> by subject) on our cluster...
>
> Another consideration is that we did preprocessing outside of TRACULA (i.e. 
> using FSL's tools directly so that we could apply a fieldmap, use new EDDY 
> with TOPUP, as well as apply a denoising algorithm). We then setup the folder 
> structure and filenames to begin TRACULA at the trac-all -intra stage, which 
> we have done successfully in the past when not using the longitudinal 
> pipeline (i.e. single-subject analyses)
>
> Still, I have a feeling that none of these customizations should have made 
> any difference as our merged outputs look excellent for both timepoints, for 
> all subjects... Any other thoughts about what might be causing this?
>
> Kind regards,
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 12, 2016 1:45 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't
> been able to replicate the problem in our own longitudinal data. Did you
> by any chance have any subjects that had only a single time point?
>
> a.y
>
> On Thu, 7 Jul 2016, Derek Pisner wrote:
>
>> Sure thing. fmajor mean.txt file is attached.
>>
>>
>> Thanks a bunch,
>> -Derek
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Thursday, July 07, 2016 4:48 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>
>> Hi Derek - this is strange. The dev and 5.3 version of freeview should
>> display them differently. Can you send me one of those mean.txt files?
>>
>> a.y
>>
>> On Wed, 6 Jul 2016, Derek Pisner wrote:
>>
>>> Hi Anastasia,
>>>
>>> This occurs for me on both stable and dev versions of freview and trac-all 
>>> -stat
>>>
>>> -Derek
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>>> [ayend...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 04, 2016 12:47 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>>
>>> Hi Derek - Are you by any chance using the dev version of freeview?
>>>
>>> a.y
>>>
>>> On Fri, 1 Jul 2016, Derek Pisner wrote:
>>>
 Dear Anastasia,
 I am running into an issue with the trac-all -stat option on our 
 longitudinal TRACULA data.

 Everything runs smoothly through all earlier stages, and I checked 
 individual subjects' merged outputs in freeview with -tv mode. Everything 
 looks fine.

 Also, then when I run trac-all -c dmric_config -stat, everything finishes 
 without error.

 But then when I open the results with the command:
 freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
 /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt

 I get the image seen in the attached .png file. Any idea what might be 
 causing this?

 Many thanks in advance for you help.

 Best,
 Derek




>>>
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>>>
>>>
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>>
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Re: [Freesurfer] Coordinates in TRACULA group analysis

2016-07-26 Thread Anastasia Yendiki



Hi Anri - The problem is in this line:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp)

It should be changed to this:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)

For this to take effect, you need to run "which trac-all" and make the 
change in the trac-all file that the which commands shows you.


Hope this helps,

a.y

On Fri, 15 Jul 2016, Anri WATANABE wrote:


Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!

Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki :

  Hi Anri - This may be a bug that was fixed at some point. Can
  you send me the scripts/trac-all.local-copy from one of your
  subjects? Thanks!

  a.y

  On Mon, 11 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,There is an error in .log files of left
corticospinal tract in cvs template and I attached
one
of file. In addition .log files of right
corticospinal tract in cvs template doesn't exist. 
Thanks in advance.

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine

**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - Is there an error in the stats/*.log
files for the different tracts?

      a.y

      On Tue, 5 Jul 2016, Anri WATANABE wrote:

            Dear Anastasia, 

            I use TRACULA to obtain diffusion
measures at each voxel in a certain pathway for
            group analysis, but
            there aren't stats/*.path.mean.txt
files. I found .log files
            (_PP.avg33_mni_bbr.log) which
exist
            1 file per 1 tract, except corticospinal
tract which has 2 .log files.

            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference
volume from
           
/Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            I attached dmrirc.example (configuration
file) and /scripts/trac-all.log.


            Thanks in advance,
            Anri




           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
University of Medicine
           

**

            2016-06-03 9:51 GMT+09:00 Anri WATANABE
:
                  Hi, Anastasia.
            There aren't any .log files but text
files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
            I guess text
            files complete all pathways and
measures.

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
University of Medicine
           

**

Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

2016-07-26 Thread Anastasia Yendiki



Hi Knut Jørgen - Do you get this error only with the dev version of 
freesurfer? The command line causing the error is:


bbregister --s 4_test --init-fsl --dti --mov 
/home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg 
/home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat 
/home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat

Can you please try running this with the 5.3 version?

Thanks!

a.y

On Wed, 13 Jul 2016, Knut J Bjuland wrote:


Hi  Anastasia

Thanks. I am sending my entire trac-all.log

Knut Jøgen


On 07/12/2016 11:19 PM, Anastasia Yendiki wrote:

  Hi Knut Jørgen - Can you please send your entire trac-all.log?
  Thanks!

  a.y

  On Mon, 11 Jul 2016, Knut J Bjuland wrote:


 


flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/ref
vol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/mov
vol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90
-searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fs
l.mat
-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fsl
mat0.trans.mat
-schedule
/usr/local/freesurfer/bin/flirt.newdefault.20080811.sch

terminate called after throwing an instance of
'NEWMAT::SingularException'

Abort (core dumped) 

ERROR: flirt





Fedora 24


glibc-2.23.1-8.fc24.x86_64

gcc-6.1.1-3.fc24.x86_64


libstdc++-6.1.1-3.fc24.x86_64

ldd /usr/local/freesurfer/bin/flirt.fsl 

    linux-vdso.so.1 (0x7ffe8b6c8000)

    libz.so.1 => /lib64/libz.so.1
(0x7feaeba06000)

    libstdc++.so.6 => /lib64/libstdc++.so.6
(0x7feaeb67e000)

    libm.so.6 => /lib64/libm.so.6
(0x7feaeb374000)

    libgcc_s.so.1 => /lib64/libgcc_s.so.1
(0x7feaeb15d000)

    libc.so.6 => /lib64/libc.so.6
(0x7feaead9a000)

    /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)







Knut Jørgen Bjuland





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Re: [Freesurfer] New hippocampal subfields

2016-07-26 Thread Iglesias, Eugenio

It need to run some additional tests, but I'm almost sure it is solved. The 
fixed code will be in the development version very soon, with some other 
updates. Stay tuned!

Cheers,

Eugenio


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jin Kyu Gahm 

Sent: Tuesday, July 26, 2016 10:17:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] New hippocampal subfields

Hello,

I was trying the new segmentation module of hippocampal subfields, but I also 
encountered the same errors as Pierre reported a week ago:

--
Invalid MEX-file 
'/tmp/MCR_1031368111/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
 libkvlGEMSCommon.so: cannot open shared object file: No such file or directory

Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)
--

Eugenio - I wonder if you already solved the problem. Thanks for your help!

Best,
Jin

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[Freesurfer] fMRI Postdoctoral Fellow

2016-07-26 Thread Thomas Yeo

Dear All,

I am looking to hire a postdoc with either strong machine learning
background OR system neuroscience background. Prior experience with
fMRI is a plus.

Topics are flexible. Example topics include individual-subject brain
parcellations, relationships between behavior and brain networks,
dynamic functional connectivity, meta-analysis, neural mass modeling,
graph theoretic modeling of brain networks, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, computer science, electrical
engineering, statistics or related fields. The successful applicant
will work with an interdisciplinary team of computer scientists and
neuroscientists.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Flattening the surface

2016-07-26 Thread Bruce Fischl

sure, you can do that with mri_vol2surf. Basically the initial surface 
and the final (inflated) surface have the same number of vertices, so the 
vertex identity is preserved and mri_vol2surf samples values from the 
volume onto the surface which can then be displayed on any surface 
configuration (like inflated)


On Tue, 26 Jul 2016, Younghoon Kim wrote:


Hi Bruce,

Thanks to your advice, I was able to obtain the surface of the segmented
brain area and its inflated surface using FreeSurfer.

