date:20160219

Re: [Freesurfer] Entorhinal thickness

2016-02-19 Thread Mohamed Ali Bahri

Thank you very much for your kind answer.

Mohamed

On 18/02/16 23:22, Bruce Fischl wrote:
> The ex vivo is probably more accurate since it was created by directly 
> visualizing the relevant cytoarchitectur
>
>> On Feb 18, 2016, at 5:17 PM, Douglas N Greve  
>> wrote:
>>
>> One (aparc) is derived from manual labels registered into the subject
>> space. The other is derived from an exvivo label.
>>
>>> On 02/18/2016 10:23 AM, Mohamed Ali Bahri wrote:
>>> Dear Freesurfer,
>>>
>>> The entorhinal has different volume and thickness in the
>>> "?h_aparc.stats" & "?h.entorhinal_exvivo.stats" files.
>>> Could any one explain way and which one should be used?
>>>
>>> Many thanks in advance,
>>>
>>> Best regards,
>>>
>>> Mohamed
>> -- 
>> 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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>>
>>
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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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-- 
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Liège, Belgium
m.ba...@ulg.ac.be

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[Freesurfer] R: Re: FS-FAST using MRS voxel or .label as seed

2016-02-19 Thread stdp82

I have also run as followed but the error persist.

mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz  
$SUBJECTS_DIR/Subj2/mri/MRS_MASK2.mgz

mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz  MRS_MASK2.mgz

fcseed-config -segid 1 -seg MRS_MASK2.mgz -fsd rest -mean -cfg MRS_MASK2.
config -overwrite

fcseed-sess -s Subj2 -cfg MRS_MASK2.config -overwrite



>Messaggio originale
>Da: Douglas N Greve 
>Data: 19-feb-2016 0.25
>A: 
>Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed
>
>
>I think it may be our fcseed-config command line
>fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd 
>rest -mean -cfg MRS_MASK.config –overwrite
>
>It should be -seg MRS_MASK.mgz
>
>They way you have it, fcseed will use the segmentation for Subj for all 
>subjects, which is why it works for one and not for others
>
>
>On 02/18/2016 06:10 PM, std...@virgilio.it wrote:
>>
>> Hi list,
>>
>> I'm having problem to use FS-FAST fMRI connectivity using as seed a 
>> mask of a MRS voxel or .label obtained by drawing it from surface. In 
>> order to resolve my concern, I'm reporting step by step the command 
>> lines which I have used. The mask, f.nii.gz, orig.nii.gz and 
>> aparc+aseg.nii.gz showed a good overlap.
>>
>> These are the features of each one:
>>
>> fslinfo orig.nii.gz
>>
>> data_type UINT8
>>
>> dim1 256
>>
>> dim2 256
>>
>> dim3 256
>>
>> dim4 1
>>
>> datatype 2
>>
>> pixdim1 1.00
>>
>> pixdim2 1.00
>>
>> pixdim3 1.00
>>
>> pixdim4 0.010747
>>
>> cal_max   0.
>>
>> cal_min 0.
>>
>> file_type NIFTI-1+
>>
>> fslinfo aparc+aseg.nii.gz
>>
>> data_type INT32
>>
>> dim1 256
>>
>> dim2 256
>>
>> dim3 256
>>
>> dim4 1
>>
>> datatype 8
>>
>> pixdim1 1.00
>>
>> pixdim2 1.00
>>
>> pixdim3 1.00
>>
>> pixdim4 0.010747
>>
>> cal_max 0.
>>
>> cal_min 0.
>>
>> file_type NIFTI-1+
>>
>> fslinfo MRS_MASK.nii.gz
>>
>> data_type FLOAT32
>>
>> dim1 256
>>
>> dim2 256
>>
>> dim3 256
>>
>> dim4 1
>>
>> datatype 16
>>
>> pixdim1 1.00
>>
>> pixdim2 1.00
>>
>> pixdim3 1.00
>>
>> pixdim4 0.00
>>
>> cal_max 0.
>>
>> cal_min 0.
>>
>> file_type NIFTI-1+
>>
>> I’m using MNI2mm for subcortical analysis.
>>
>> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz 
>> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz
>>
>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd 
>> rest -mean -cfg MRS_MASK.config –overwrite
>>
>> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite
>>
>> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh 
>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg 
>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run 
>> -overwrite
>>
>> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh 
>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg 
>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run 
>> -overwrite
>>
>> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask 
>> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 
>> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite
>>
>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh
>>
>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh
>>
>> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305
>>
>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast 
>> MRS_MASK -o my-group
>>
>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast 
>> MRS_MASK -o my-group
>>
>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast 
>> MRS_MASK -o my-group
>>
>> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, 
>> it seem to be functioning for the first subj, but the next subj2 show 
>> this error
>>
>> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz
>>
>> Voxel Volume is 64.5752 mm^3
>>
>> Generating list of segmentation ids
>>
>> Found   1 segmentations
>>
>> Computing statistics for each segmentation
>>
>>   0 1 0   0.000
>>
>> MRIalloc(0, 1, 1): bad parm
>>
>> Reporting on 0 segmentations
>>
>> Computing spatial average of each frame
>>
>> Writing to 
>> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess.
28328/avgwf.mgh
>>
>> Segmentation fault
>>
>>
>>
>> ___
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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] Building from source -- autoconf error