The generated surface however does not contain any texture, which is needed
for further steps in my project.

I am considering to project the texture of the segmented brain area (the
pixel intensity on the surface of the volumetric data) to the generated
surface (vectorized surface). I wonder whether this can be done in a similar
way to the way you project fMRI signal to the surface.

Thanks,

Younghoon Kim
--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:

and 255 is the label that you want to cover? 16G may not be enough. Do
you
have any machines with more RAM?

On Thu, 21 Jul 2016, Younghoon
Kim wrote:

> Hi Bruce,
>
> Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using
different imaging methods)
>
> Our machine has 16GB RAM.
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
>
> On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fis...@nmr.mgh.harvard.edu) wrote:
>
> is Brain_FS.mgz a segmented volume? How much memory do you have on
that
> machine?
>
> On Wed, 20 Jul 2016, Younghoon Kim wrote:
>
> > Hi Bruce,
> >
> > I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix”
command to generate a
> > surface, but received an error message as below:
> >
> > changing type of input volume to 8 bits/voxel...
> > $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
> >   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
> > Cannot calloc()
> >
> > Would this be because my input data is not compatible with the
mri_tessellate
> > command?
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> > On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fis...@nmr.mgh.harvard.edu) wrote:
> >
> > If you have a segmented volume, you can use mri_tessellate to
create the
> > surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
> > patch. You can check out our wiki
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki
> >
> > which has info on this process, although the flattening isn't
terribly well
> > documented. You need the -1 flag to tell it to only use that one
surface
> > that you are giving it, and not to assume that the entire FS
directory
> > structure exists.
> >
> > cheers
> > Bruce
> >
> >
> > On Wed, 20 Jul 2016, Younghoon Kim wrote:
> >
> > > Hi Bruce,
> > >
> > > Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
> > to
> > > generate a surface of our volumetric data and flatten it?
> > >
> > > Thanks,
> > >
> > > Younghoon Kim
> > >
> > > --
> > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > OMICS Lab
> > > Wellman Center, Massachusetts General Hospital
> > > Bouma’s Lab
> > > --
> > > younghoon.h@gmail.com
> > > aktivh...@kaist.ac.kr
> > >
> > > On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fis...@nmr.mgh.harvard.edu)
> > wrote:
> > >
> > > HI Younghoon
> > >
> > > I guess that could work. You will need to introduce at least one
cut if not
> > > more if you surface has substantial Gaussian curvature
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Wed,
> > > 20 Jul 2016, Younghoon Kim wrote:
> > >
> > > > Hi Bruce,
> > > >
> > > > We are only interested in the surface image of the volumetric
data.
> > > >
> > > > For flattening, we do not care about the interior of the
volume, so we
> > > would like
> > > > to remove the volume data inside.
> > > >
> > > > So what we want is to peel off the surface from the segmented
brain area
> > > and
> > > > flatten that surface.
> > > >
> > > > Thanks,
> > > >
> > > > Younghoon Kim
> > > >
> > > > --
> > > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > > OMICS Lab
> > > > Wellman Center, Massachusetts General Hospital
> > > > Bouma’s Lab
> > > > --
> > > >

[Freesurfer] New hippocampal subfields

2016-07-26 Thread Jin Kyu Gahm

Hello,

I was trying the new segmentation module of hippocampal subfields, but I also 
encountered the same errors as Pierre reported a week ago:

--
Invalid MEX-file 
'/tmp/MCR_1031368111/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
 libkvlGEMSCommon.so: cannot open shared object file: No such file or directory

Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)
--

Eugenio - I wonder if you already solved the problem. Thanks for your help!

Best,
Jin

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Re: [Freesurfer] Flattening the surface

2016-07-26 Thread Younghoon Kim

Hi Bruce,

Thanks to your advice, I was able to obtain the surface of the segmented
brain area and its inflated surface using FreeSurfer.

The generated surface however does not contain any texture, which is needed
for further steps in my project.

I am considering to project the texture of the segmented brain area (the
pixel intensity on the surface of the volumetric data) to the generated
surface (vectorized surface). I wonder whether this can be done in a
similar way to the way you project fMRI signal to the surface.

Thanks,

Younghoon Kim
--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:

and 255 is the label that you want to cover? 16G may not be enough. Do you
have any machines with more RAM?

On Thu, 21 Jul 2016, Younghoon
Kim wrote:

> Hi Bruce,
>
> Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the
size is about 3000x2000x140. (We obtained this brain image using different
imaging methods)
>
> Our machine has 16GB RAM.
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
>
> On July 21, 2016 at 10:35:18 AM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
>
> is Brain_FS.mgz a segmented volume? How much memory do you have on that
> machine?
>
> On Wed, 20 Jul 2016, Younghoon Kim wrote:
>
> > Hi Bruce,
> >
> > I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to
generate a
> > surface, but received an error message as below:
> >
> > changing type of input volume to 8 bits/voxel...
> > $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
> >   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
> > Cannot calloc()
> >
> > Would this be because my input data is not compatible with the
mri_tessellate
> > command?
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> > On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
> >
> > If you have a segmented volume, you can use mri_tessellate to create
the
> > surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
> > patch. You can check out our wiki
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki
> >
> > which has info on this process, although the flattening isn't terribly
well
> > documented. You need the -1 flag to tell it to only use that one
surface
> > that you are giving it, and not to assume that the entire FS directory
> > structure exists.
> >
> > cheers
> > Bruce
> >
> >
> > On Wed, 20 Jul 2016, Younghoon Kim wrote:
> >
> > > Hi Bruce,
> > >
> > > Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
> > to
> > > generate a surface of our volumetric data and flatten it?
> > >
> > > Thanks,
> > >
> > > Younghoon Kim
> > >
> > > --
> > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > OMICS Lab
> > > Wellman Center, Massachusetts General Hospital
> > > Bouma’s Lab
> > > --
> > > younghoon.h@gmail.com
> > > aktivh...@kaist.ac.kr
> > >
> > > On July 20, 2016 at 5:12:59 PM, Bruce Fischl (
fis...@nmr.mgh.harvard.edu)
> > wrote:
> > >
> > > HI Younghoon
> > >
> > > I guess that could work. You will need to introduce at least one cut
if not
> > > more if you surface has substantial Gaussian curvature
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Wed,
> > > 20 Jul 2016, Younghoon Kim wrote:
> > >
> > > > Hi Bruce,
> > > >
> > > > We are only interested in the surface image of the volumetric data.
> > > >
> > > > For flattening, we do not care about the interior of the volume, so
we
> > > would like
> > > > to remove the volume data inside.
> > > >
> > > > So what we want is to peel off the surface from the segmented brain
area
> > > and
> > > > flatten that surface.
> > > >
> > > > Thanks,
> > > >
> > > > Younghoon Kim
> > > >
> > > > --
> > > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > > OMICS Lab
> > > > Wellman Center, Massachusetts General Hospital
> > > > Bouma’s Lab
> > > > --
> > > > younghoon.h@gmail.com
> > > > aktivh...@kaist.ac.kr
> > > >
> > > > On July 20, 2016 at 5:00:55 PM, Bruce Fischl (
fis...@nmr.mgh.harvard.edu)
> > > wrote:
> > > >
> > > > Hi Younghoon
> > > >
> > > > what structure are you talking about? In general it doesn't make
sense to
> > > > flatten volumetric structures. We flatten the cortex, which is a
folded
> > > > 2D

Re: [Freesurfer] Freesurfer 6.0?