2016-02-19 Thread Yaroslav Halchenko


On Thu, 18 Feb 2016, Z K wrote:
> > is there a public clone of freesurfer on github?

> Sorry, their is no public freesurfer on github. But at the current 
> moment (and forseeable future) the public repo is an exact mirro of the 
> private repo.


> > --disable-GUI-build  -- wouldn't it disable then building all so necessary 
> > GUI
> > tools?  is there  a way to overcome the shortcoming?


> I was never able to get the GUI tools to build on Ubuntu. It is 
> something I may revisit in the near future, but as of now, in order to 
> build on an Ubuntu platform you will need to disable GUI building.

just confirming that I have managed to build it under 14.04 -- hip hip
hoorray! ;)  next one will be to try with GUI ;)

the only concern is that currently some subdirs makefiles do not care about
DESTDIR, which is generally respected by autotools... attached patch should
help (if only there was a public github... ;)) to make it 'installable' e.g. via

make install DESTDIR=$PWD/INSTALL-DIR/

it would be a nice "test" to add to .travis.yml upon successful build, without
system wide installation with sudo ;)

> We simply dont have the resources to ensure build capability on all 
> linux (and mac) based OSes. For now simply we make the claim that 
> freesurfer will build on centos, and will run on nearly all the major 
> linux distros.

Fair enough.  but may be together we could push it forward step by step
;)

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
From 1983364a101d9543f6d80c45b968aa194e023288 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko 
Date: Fri, 19 Feb 2016 05:06:24 +
Subject: [PATCH] BF: adjusted use of $(DESTDIR) so installs fine under DESTDIR

---
 BrainstemSS/Makefile.am | 4 ++--
 BrainstemSS/linux_x86_64/Makefile.am| 4 ++--
 GEMS/data/Makefile.am   | 4 ++--
 HippoSF/Makefile.am | 4 ++--
 HippoSF/linux_x86_64/Makefile.am| 4 ++--
 distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile.am | 4 ++--
 distribution/average/Choi_JNeurophysiol12_MNI152/Makefile.am| 4 ++--
 distribution/average/Makefile.am| 4 ++--
 distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile.am | 4 ++--
 distribution/average/surf/Makefile.am   | 4 ++--
 distribution/fsafd/Makefile.am  | 4 ++--
 distribution/fsl-extra/Makefile.am  | 2 +-
 distribution/lib/bem/Makefile.am| 4 ++--
 distribution/subjects/Makefile.am   | 4 ++--
 fsfast/docs/Makefile.am | 4 ++--
 images/Makefile.am  | 4 ++--
 matlab/Makefile.am  | 8 
 mri_cvs_register/Makefile.am| 2 +-
 qdec/Makefile.am| 8 
 talairach_avi/Makefile.am   | 4 ++--
 20 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/BrainstemSS/Makefile.am b/BrainstemSS/Makefile.am
index d0d505e..3bcf40e 100644
--- a/BrainstemSS/Makefile.am
+++ b/BrainstemSS/Makefile.am
@@ -21,8 +21,8 @@ segmentBS.sh \
 quantifyBrainstemStructures.sh
 
 install-data-local:
-	test -z $(foodir) || $(mkdir_p) $(foodir)
-	$(INSTALL_DATA) $(foo_datafiles) $(foodir)
+	test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir)
+	$(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir)
 
 # Our release target. Include files to be excluded here. They will be
 # found and removed after 'make install' is run during the 'make
diff --git a/BrainstemSS/linux_x86_64/Makefile.am b/BrainstemSS/linux_x86_64/Makefile.am
index 3543581..0f47fd7 100644
--- a/BrainstemSS/linux_x86_64/Makefile.am
+++ b/BrainstemSS/linux_x86_64/Makefile.am
@@ -17,8 +17,8 @@ foo_binaryfiles = \
 	SegmentSubject.bin
 
 install-data-local:
-	test -z $(foodir) || $(mkdir_p) $(foodir)
-	$(INSTALL) -m 755 $(foo_binaryfiles) $(foodir)
+	test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir)
+	$(INSTALL) -m 755 $(foo_binaryfiles) $(DESTDIR)$(foodir)
 
 # Our release target. Include files to be excluded here. They will be
 # found and removed after 'make install' is run during the 'make
diff --git a/GEMS/data/Makefile.am b/GEMS/data/Makefile.am
index 97a7eb1..cf29198 100644
--- a/GEMS/data/Makefile.am
+++ b/GEMS/data/Makefile.am
@@ -15,8 +15,8 @@ kvlQuantifyHippocampalSubfieldSegmentations.sh.help.xml \
 kvlSegmentHippocampalSubfields.sh.help.xml
 
 install-data-local:
-	test -z $(

[Freesurfer] comparison between two hemisphere in single

2016-02-19 Thread Ashkan Faghiri

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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Re: [Freesurfer] comparison between two hemisphere in single

2016-02-19 Thread Douglas Greve

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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Re: [Freesurfer] Paired t-test for correlation analysis on two time points

2016-02-19 Thread Douglas Greve

I think so. Just make sure you don't try to draw conclusions from the 
ROI or area around it.


On 2/19/16 2:02 AM, amirhossein manzouri wrote:
Yes, I extracted the mean thickness of the ROI label from each 
timepoint to use it as a continuous variable and study the correlation 
of whole brain thickness with this region, is this ok?


On Friday, 19 February 2016, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Hmmm, I think I'm more confused. what do you mean by "mean
thickness of ROI from longitudinal group comparison"? You are
looking at how the thickness across cortex correlates with the
mean thickness in your ROI?

On 02/18/2016 05:50 PM, amirhossein manzouri wrote:

I just wanted to clarify a bit more to see if makes more sense
now ?

On Thursday, 18 February 2016, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

Hi Amirhossein,  I can't tell from below if you have a
question or not

On 02/18/2016 05:32 PM, amirhossein manzouri wrote:

Hi and thanks, tp1 is before and tp2 after treatment,
and the
measurement is the mean thickness of ROI  from
longitudinal
group comparison, so we basically want to see effect of
treatment on cortico cortical correlation.

On Thursday, 18 February 2016, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

so you want to test whether the cross-sectional
slope changes
across time? That is unusual, but you can do it by
specifying two
classes in the FSGD file, one for each time point.
Also
specify a
variable which is your measurement. Then create a
contrast
0 0 1
-1. This will test whether the slopes change
between "groups",
where a "group" is the given time point. This analysis
does not
make sense to me, but that is how to do it.
doug

On 02/18/2016 12:16 PM, amirhossein manzouri wrote:

Hi,
We would like to run paired t-test on
longitudinal within
group data for correlation analysis of one
measurement and
cortical thickness, not cortical thickness
comparison
at the
respective time point .
I found the paired analysis and read that but
in fact
we need
to see if correlation between our measure and CTH
differs from
time point one to time point 2. So the
question will
does the
thickness  and measure1 correlation differs
between time
point1 and tp2?