2016-07-26 Thread Trisanna Sprung-Much

thanks, Doug!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve 
wrote:

> We are working pretty hard to get it out but we are still reluctant to set
> a hard date. I think we'll have a beta version in two weeks, but that's
> just a guess.
>
> doug
>
>
>
> On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:
>
>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create better surfaces using
> Freesurfer 6.0 and I am wondering if it really will improve surface
> extraction that much.
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] question about reslicing

2016-07-26 Thread Dorsa Haji Ghaffari

Hi,
Yes my original data has 1x1x1mm voxel dimension but I prefer to work with
the upsampled data. I am satisfied with the results I get from Freesurfer
and the results actually look better than the results I get with the 1mm
data, the only problem I have is that the thalamus mask does not keep the
original dimensions in both cases. It is 256x256x256 ,so in terms of the
thalamus position I do not know if it is at the right place. I will need to
combine the STN that I have traced out in Analyze with the thalamus, thats
why I need to make sure everything are in the correct position with respect
to others.

Thank you

Dorsa

On Tue, Jul 26, 2016 at 1:58 PM, Bruce Fischl 
wrote:

> sorry, I'm confused about what you are trying to do. Can you start from
> the beginning and explain? If the data you have is 1mm but upsampled by the
> scanner there is really nothing to be gained by processing the upsampled
> data and it will waste lots of time
>
>
> cheers
> Bruce
>
> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Yes I created it using the higher resolution and I think it looks fine. I
>> attached the aseg.mgz. Is there any way to create the thalamus mask with
>> the
>> original properties ( same as the original mri) at the first place? I need
>> to make sure the size and position of the thalamus corresponds to the
>> original mri.
>>
>> Thank you!
>>
>> Dorsa
>>
>> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl > >
>> wrote:
>>   Hi Dorsa
>>
>>   did you create the aseg.mgz from 1mm data (using the standard
>>   "conform" process), or higher res? The file you sent is higher:
>>
>>   mri_info resliceduncoregtahalmus.nii.gz
>>   Volume information for resliceduncoregtahalmus.nii.gz
>> type: nii
>>   dimensions: 512 x 512 x 288
>>  voxel sizes: 0.488281, 0.488281, 0.625000
>> type: SHORT (4)
>>  fov: 250.000
>>  dof: 0
>>   xstart: -125.0, xend: 125.0
>>   ystart: -125.0, yend: 125.0
>>   zstart: -90.0, zend: 90.0
>>   TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>   angle: 0.00 degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>  FieldStrength: 0.00
>>   ras xform present
>>
>>
>>   it also has strange values in it (-32K and 32K, so probably
>>   things that can't be represented as a short). Does your aseg.mgz
>>   look right?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>>
>> Hi, This is the command line for reslicing:
>> mri_convert -rl aseg.mgz thalamus.nii
>> resliceduncoregtahalmus.nii
>>
>> thalamus.nii is the thalamus mask obtained by using
>> the following command:
>> mri_binarize --i aseg.mgz --match 10 --o
>> thalamus.mask.nii.gz
>>
>> and I have attached the out put.
>>
>> Thank you!
>>
>> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl
>> 
>> wrote:
>>   Hi Dorsa
>>
>>   you need to give us more details. What was
>> your reslicing
>>   command line? And the screen output?
>>
>>   Bruce
>>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari
>> wrote:
>>
>>
>> Hi,
>>
>> I re-sliced my left thalamus so that the
>> size and
>> number of slices correspond with the
>> original MRI,
>> but when I open it in freeview, it shows
>> an extra
>> part(
>> like a cube) on the bottom of the image
>> ( I have
>> attached the  mask). do you have any
>> idea how to
>> solve that?
>> Also how can I make sure that the
>> position and size
>> of the thalamus makes sense since the
>> thalamus mask
>> has a different slice size and number
>> than the
>> original mri?
>>
>> Thank you
>>
>> Dorsa
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>> 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,

Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

2016-07-26 Thread Harms, Michael








Hi,
Bumping this up for AY.  


We have a bunch of jobs we want to send to our cluster, and we are wondering if we need a revised version of dmri_paths to properly handle single time points in the TRACULA longitudinal stream.


thanks,
-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  63110 
Email: mha...@wustl.edu







From:  on behalf of "Harms, Michael" 
Reply-To: freesurfer 
Date: Wednesday, July 20, 2016 at 11:59 AM
To: freesurfer 
Cc: Dillan Newbold 
Subject: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream









Hi Anastasia,


I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html


It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal TRACULA stream, but Janosch’s last post seemed to indicate that her issue wasn’t resolved even with the new build of dmri_paths
 that you generated.


thanks,
-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  63110 
Email: mha...@wustl.edu






 



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Re: [Freesurfer] question about reslicing

2016-07-26 Thread Bruce Fischl

sorry, I'm confused about what you are trying to do. Can you start from the 
beginning and explain? If the data you have is 1mm but upsampled by 
the scanner there is really nothing to be gained by processing the 
upsampled data and it will waste lots of time


cheers
Bruce

On Mon, 25 Jul 2016, 
Dorsa Haji Ghaffari wrote:



Yes I created it using the higher resolution and I think it looks fine. I
attached the aseg.mgz. Is there any way to create the thalamus mask with the
original properties ( same as the original mri) at the first place? I need
to make sure the size and position of the thalamus corresponds to the
original mri.

Thank you!

Dorsa

On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  did you create the aseg.mgz from 1mm data (using the standard
  "conform" process), or higher res? The file you sent is higher:

  mri_info resliceduncoregtahalmus.nii.gz
  Volume information for resliceduncoregtahalmus.nii.gz
            type: nii
      dimensions: 512 x 512 x 288
     voxel sizes: 0.488281, 0.488281, 0.625000
            type: SHORT (4)
             fov: 250.000
             dof: 0
          xstart: -125.0, xend: 125.0
          ystart: -125.0, yend: 125.0
          zstart: -90.0, zend: 90.0
              TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
  angle: 0.00 degrees
         nframes: 1
         PhEncDir: UNKNOWN
         FieldStrength: 0.00
  ras xform present


  it also has strange values in it (-32K and 32K, so probably
  things that can't be represented as a short). Does your aseg.mgz
  look right?

  cheers
  Bruce


  On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:

Hi, This is the command line for reslicing:
mri_convert -rl aseg.mgz thalamus.nii
resliceduncoregtahalmus.nii

thalamus.nii is the thalamus mask obtained by using
the following command:
mri_binarize --i aseg.mgz --match 10 --o
thalamus.mask.nii.gz

and I have attached the out put.

Thank you!

On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl

wrote:
      Hi Dorsa

      you need to give us more details. What was
your reslicing
      command line? And the screen output?

      Bruce
      On Mon, 25 Jul 2016, Dorsa Haji Ghaffari
wrote:


            Hi,

            I re-sliced my left thalamus so that the
size and
            number of slices correspond with the
original MRI,
            but when I open it in freeview, it shows
an extra
            part(
            like a cube) on the bottom of the image
( I have
            attached the  mask). do you have any
idea how to
            solve that? 
            Also how can I make sure that the
position and size
            of the thalamus makes sense since the
thalamus mask
            has a different slice size and number
than the
            original mri?

            Thank you

            Dorsa



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HelpLine at
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[Freesurfer] TRACULA: 20% default threshold

2016-07-26 Thread Newbold, Dillan

Hi everyone,

I’m having a little trouble understanding the exact meaning of the 20% default 
threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen 
multiple threads where Anastasia said that it is 20% of the maximum value in 
the probability distribution—which corresponds to the maximum number of sample 
paths intersecting a single voxel—but the default thresholds I’ve seen set by 
the -tv option are generally lower than that. For example, I have one subject 
in whom the right CST has a maximum value in its path.pd.nii.gz file of 300. I 
would expect based on what I’ve read in the mail archives that the threshold 
would be set at 60, but when I open the merged file with the -tv option the 
default threshold for the right CST is 35.

My current best guess is that the default threshold is set to produce a volume 
that has a probability sum equal to 20% of the sum of the pre-threshold volume. 
(That is, the sum of intensities of all voxels in the path.pd.nii.gz file 
should be 5 times the sum of the voxels above the default threshold.) Is that 
accurate?

Thanks for all you’ve done to develop this tool. It’s brilliant and I want to 
understand as much of it as I can.

-Dillan

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Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

2016-07-26 Thread miracle ozzoude

Here's my design matrix
1.000   0.000  -0.960   0.000  -0.170   0.000   1.860   0.000   1.970
0.000   2.010   0.000   2.140   0.000;
 1.000   0.000   0.170   0.000   0.290   0.000  -0.560   0.000  -0.400
0.000   0.110   0.000  -0.260   0.000;
 1.000   0.000  -0.050   0.000   0.750   0.000  -0.700   0.000  -0.530
0.000   0.170   0.000  -0.330   0.000;
 1.000   0.000  -1.190   0.000  -1.100   0.000  -0.560   0.000   0.060
0.000   0.250   0.000  -0.050   0.000;
 1.000   0.000  -0.680   0.000  -1.100   0.000   0.080   0.000   0.210
0.000   0.480   0.000   0.310   0.000;
 1.000   0.000  -0.680   0.000   1.210   0.000  -0.180   0.000   0.590
0.000   0.400   0.000   0.320   0.000;
 1.000   0.000  -0.170   0.000   0.290   0.000  -0.470   0.000   0.290
0.000   0.480   0.000   0.160   0.000;
 1.000   0.000  -1.130   0.000  -0.630   0.000  -0.100   0.000   0.880
0.000   0.640   0.000   0.550   0.000;
 1.000   0.000   1.030   0.000   0.290   0.000  -0.180   0.000   0.210
0.000   0.560   0.000   0.260   0.000;
 1.000   0.000  -0.680   0.000   1.210   0.000  -0.470   0.000  -0.100
0.000  -0.290   0.000  -0.310   0.000;
 1.000   0.000   0.340   0.000   0.290   0.000  -0.760   0.000   0.060
0.000   0.910   0.000   0.180   0.000;
 1.000   0.000  -1.080   0.000   0.290   0.000   1.570   0.000   1.970
0.000   1.320   0.000   1.740   0.000;
 1.000   0.000  -1.020   0.000   0.290   0.000   1.340   0.000   0.480
0.000   1.010   0.000   1.030   0.000;
 1.000   0.000  -1.190   0.000  -1.100   0.000   1.460   0.000   1.700
0.000   2.010   0.000   1.920   0.000;
 1.000   0.000  -1.300   0.000  -1.560   0.000  -0.100   0.000   0.140
0.000   0.330   0.000   0.160   0.000;
 1.000   0.000   0.630   0.000   0.290   0.000  -0.270   0.000   1.330
0.000   1.120   0.000   0.860   0.000;
 1.000   0.000   0.230   0.000   0.290   0.000   0.540   0.000   0.690
0.000   0.750   0.000   0.730   0.000;
 1.000   0.000   2.160   0.000  -1.560   0.000  -1.220   0.000   0.210
0.000   0.020   0.000  -0.300   0.000;
 1.000   0.000   0.910   0.000  -1.100   0.000  -1.250   0.000  -1.090
0.000  -0.880   0.000  -1.150   0.000;
 0.000   1.000   0.000   0.570   0.000   1.210   0.000   0.250   0.000
-0.260   0.000  -0.410   0.000  -0.190;
 0.000   1.000   0.000  -1.130   0.000  -0.170   0.000   0.250   0.000
-0.530   0.000  -1.110   0.000  -0.590;
 0.000   1.000   0.000   0.460   0.000   0.290   0.000  -1.740   0.000
-1.830   0.000  -1.630   0.000  -1.890;
 0.000   1.000   0.000  -0.960   0.000   0.290   0.000   1.570   0.000
0.480   0.000   0.170   0.000   0.730;
 0.000   1.000   0.000  -1.300   0.000  -2.020   0.000   1.340   0.000
0.590   0.000   0.110   0.000   0.670;
 0.000   1.000   0.000   0.630   0.000   1.210   0.000  -0.820   0.000
-0.930   0.000  -1.110   0.000  -1.060;
 0.000   1.000   0.000   0.170   0.000   1.210   0.000   0.850   0.000
-0.400   0.000  -0.550   0.000  -0.110;
 0.000   1.000   0.000   1.080   0.000   0.290   0.000  -0.620   0.000
-1.170   0.000  -1.110   0.000  -1.080;
 0.000   1.000   0.000   0.340   0.000   1.670   0.000  -0.620   0.000
-0.660   0.000  -0.880   0.000  -0.810;
 0.000   1.000   0.000   1.370   0.000  -1.100   0.000  -0.330   0.000
-1.300   0.000  -1.400   0.000  -1.160;
 0.000   1.000   0.000   0.510   0.000   0.290   0.000   1.570   0.000
-0.020   0.000  -0.510   0.000   0.260;
 0.000   1.000   0.000   2.160   0.000  -1.560   0.000  -1.830   0.000
-2.470   0.000  -2.140   0.000  -2.360;
 0.000   1.000   0.000   0.740   0.000   1.210   0.000   0.080   0.000
-0.180   0.000  -0.800   0.000  -0.390;

On Tue, Jul 26, 2016 at 12:19 PM, Douglas N Greve  wrote:

> Can you resend the design matrix?
>
> On 07/26/2016 11:46 AM, miracle ozzoude wrote:
> > Hello Doug,
> > Sure. Here are my  new fsgd file and new contrast matrix ( matrix is
> > the same as the old one).
> > Best,
> > Paul
> > GroupDescriptorFile 1
> > Title MOT
> > Class Group1
> > Class Group2
> > Variables Age Education Firstscore Secondscore Thirdscore Averagescore
> > Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14
> > Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26
> > Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33
> > Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05
> > Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31
> > Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32
> > Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16
> > Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55
> > Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21  0.56 0.26
> > Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31
> > Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18
> > Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74
> > Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03
> > Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92
> > Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16
> > Input 1044pp/fsdir Group1 0.63 0.29 -0.27

Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread miracle ozzoude

I added normalizing and demeaning code like you suggested in my fsgd file
and perform the GLM analysis (mri_glmfit). However, my covariates were only
demeaned (DeMeanFlag 1) but they were not normalized (ReScaleFlag 1). Hence
I received this error from freesurfer. I have attached my fsgd files and
contrast matrix
INFO: demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
1 Education 15.5625 1.99902
2 Firstscore 1.03375 0.341785
3 Secondscore 1.03906 0.370678
4 Thirdscore 1.13844 0.4768
5 Averagescore 1.07375 0.364046
Class Means of each Continuous Variable
1 Group1  35.6316  15.0526   1.0342   1.2111   1.4289   1.2305
2 Group2  46.2308  16.3077   1.0331   0.7877   0.7138   0.8446
INFO: gd2mtx_method is dods
Reading source surface
/Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/ctartaglia/Desktop/improvervsdeclinermri
cmdline mri_glmfit --y lh.NeuroTrackerscore.thickness.10B.mgh --fsgd
NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C
new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C
new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C
new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf
fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir
sysname  Darwin
hostname twh-ct-lab4-imac.uhn.ca
machine  x86_64
user ctartaglia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
logyflag 0
usedti  0
FSGD NeuroTrackerscore.fsgd
labelmask
/Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.NeuroTrackerscore.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.NeuroTrackerscore.glmdir
Loading y from
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to lh.NeuroTrackerscore.glmdir/Xg.dat
Normalized matrix condition is 115605
Design matrix --
 1.000   0.000  -0.729   0.000  -0.026   0.000   1.889   0.000   1.535
0.000   1.428   0.000   1.729   0.000;
 1.000   0.000   0.425   0.000   0.474   0.000  -0.568   0.000  -0.866
0.000  -0.501   0.000  -0.716   0.000;
 1.000   0.000   0.194   0.000   0.974   0.000  -0.715   0.000  -1.001
0.000  -0.438   0.000  -0.771   0.000;
 1.000   0.000  -0.960   0.000  -1.027   0.000  -0.568   0.000  -0.408
0.000  -0.354   0.000  -0.496   0.000;
 1.000   0.000  -0.440   0.000  -1.027   0.000   0.075   0.000  -0.246
0.000  -0.124   0.000  -0.139   0.000;
 1.000   0.000  -0.440   0.000   1.474   0.000  -0.188   0.000   0.132
0.000  -0.208   0.000  -0.111   0.000;
 1.000   0.000   0.079   0.000   0.474   0.000  -0.480   0.000  -0.165
0.000  -0.124   0.000  -0.276   0.000;
 1.000   0.000  -0.902   0.000  -0.527   0.000  -0.100   0.000   0.429
0.000   0.044   0.000   0.108   0.000;
 1.000   0.000   1.291   0.000   0.474   0.000  -0.188   0.000  -0.246
0.000  -0.040   0.000   0.108   0.000;
 1.000   0.000  -0.440   0.000   1.474   0.000  -0.480   0.000  -0.569
0.000  -0.900   0.000  -0.743   0.000;
 1.000   0.000   0.598   0.000   0.474   0.000  -0.773   0.000  -0.408
0.000   0.317   0.000  -0.249   0.000;
 1.000   0.000  -0.844   0.000   0.474   0.000   1.597   0.000   1.535
0.000   0.736   0.000   1.317   0.000;
 1.000   0.000  -0.787   0.000   0.474   0.000   1.363   0.000   0.024
0.000   0.422   0.000   0.603   0.000;
 1.000   0.000  -0.960   0.000  -1.027   0.000   1.480   0.000   1.265
0.000   1.428   0.000   1.509   0.000;
 1.000   0.000  -1.075   0.000  -1.527   0.000  -0.100   0.000  -0.327
0.000  -0.270   0.000  -0.276   0.000;
 1.000   0.000   0.887   0.000   0.474   0.000  -0.276   0.000   0.887
0.000   0.527   0.000   0.438   0.000;
 1.000   0.000   0.483   0.000   0.474   0.000   0.544   0.000   0.240
0.000   0.149   0.000   0.301   0.000;
 1.000   0.000   2.445   0.000  -1.527   0.000  -1.241   0.000  -0.246
0.000  -0.585   0.000  -0.743   0.000;
 1.000   0.000   1.175   0.000  -1.027   0.000  -1.270   0.000  -1.568
0.000  -1.508   0.000  -1.595   0.000;
 0.000   1.000   0.000   0.217   0.000   0.847   0.000   0.254   0.000
0.411   0.000   0.474   0.000   0.427;
 0.000   1.000   0.000  -1.513   0.000  -0.654   0.000   0.254   0.000
0.141   0.000  -0.239   0.000   0.015;
 0.000   1.000   0.000   0.102   0.000  -0.154   0.000  -1.764   0.000
-1.181   0.000  -0.763   0.000  -1.276;
 0.000   1.000   0.000  -1.340   0.000  -0.154   0.000   1.600   0.000
1.166   0.000   1.062   0.000   1.361;
 0.000   1.000   0.000  -1.687   0.000   0.346   0.000   1.366   0.000
1.274   0.000   0.999   0.000   1.306;
 0.000   1.000   0.000   0.275   0.000   0.847

Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread Douglas N Greve

what do you mean it did not work? can you be more specific?


On 07/26/2016 12:21 PM, miracle ozzoude wrote:
> Hello Doug,
> The ReScaleFlag 1 command did not work. Only the demean command.
> Paul
>
>
> On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve 
> > wrote:
>
> Actually, I checked the code and found that I had already put a
> flag in there to do this (I'm so clever). Add
>
> ReScaleFlag 1
>
> in addition to
>
> DeMeanFlag 1
>
>
>
>
> On 7/25/16 11:22 AM, Douglas Greve wrote:
>>
>> No, that flag does not exist, but it is a good idea! You'll have
>> to normalize them by hand.
>>
>>
>> On 7/24/16 1:33 PM, miracle ozzoude wrote:
>>> Hello freesurfer experts,
>>> I am trying to normalize my continuous variables in my fsgd
>>> file. Is this the correct term to add to my fsgd file in order
>>> for mri_glmfit to normalize it?
>>>
>>> GroupDescriptorFile 1
>>> Title PCS
>>> Class group1
>>> Class group2
>>> Normalize 1
>>> Variables Age Education Scoreone Scoretwo
>>> Input 053 group1 47 18 3.4 5.6
>>> Input 054 group2 50 16 5.3 2.8
>>>
>>> Thank you,
>>> Paul
>>>
>>>
>>> ___
>>> 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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gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] question about reslicing

2016-07-26 Thread Douglas N Greve

Does this wiki page help?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 07/25/2016 04:22 PM, Dorsa Haji Ghaffari wrote:
> Yes I created it using the higher resolution and I think it looks 
> fine. I attached the aseg.mgz. Is there any way to create the thalamus 
> mask with the original properties ( same as the original mri) at the 
> first place? I need to make sure the size and position of the thalamus 
> corresponds to the original mri.
>
> Thank you!
>
> Dorsa
>
> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl 
> > wrote:
>
> Hi Dorsa
>
> did you create the aseg.mgz from 1mm data (using the standard
> "conform" process), or higher res? The file you sent is higher:
>
> mri_info resliceduncoregtahalmus.nii.gz
> Volume information for resliceduncoregtahalmus.nii.gz
>   type: nii
> dimensions: 512 x 512 x 288
>voxel sizes: 0.488281, 0.488281, 0.625000
>   type: SHORT (4)
>fov: 250.000
>dof: 0
> xstart: -125.0, xend: 125.0
> ystart: -125.0, yend: 125.0
> zstart: -90.0, zend: 90.0
> TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
>
>
> it also has strange values in it (-32K and 32K, so probably things
> that can't be represented as a short). Does your aseg.mgz look right?
>
> cheers
>
> Bruce
>
>
> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Hi, This is the command line for reslicing:
> mri_convert -rl aseg.mgz thalamus.nii resliceduncoregtahalmus.nii
>
> thalamus.nii is the thalamus mask obtained by using the
> following command:
> mri_binarize --i aseg.mgz --match 10 --o thalamus.mask.nii.gz
>
> and I have attached the out put.
>
> Thank you!
>
> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl
> >
> wrote:
>   Hi Dorsa
>
>   you need to give us more details. What was your reslicing
>   command line? And the screen output?
>
>   Bruce
>   On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
>
>
> Hi,
>
> I re-sliced my left thalamus so that the size and
> number of slices correspond with the original MRI,
> but when I open it in freeview, it shows an extra
> part(
> like a cube) on the bottom of the image ( I have
> attached the  mask). do you have any idea how to
> solve that?
> Also how can I make sure that the position and size
> of the thalamus makes sense since the thalamus mask
> has a different slice size and number than the
> original mri?
>
> Thank you
>
> Dorsa
>
>
>
> ___
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> 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.
>
>
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Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread miracle ozzoude