Best regards,
Amirhossein Manzouri



-- 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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for the
person to
whom it is
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you in
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the e-mail
contains patient information, please contact the
Partners
Compliance HelpLine at
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-- Best regards,
Amirhossein Manzouri




-- Douglas N. Greve, Ph.D.

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

2016-02-19 Thread María Díez Cirarda

Thank you very much for your prompt response.
However, I am doing the same analysis (with Repeated Measures ANOVA 2x2) in
different MRI acquisitions, so I would like to do the same analysis in
freesurfer.

Could you please help me?

Thank you,

Best regards,

Maria.

2016-02-18 23:22 GMT+01:00 Douglas N Greve :

> It will be much easier if you subtract time point 1 from 2 then do a
> two-group t-test. See
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>
> On 02/18/2016 05:37 AM, María Díez Cirarda wrote:
> > Dear FS experts,
> >
> > I am trying to do a longitudinal analysis with a Repeated Measures
> > ANOVA 2x2, with two groups (experimental and control group) and two
> > times (pre and post treatment).
> >
> > First, I have followed the Longitudinal Processing Tutorial:
> > 1) I have 2 acquisitions per subject so, I created a subject template
> > (BASE) for each pair of subjects
> > 2) I created the two longitudinal runs
> >
> > Now I am confused, because I don´t know wether I have to:
> > 1) do a Longitudinal QDEC table with two columns (time and group)
> > or 2) create a FSGD File, (or a DOSS file?) and create the contrasts.
> >
> > If I have to create the FSGD file, Would this be OK?
> >
> > GroupDescriptorFile 1
> > Class Subject 1
> > Class Subject 2
> > Variables   Tp1vsTp2.Gr1Exp
> >   Tp1vsTp2.Gr2Control
> > Input Subject1-tp1  Subject110
> > Input Subject1-tp2  Subject1   -10
> > Input Subject2-tp1  Subject2 0 1
> > Input Subject2-tp2  Subject2 0-1
> >
> > Contrasts:
> > Mtx file:
> > 0 0 1 0
> > 0 0 0 -1
> > 0 0 1 -1
> >
> > Were do I have to create the FSGD file? In subjects folder or inside
> > qdec folder?
> > The group descriptor file must be "subject1" "subject2", or should I
> > introduce the specific names of the folders from the subjects of my
> study?
> >
> > Thank you in advance,
> >
> > Maria.
> >
> >
> >
> > ___
> > 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/
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
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Re: [Freesurfer] Paired t-test for correlation analysis on two time points

2016-02-19 Thread amirhossein manzouri

Of course. Just another question to make sure I understand your answer
correctly. What you suggested with the fsgd file and contrast is the same
as running Qdec on the two time points as two groups and ROI as variable in
the dec table and then select the ROI as continuous and group as discreet
with DODS, right?

Best regards,
Amirhossein Manzouri




On Fri, Feb 19, 2016 at 4:28 PM, Douglas Greve 
wrote:

> I think so. Just make sure you don't try to draw conclusions from the ROI
> or area around it.
>
>
> On 2/19/16 2:02 AM, amirhossein manzouri wrote:
>
> Yes, I extracted the mean thickness of the ROI label from each timepoint
> to use it as a continuous variable and study the correlation of whole brain
> thickness with this region, is this ok?
>
> On Friday, 19 February 2016, Douglas N Greve < 
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hmmm, I think I'm more confused. what do you mean by "mean thickness of
>> ROI  from longitudinal group comparison"? You are looking at how the
>> thickness across cortex correlates with the mean thickness in your ROI?
>>
>> On 02/18/2016 05:50 PM, amirhossein manzouri wrote:
>>
>>> I just wanted to clarify a bit more to see if makes more sense now ?
>>>
>>> On Thursday, 18 February 2016, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu > wrote:
>>>
>>> Hi Amirhossein,  I can't tell from below if you have a question or
>>> not
>>>
>>> On 02/18/2016 05:32 PM, amirhossein manzouri wrote:
>>>
>>> Hi and thanks, tp1 is before and tp2 after treatment, and the
>>> measurement is the mean thickness of ROI  from longitudinal
>>> group comparison, so we basically want to see effect of
>>> treatment on cortico cortical correlation.
>>>
>>> On Thursday, 18 February 2016, Douglas N Greve
>>> mailto:gr...@nmr.mgh.harvard.edu>>
>>> wrote:
>>>
>>> so you want to test whether the cross-sectional slope changes
>>> across time? That is unusual, but you can do it by
>>> specifying two
>>> classes in the FSGD file, one for each time point. Also
>>> specify a
>>> variable which is your measurement. Then create a contrast
>>> 0 0 1
>>> -1. This will test whether the slopes change between
>>> "groups",
>>> where a "group" is the given time point. This analysis
>>> does not
>>> make sense to me, but that is how to do it.
>>> doug
>>>
>>> On 02/18/2016 12:16 PM, amirhossein manzouri wrote:
>>>
>>> Hi,
>>> We would like to run paired t-test on longitudinal within
>>> group data for correlation analysis of one measurement
>>> and
>>> cortical thickness, not cortical thickness comparison
>>> at the
>>> respective time point .
>>> I found the paired analysis and read that but in fact
>>> we need
>>> to see if correlation between our measure and CTH
>>> differs from
>>> time point one to time point 2. So the question will
>>> does the
>>> thickness  and measure1 correlation differs between time
>>> point1 and tp2?
>>>
>>>
>>>
>>> Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
>>> -- 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/
>>>
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>> -- Best regards,
>>> Amirhossein Manzouri
>>>
>>>
>>>
>>>
>>> -- Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr.

[Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

2016-02-19 Thread Afzal, Afsana

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

2016-02-19 Thread Thomas Jacquemont

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?

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...

Thank you for your help,

Yours faithfully,

Thomas

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Re: [Freesurfer] Paired t-test for correlation analysis on two time points

2016-02-19 Thread Douglas Greve


right

On 2/19/16 10:48 AM, amirhossein manzouri wrote:
Of course. Just another question to make sure I understand your answer 
correctly. What you suggested with the fsgd file and contrast is the 
same as running Qdec on the two time points as two groups and ROI as 
variable in the dec table and then select the ROI as continuous and 
group as discreet with DODS, right?


Best regards,
Amirhossein Manzouri



On Fri, Feb 19, 2016 at 4:28 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I think so. Just make sure you don't try to draw conclusions from
the ROI or area around it.


On 2/19/16 2:02 AM, amirhossein manzouri wrote:

Yes, I extracted the mean thickness of the ROI label from each
timepoint to use it as a continuous variable and study the
correlation of whole brain thickness with this region, is this ok?

On Friday, 19 February 2016, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Hmmm, I think I'm more confused. what do you mean by "mean
thickness of ROI  from longitudinal group comparison"? You
are looking at how the thickness across cortex correlates
with the mean thickness in your ROI?

On 02/18/2016 05:50 PM, amirhossein manzouri wrote:

I just wanted to clarify a bit more to see if makes more
sense now ?

On Thursday, 18 February 2016, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>
> wrote:

Hi Amirhossein,  I can't tell from below if you have
a question or not

On 02/18/2016 05:32 PM, amirhossein manzouri wrote:

Hi and thanks, tp1 is before and tp2 after
treatment, and the
measurement is the mean thickness of ROI  from
longitudinal
group comparison, so we basically want to see
effect of
treatment on cortico cortical correlation.