Hello Doug,
The ReScaleFlag 1 command did not work. Only the demean command.
Paul


On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve 
wrote:

> Actually, I checked the code and found that I had already put a flag in
> there to do this (I'm so clever). Add
>
> ReScaleFlag 1
>
> in addition to
>
> DeMeanFlag 1
>
>
>
>
> On 7/25/16 11:22 AM, Douglas Greve wrote:
>
> No, that flag does not exist, but it is a good idea! You'll have to
> normalize them by hand.
>
> On 7/24/16 1:33 PM, miracle ozzoude wrote:
>
> Hello freesurfer experts,
> I am trying to normalize my continuous variables in my fsgd file. Is this
> the correct term to add to my fsgd file in order for mri_glmfit to
> normalize it?
>
> GroupDescriptorFile 1
> Title PCS
> Class group1
> Class group2
> Normalize 1
> Variables Age Education Scoreone Scoretwo
> Input 053 group1 47 18 3.4 5.6
> Input 054 group2 50 16 5.3 2.8
>
> Thank you,
> Paul
>
>
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Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

2016-07-26 Thread Douglas N Greve

Can you resend the design matrix?

On 07/26/2016 11:46 AM, miracle ozzoude wrote:
> Hello Doug,
> Sure. Here are my  new fsgd file and new contrast matrix ( matrix is 
> the same as the old one).
> Best,
> Paul
> GroupDescriptorFile 1
> Title MOT
> Class Group1
> Class Group2
> Variables Age Education Firstscore Secondscore Thirdscore Averagescore
> Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14
> Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26
> Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33
> Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05
> Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31
> Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32
> Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16
> Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55
> Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21  0.56 0.26
> Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31
> Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18
> Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74
> Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03
> Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92
> Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16
> Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86
> Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73
> Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30
> Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15
> Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19
> Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59
> Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89
> Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73
> Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67
> Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06
> Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11
> Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08
> Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81
> Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16
> Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26
> Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36
> Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39
>
> New Contrast Matrix
>
> first contrast matrix
>
> 1 -1 0 0 0 0 0 0 0 0 0 0 0 0
>
> group1 greater than group 2 regressing out age, education, first, 
> second, third and average
>
> second constrast matrix
>
> -1 1 0 0 0 0 0 0 0 0 0 0 0 0
>
> group 2 greater than group 1 regressing out age, education, first, 
> second, third and average
>
> third contrast matrix
>
> 0 0 0 0 0 0 0.5 -0.5 0 0 0 0 0 0
>
> group 1 showing increasing correlation with first score compared to 
> group 2
>
> fourth contrast matrix
>
> 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 0 0
>
> group2 showing showing increasing correlation with first score 
> compared to group 1
>
> fifth contrast matrix
>
> 0 0 0 0 0 0 0 0 0.5 -0.5 0 0 0 0
>
> group1 showing showing increasing correlation with second score 
> compared to group 2
>
> sixth contrast matrix
>
> 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0
>
> group2 showing showing increasing correlation with second score 
> compared to group 1
>
> seventh contrast matrix
>
> 0 0 0 0 0 0 0 0 0 0 0.5 -0.5 0 0
>
> group1 showing showing increasing correlation with third score 
> compared to group 2
>
> eighth contrast matrix
>
> 0 0 0 0 0 0 0 0 0 0 -0.5 0.5 0 0
>
> group2 showing showing increasing correlation with third score 
> compared to group 1
>
> ninety contrast matrix
>
> 0 0 0 0 0 0 0 0 0 0 0 0 0.5 -0.5
>
> group1 showing showing increasing correlation with average score 
> compared to group 2
>
> tenth contrast matrix
>
> 0 0 0 0 0 0 0 0 0 0 0 0 -0.5 0.5
>
> group2 showing showing increasing correlation with average score 
> compared to group 1
>
>
>
>
> On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve 
> > wrote:
>
> Can you send your new fsgd file and new design matrix?
>
>
> On 7/24/16 6:06 PM, miracle ozzoude wrote:
>> Hello Doug or Bruce,
>> I demeaned and normalize like you suggested but I'm still getting
>> the same results. I created a new fsgd file using the demeaned
>> and normalized variables (n = (x-mean)/std(x). Any reason why?
>> Thank you very much.
>> Paul
>>
>> On Fri, Jul 22, 2016 at 6:43 PM, Douglas N Greve
>> > wrote:
>>
>> Try demeaning and normalizing your continuous covariates in
>> the FSGD file.
>>
>> On 07/22/2016 06:17 PM, miracle ozzoude wrote:
>> >
>> > Hello doug,
>> >
>> > while running the mir_glmfit problem, i encountered this
>> problem “
>> >
>> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> >
>> > Continuous Variable Means (all subjects)
>>

Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates

2016-07-26 Thread miracle ozzoude

Hello Doug,
Sure. Here are my  new fsgd file and new contrast matrix ( matrix is the
same as the old one).
Best,
Paul
GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age Education Firstscore Secondscore Thirdscore Averagescore
Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14
Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26
Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33
Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05
Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31
Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32
Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16
Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55
Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21  0.56 0.26
Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31
Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18
Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74
Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03
Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92
Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16
Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86
Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73
Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30
Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15
Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19
Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59
Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89
Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73
Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67
Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06
Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11
Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08
Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81
Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16
Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26
Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36
Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39

New Contrast Matrix

first contrast matrix

1 -1 0 0 0 0 0 0 0 0 0 0 0 0

group1 greater than group 2 regressing out age, education, first, second,
third and average

second constrast matrix

-1 1 0 0 0 0 0 0 0 0 0 0 0 0

group 2 greater than group 1 regressing out age, education, first, second,
third and average

third contrast matrix

0 0 0 0 0 0 0.5 -0.5 0 0 0 0 0 0

group 1 showing increasing correlation with first score compared to group 2

fourth contrast matrix

0 0 0 0 0 0 -0.5 0.5 0 0 0 0 0 0

group2 showing showing increasing correlation with first score compared to
group 1

fifth contrast matrix

0 0 0 0 0 0 0 0 0.5 -0.5 0 0 0 0

group1 showing showing increasing correlation with second score compared to
group 2

sixth contrast matrix

0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0

group2 showing showing increasing correlation with second score compared to
group 1

seventh contrast matrix

0 0 0 0 0 0 0 0 0 0 0.5 -0.5 0 0

group1 showing showing increasing correlation with third score compared to
group 2

eighth contrast matrix

0 0 0 0 0 0 0 0 0 0 -0.5 0.5 0 0

group2 showing showing increasing correlation with third score compared to
group 1

ninety contrast matrix

0 0 0 0 0 0 0 0 0 0 0 0 0.5 -0.5

group1 showing showing increasing correlation with average score compared
to group 2

tenth contrast matrix

0 0 0 0 0 0 0 0 0 0 0 0 -0.5 0.5

group2 showing showing increasing correlation with average score compared
to group 1



On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve 
wrote:

> Can you send your new fsgd file and new design matrix?
>
> On 7/24/16 6:06 PM, miracle ozzoude wrote:
>
> Hello Doug or Bruce,
> I demeaned and normalize like you suggested but I'm still getting the same
> results. I created a new fsgd file using the demeaned and normalized
> variables (n = (x-mean)/std(x). Any reason why? Thank you very much.
> Paul
>
> On Fri, Jul 22, 2016 at 6:43 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Try demeaning and normalizing your continuous covariates in the FSGD file.
>>
>> On 07/22/2016 06:17 PM, miracle ozzoude wrote:
>> >
>> > Hello doug,
>> >
>> > while running the mir_glmfit problem, i encountered this problem “
>> >
>> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> >
>> > Continuous Variable Means (all subjects)
>> >
>> > 0 Age 39.9375 17.3312
>> >
>> > 1 Education 15.5625 1.99902
>> >
>> > 2 Firstscore 1.03375 0.341785
>> >
>> > 3 Secondscore 1.03906 0.370678
>> >
>> > 4 Thirdscore 1.13844 0.4768
>> >
>> > 5 Averagescore 1.07375 0.364046
>> >
>> > Class Means of each Continuous Variable
>> >
>> > 1 Group1  35.6316  15.0526   1.0342 1.2111   1.4289   1.2305
>> >
>> > 2 Group2  46.2308  16.3077   1.0331 0.7877   0.7138   0.8446
>> >
>> > INFO: gd2mtx_method is dods
>> >
>> > Reading source surface
>> >

Re: [Freesurfer] GLM significance table

2016-07-26 Thread Douglas Greve

The -log10(p) is signed by the sign of the contrast, so to get back to 
the p value you must compute 10^-abs(sig).



On 7/26/16 10:42 AM, Caroline Beelen wrote:


Dear FS team,

I tried to run GLM-analysis using aparc stats files. At first I 
created these files for a few subjects of interest (e.g. 
aparc_rh_thickness_stats.txt) and checked whether they looked ok, 
which they did (values were pretty similar). Then I used the following 
command (for example):


Mri_glmfit

-- table aparc_rh_thickness_stats.txt

-- fsgd gender_dys.fsgd (see attached; example of a fsgd-file)

-- C Int.mtx

-- C Dys.mtx

-- C Gender.mtx

-- glmdir roi.gender_dyslect.rh.thickness.glmdir

The file was created and it contained a sig.table.dat folder. However, 
the values in this folder are all quite low. According to information 
found on your website they should correspond to (-)log10(p) values. I 
found mainly values between -1 and 1, but even of -0.03, which would 
correspond to a p-value of 1.5 (non-existing). Could you please 
explain to me what I did wrong?


Thank you very much!

Kind regards,

Caroline



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[Freesurfer] GLM significance table

2016-07-26 Thread Caroline Beelen

Dear FS team,

I tried to run GLM-analysis using aparc stats files. At first I created these 
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and 
checked whether they looked ok, which they did (values were pretty similar). 
Then I used the following command (for example):

Mri_glmfit
-- table aparc_rh_thickness_stats.txt
-- fsgd gender_dys.fsgd (see attached; example of a fsgd-file)
-- C Int.mtx
-- C Dys.mtx
-- C Gender.mtx
-- glmdir roi.gender_dyslect.rh.thickness.glmdir

The file was created and it contained a sig.table.dat folder. However, the 
values in this folder are all quite low. According to information found on your 
website they should correspond to (-)log10(p) values. I found mainly values 
between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 
(non-existing). Could you please explain to me what I did wrong?

Thank you very much!

Kind regards,
Caroline



gender_dys.fsgd.docx
Description: gender_dys.fsgd.docx
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[Freesurfer] GLM significance table

2016-07-26 Thread Caroline Beelen

Dear FS team,

I tried to run GLM-analysis using aparc stats files. At first I created these 
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and 
checked whether they looked ok, which they did (values were pretty similar). 
Then I used the following command (for example):

Mri_glmfit
-- table aparc_rh_thickness_stats.txt
-- fsgd gender_dys.fsgd (see attached; example of a fsgd-file)
-- C Int.mtx
-- C Dys.mtx
-- C Gender.mtx
-- glmdir roi.gender_dyslect.rh.thickness.glmdir

The file was created and it contained a sig.table.dat folder. However, the 
values in this folder are all quite low. According to information found on your 
website they should correspond to (-)log10(p) values. I found mainly values 
between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 
(non-existing). Could you please explain to me what I did wrong?

Thank you very much!

Kind regards,
Caroline



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Re: [Freesurfer] How to apply ACPC alignment to Freesurfer output

2016-07-26 Thread Sandra Hanekamp

Dear Douglas,

Thank you for your input. Additional background information to answer your 
question (why not register the anatomical to the DTI):

Freesurfer segmentation was done in a previous project and used the native 
space T1 scans. For this DTI project, I would like to use the Freesurfer 
segmentation so I can do (amongst other analyses) ROI to ROI tracking. To be 
able to use this previously segmented data, I used the native space anatomical 
scans and registered them successfully to the DTI scans and continued my 
analysis. Although it seems to work initially (they overlap and I can 
successfully do tracking with mrtrix), it gives dimension mismatch errors later 
in my pipeline. My pipeline assumes that my data is in MNI space and assumes a 
specific size for the bounding box of the scans. The anatomical native scans do 
not fit this criteria and my code crashes later in my pipeline. I have not been 
able to work around this issue. 

I would like to register a MNI T1 scan and register this to my DTI data, and 
have the freesurfer output in the same space. Do I understand correctly that I 
could extract a registration matrix from a realigned MNI T1 scan and then apply 
this to a segmentation with mri_label2vol?

Thank you for your time and effort.

Sandra

> On 25 Jul 2016, at 17:11, Douglas Greve  wrote:
> 
> If you have a registration matrix that maps to the desired orientation, then 
> you can apply it to a segmentation with mri_label2vol. But why not just 
> register the anatomical to the DTI (bbregister) and then run mri_label2vol 
> with that registration to map the WM mask directly into the native DTI space?
> 
> On 7/25/16 7:56 AM, Sandra Hanekamp wrote:
>> Dear Freesurfer community,
>> 
>> I would like to apply ACPC alignment to Freesurfer output. 
>> 
>> Data was previously segmented with recon -all and a lot of manual editing 
>> using ITK. Unfortunately, the data was not aligned to ACPC and this causes 
>> errors in my pipeline (I am using the labels and white matter mask from 
>> Freesurfer for my DTI analysis). 
>> 
>> Re-doing the segmentation plus necessary edits would be very time-consuming 
>> due to a poor contrast between white and grey matter and the number of scans 
>> that I have, so I would prefer to align the current output to ACPC. Does 
>> anyone know a solution that does not involve re-doing the segmentation? How 
>> can I apply ACPC alignment to Freesurfer output?
>> 
>> Thank you so much for any thoughts or recommendations you might be able to 
>> provide. 
>> 
>> Sandra Hanekamp
>> Laboratory for Experimental Ophthalmology
>> University Medical Center Groningen
>> 
>> 
>> 
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Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-26 Thread Falk Lüsebrink

Hi Bruce,

thanks. Keep up the fantastic work!