On Thursday, 18 February 2016, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

so you want to test whether the
cross-sectional slope changes
across time? That is unusual, but you can do
it by
specifying two
classes in the FSGD file, one for each time
point. Also
specify a
variable which is your measurement. Then
create a contrast
0 0 1
-1. This will test whether the slopes change
between "groups",
where a "group" is the given time point. This
analysis
does not
make sense to me, but that is how to do it.
doug

On 02/18/2016 12:16 PM, amirhossein manzouri
wrote:

Hi,
We would like to run paired t-test on
longitudinal within
group data for correlation analysis of
one measurement and
cortical thickness, not cortical
thickness comparison
at the
respective time point .
I found the paired analysis and read that
but in fact
we need
to see if correlation between our measure
and CTH
differs from
time point one to time point 2. So the
question will
does the
thickness  and measure1 correlation
differs between time
point1 and tp2?



Best regards,
Amirhossein Manzouri



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

2016-02-19 Thread Douglas Greve



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] R: Re: FS-FAST using MRS voxel or .label as seed

2016-02-19 Thread Douglas N Greve


Make sure that the MRS_MASK.mgz itself has some voxels with value=1, and 
make sure that there are enough of them to fit into at least one 
functional voxel.

Make sure that the registration is accurate.

When you run run fcseed-sess, add -debug, capture the output, and send 
it to me.


On 02/18/2016 06:43 PM, std...@virgilio.it wrote:
> The problem persist.
>
> Stefano
>
>
>> Messaggio originale
>> Da: Douglas N Greve 
>> Data: 19-feb-2016 0.25
>> A: 
>> Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed
>>
>>
>> I think it may be our fcseed-config command line
>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd
>> rest -mean -cfg MRS_MASK.config –overwrite
>>
>> It should be -seg MRS_MASK.mgz
>>
>> They way you have it, fcseed will use the segmentation for Subj for all
>> subjects, which is why it works for one and not for others
>>
>>
>> On 02/18/2016 06:10 PM, std...@virgilio.it wrote:
>>> Hi list,
>>>
>>> I'm having problem to use FS-FAST fMRI connectivity using as seed a
>>> mask of a MRS voxel or .label obtained by drawing it from surface. In
>>> order to resolve my concern, I'm reporting step by step the command
>>> lines which I have used. The mask, f.nii.gz, orig.nii.gz and
>>> aparc+aseg.nii.gz showed a good overlap.
>>>
>>> These are the features of each one:
>>>
>>> fslinfo orig.nii.gz
>>>
>>> data_type UINT8
>>>
>>> dim1 256
>>>
>>> dim2 256
>>>
>>> dim3 256
>>>
>>> dim4 1
>>>
>>> datatype 2
>>>
>>> pixdim1 1.00
>>>
>>> pixdim2 1.00
>>>
>>> pixdim3 1.00
>>>
>>> pixdim4 0.010747
>>>
>>> cal_max   0.
>>>
>>> cal_min 0.
>>>
>>> file_type NIFTI-1+
>>>
>>> fslinfo aparc+aseg.nii.gz
>>>
>>> data_type INT32
>>>
>>> dim1 256
>>>
>>> dim2 256
>>>
>>> dim3 256
>>>
>>> dim4 1
>>>
>>> datatype 8
>>>
>>> pixdim1 1.00
>>>
>>> pixdim2 1.00
>>>
>>> pixdim3 1.00
>>>
>>> pixdim4 0.010747
>>>
>>> cal_max 0.
>>>
>>> cal_min 0.
>>>
>>> file_type NIFTI-1+
>>>
>>> fslinfo MRS_MASK.nii.gz
>>>
>>> data_type FLOAT32
>>>
>>> dim1 256
>>>
>>> dim2 256
>>>
>>> dim3 256
>>>
>>> dim4 1
>>>
>>> datatype 16
>>>
>>> pixdim1 1.00
>>>
>>> pixdim2 1.00
>>>
>>> pixdim3 1.00
>>>
>>> pixdim4 0.00
>>>
>>> cal_max 0.
>>>
>>> cal_min 0.
>>>
>>> file_type NIFTI-1+
>>>
>>> I’m using MNI2mm for subcortical analysis.
>>>
>>> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz
>>> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz
>>>
>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd
>>> rest -mean -cfg MRS_MASK.config –overwrite
>>>
>>> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite
>>>
>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh
>>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg
>>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run
>>> -overwrite
>>>
>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh
>>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg
>>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run
>>> -overwrite
>>>
>>> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask
>>> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5
>>> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite
>>>
>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh
>>>
>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh
>>>
>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305
>>>
>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast
>>> MRS_MASK -o my-group
>>>
>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast
>>> MRS_MASK -o my-group
>>>
>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast
>>> MRS_MASK -o my-group
>>>
>>> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite,
>>> it seem to be functioning for the first subj, but the next subj2 show
>>> this error
>>>
>>> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz
>>>
>>> Voxel Volume is 64.5752 mm^3
>>>
>>> Generating list of segmentation ids
>>>
>>> Found   1 segmentations
>>>
>>> Computing statistics for each segmentation
>>>
>>>0 1 0   0.000
>>>
>>> MRIalloc(0, 1, 1): bad parm
>>>
>>> Reporting on 0 segmentations
>>>
>>> Computing spatial average of each frame
>>>
>>> Writing to
>>> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess.
> 28328/avgwf.mgh
>>> Segmentation fault
>>>
>>>
>>>
>>> ___
>>> 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/o

Re: [Freesurfer] R: Re: R: FS-FAST using MRS voxel or .label as seed

2016-02-19 Thread Douglas N Greve

Yes, that is expected given your command line.

On 02/18/2016 06:52 PM, std...@virgilio.it wrote:
> By running
> mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label
>
> and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay 
> MRS.
> label
> the inflate is empty.
>
>
> Stefano
>
>
>
>> Messaggio originale
>> Da: Douglas N Greve 
>> Data: 19-feb-2016 0.34
>> A: 
>> Ogg: Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed
>>
>> That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a
>> volume, not a surface overlay. By using --surf, you are indicating that
>> it is a surface overlay
>>
>> On 02/18/2016 06:30 PM, std...@virgilio.it wrote:
>>> Furthermore, if I use mir_cor2label in order to show the location of
>>> MRS voxel (in native space) this error occurs:
>>>
>>> mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l
>>> MRS.label --surf fsaverage lh
>>> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
>>> Loading mri
>>> /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz
>>> Loading
>>> /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white
>>> ERROR: dim mismatch between surface (163842) and input (16777216)
>>>
>>>  Messaggio originale
>>>  Da: std...@virgilio.it
>>>  Data: 19-feb-2016 0.10
>>>  A: 
>>>  Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed
>>>
>>>  Hi list,
>>>
>>>  I'm having problem to use FS-FAST fMRI connectivity using as seed
>>>  a mask of a MRS voxel or .label obtained by drawing it from
>>>  surface. In order to resolve my concern, I'm reporting step by
>>>  step the command lines which I have used. The mask, f.nii.gz,
>>>  orig.nii.gz and aparc+aseg.nii.gz showed a good overlap.
>>>
>>>  These are the features of each one:
>>>
>>>  fslinfo orig.nii.gz
>>>
>>>  data_type UINT8
>>>
>>>  dim1   256
>>>
>>>  dim2   256
>>>
>>>  dim3   256
>>>
>>>  dim4   1
>>>
>>>  datatype   2
>>>
>>>  pixdim1 1.00
>>>
>>>  pixdim2 1.00
>>>
>>>  pixdim3 1.00
>>>
>>>  pixdim4 0.010747
>>>
>>>  cal_max   0.
>>>
>>>  cal_min 0.
>>>
>>>  file_type NIFTI-1+
>>>
>>>  fslinfo aparc+aseg.nii.gz
>>>
>>>  data_type INT32
>>>
>>>  dim1   256
>>>
>>>  dim2   256
>>>
>>>  dim3   256
>>>
>>>  dim4   1
>>>
>>>  datatype   8
>>>
>>>  pixdim1 1.00
>>>
>>>  pixdim2 1.00
>>>
>>>  pixdim3 1.00
>>>
>>>  pixdim4 0.010747
>>>
>>>  cal_max 0.
>>>
>>>  cal_min 0.
>>>
>>>  file_type NIFTI-1+
>>>
>>>  fslinfo MRS_MASK.nii.gz
>>>
>>>  data_type FLOAT32
>>>
>>>  dim1   256
>>>
>>>  dim2   256
>>>
>>>  dim3   256
>>>
>>>  dim4   1
>>>
>>>  datatype   16
>>>
>>>  pixdim1 1.00
>>>
>>>  pixdim2 1.00
>>>
>>>  pixdim3 1.00
>>>
>>>  pixdim4 0.00
>>>
>>>  cal_max 0.
>>>
>>>  cal_min 0.
>>>
>>>  file_type NIFTI-1+
>>>
>>>  I’m using MNI2mm for subcortical analysis.
>>>
>>>  mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz
>>>  $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz
>>>
>>>  fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz
>>>  -fsd rest -mean -cfg MRS_MASK.config –overwrite
>>>
>>>  fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite
>>>
>>>  mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage
>>>  lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5
>>>  -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1
>>>  -per-run -overwrite
>>>
>>>  mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage
>>>  rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5
>>>  -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1
>>>  -per-run -overwrite
>>>
>>>  mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8
>>>  -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
>>>  -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite
>>>
>>>  selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh
>>>
>>>  selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh
>>>
>>>  selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305
>>>
>>>  isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast
>>>  MRS_MASK -o my-group
>>>
>>>  isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast
>>>  MRS_MASK -o my-group
>>>
>>>  isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast
>>>  MRS_MASK -o my-group
>>>
>>>  When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite,
>>>  it seem to be functioning for the first subj, but the next subj2
>>>  show this error
>>>
>>>  Loading
>>>  /Applications/freesurfer/subjec