Best,
Falk

-Ursprüngliche Nachricht-
Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Gesendet: Donnerstag, 21. Juli 2016 16:44
An: Falk Lüsebrink
Cc: Freesurfer support list
Betreff: Re: AW: AW: AW: [Freesurfer] mri_ca_label with high resolution data

Hi Falk

yes, it's an active area of devlopment for us cheers Bruce

On Thu, 21 Jul 2016, Falk
Lüsebrink wrote:

> Hi Bruce,
>
> I thought so. Are there any other means to accelerate this procedure (in the 
> future)?
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Gesendet: Donnerstag, 21. Juli 2016 15:52
> An: Falk Lüsebrink
> Cc: Freesurfer support list
> Betreff: Re: AW: AW: [Freesurfer] mri_ca_label with high resolution 
> data
>
> Hi Falk
>
> not every part of it is accelerated, but some are
>
> cheers
> Bruce
>
>
> On Thu, 21 Jul 2016, Falk Lüsebrink wrote:
>
>> Hi Bruce,
>>
>> I'm using the current dev build:
>>
>> ProgramName: mri_ca_label  ProgramArguments: --all-info
>> ProgramVersion: $Name:  $  TimeStamp: 2016/07/21-13:42:39-GMT
>> BuildTimeStamp: Jul 12 2016 13:31:56  CVS: $Id: mri_ca_label.c,v 
>> 1.113
>> 2016/05/13 18:02:49 fischl Exp $  User: luesebrink  Machine: reco
>> Platform: Linux  PlatformVersion: 3.16.0-4-amd64  CompilerName: GCC
>> CompilerVersion: 40400
>>
>> and in the log it says to use 12 threads
>>
>> == Number of threads available to mri_ca_label for OpenMP = 12 ==
>>
>> however, at least while saving the intensity scale
>>
>> saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
>> saving sequentially combined intensity scales to 
>> aseg.auto_noCCseg.label_intensities.txt
>>
>> it doesn't seem to help.
>>
>> Best,
>> Falk
>>
>> 
>> Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Gesendet: Donnerstag, 21. Juli 2016 15:30
>> An: Falk Lüsebrink
>> Cc: Freesurfer support list
>> Betreff: Re: AW: [Freesurfer] mri_ca_label with high resolution data
>>
>> Hi Falk
>>
>> the dev version of mri_ca_label does use openmp, so should be faster.
>>
>> cheers
>> Bruce
>> On
>> Thu, 21 Jul 2016, Falk Lüsebrink wrote:
>>
>>> Hi Bruce,
>>>
>>> I started the process again with openmp set to 12 using the dev build from 
>>> 12th July. However, mri_ca_label uses only 1 thread at that point. So I 
>>> don't assume any faster processing.
>>>
>>> Best,
>>> Falk
>>>
>>>
>>> -Ursprüngliche Nachricht-
>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce 
>>> Fischl
>>> Gesendet: Dienstag, 19. Juli 2016 15:37
>>> An: Freesurfer support list
>>> Betreff: Re: [Freesurfer] mri_ca_label with high resolution data
>>>
>>> Hi Falk
>>>
>>> I think openmp will help with this in V6, but probably not before 
>>> Bruce
>>>
>>> On Tue, 19
>>> Jul 2016, Falk Lüsebrink wrote:
>>>

 Hi all,



 I'm currently processing a 250 µm MPRAGE with a dev build from mid of May.
 Running recon-all with default parameters ran flawlessly. 
 Afterwards I added the -hires flag to process the data without 
 conformation.
 However, since Saturday morning it is kind of stuck at mri_ca_label 
 stating:



 saving sequentially combined intensity scales to 
 aseg.auto_noCCseg.label_intensities.txt



 while  consuming around 30 GB of memory. I ran something similar 
 before and processing works, it's just terribly slow. Maybe this 
 particular stage is just not very efficient as it does take a few minutes 
 on 1 mm data only?
 Would it help to add the openmp flag in that case?



 Best,

 Falk



 

 Falk Lüsebrink, M. Sc.



 Otto-von-Guericke-Universität Magdeburg

 Forschungscampus STIMULATE

 http://www.forschungscampus-stimulate.de/



 Universitätsplatz 2

 39106 Magdeburg



 Raum:ExFa - 4.06

 Telefon: 0391-67-19366

 Fax:   0391-67-19347





>>>
>>>
>>>
>>
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Re: [Freesurfer] Hippocampal subfields total volume differences

2016-07-26 Thread Mojmír Vinkler

Wow, longitudinal segmentation is absolutely awesome! It reduced our
measurement error by more than 30%. I can't wait when the hippocampal
longitudinal segmentation is ready.

By the way, I want to run (cross-sectional) hippocampal subfields on
longitudinal data using additional T2 with lower resolution and I was
wondering if I should use multispectral segmentation

recon-all -s  -hippocampal-subfields-T1T2  

or just additional scan

recon-all -s  -hippocampal-subfields-T2   

Since my T1 and T2 scans are quite well aligned, I wanted to use
-hippocampal-subfields-T2,
but I saw you recommending T1T2 in mailing list. Thanks!

(I'm also blocked by a bug with .ctf files
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html,
but I'm fine with waiting for fix)

Thanks!
Mojmir

On Fri, Jul 15, 2016 at 12:33 PM Iglesias, Eugenio 
wrote:

> Dear Mojmir,
> using ~400 subjects, we found that the subfield module was a bit better
> than the ASEG volumes at discriminating Alzheimer’s patients from controls
> (see the Neuorimage paper). But, in any case, the difference is small.
> Regarding longitudinal segmentation: we just got a paper about this
> accepted, see
>
> http://www.nmr.mgh.harvard.edu/~iglesias/pdf/Neuroimage_2016_longitudinal.pdf
> I still need to find time to clean up the code and put it up on
> FreeSurfer. For the time being, you can run the subfield module on the
> longitudinally analyzed recons (method “L-INIT” in the paper).
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 15 Jul 2016, at 09:00, Mojmír Vinkler  wrote:
>
> Hi Juan,
>
> Thanks! You're right, they really are tightly correlated (although their
> absolute values differ by 30%). We tried it on couple of subjects, but
> didn't find subfields to be significantly better than aseg stats though. By
> the way, is Freesurfer capable of using multiple scans from the same
> subject (longitudinal study, same modality) to make more precise
> measurements? For example by using T1 from the same subject / different
> time instead of T2 in subfields?
>
> Thanks!
> Mojmir
>
> On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio 
> wrote:
>
>> Hi Mojmir,
>> ASEG typically gives a larger estimate of the volume, though highly
>> correlated with that from the subfield package. We have found the
>> measurements from the subfield package to be a bit more reliable, though.
>> Cheers,
>> Eugenio
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 13 Jul 2016, at 16:07, Mojmír Vinkler 
>> wrote:
>>
>> Hi experts,
>>
>> I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal
>> subfields segmentation. I only need to measure total hippocampus volume,
>> but measurements from basic `recon-all` were too volatile and I was hoping
>> that using subfields with T2 modality would reduce variance. However,
>> volume measured by hippocampal subfields is significantly different from
>> volume in aseg.stats.
>>
>> Here are volumes for right hippocampus from various methods:
>> aseg.stats - 3312.8
>> rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
>> rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) -
>> 2503.97
>> rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation)
>> - 2596.09
>>
>> I checked labeling visually and there were no obvious problems. Is such
>> a large difference common? Am I missing something? What number should be
>> most trusted?
>>
>> Thanks for any hints!
>> Mojmir
>>
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>> The information in this e-mail is intended only for the person to whom it
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>> contains patient information, please contact the Partners Compliance
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>> 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
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>> in error
>> but does not contain patient information, please

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