Re: [Freesurfer] Building from source -- autoconf error

2016-02-19 Thread Z K

Hello Yaroslav,

Ive built freesurfer on Debian "Jessie" platform. It was just a matter 
of adding "libtool-bin" and "tcsh" to the list of packages that need to 
be installed. Ive update the wiki page:

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

I still wasnt quite able to get the freeview GUI to build. But If you 
change the "--disable-GUI-build" flag to "--without-qt" then you will 
get all the tktool GUIs except freeview. Im working on getting freeview 
to build at the moment and will update the wiki page once I figure it out.

-Zeke




On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
> Gotcha, thanks!
>
> On February 18, 2016 3:27:21 PM EST, Z K  wrote:
>>
>>> I would be infinitely grateful if freesurfer could build natively on
>> Debian
>>> stable! ;)  Thanks for trying.  In my case I am trying the build
>> under jessie
>>> chroot (using schroot helper), so I could quickly setup/enter such
>> environment
>>> while maintaining user/directory.  I will do the same now for 14.04.
>> If you
>>> would like more -- let me know I could give a bit more detailed
>>> instructions.
>>>
>>
>> I have a debian jessie system just setup, but I have a high priority
>> project due Monday, so I would be able to begin determining the exact
>> build procedure on Debian jessie until beginning of next week. It is
>> something I have been meaning to do so I plan on getting to it. If you
>> dont hear from me by Tuesday/Wedensday feel free to shoot me an email
>> for an update. Thanks.
>>
>> -Zeke
>>
>>
>> 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] Building from source -- autoconf error

2016-02-19 Thread Rudolph Pienaar

I have been able to build the FS GUI tools succesfully on Ubuntu in the 
past... Admittedly this was a long time ago (pre 14.04 days). I can dig 
through my notes and see if they are still applicable. We no longer have 
any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose 
in a few weeks will be superseded by 16.04's release.


On 2/19/16 12:45 , Z K wrote:
> Hello Yaroslav,
>
> Ive built freesurfer on Debian "Jessie" platform. It was just a matter
> of adding "libtool-bin" and "tcsh" to the list of packages that need to
> be installed. Ive update the wiki page:
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>
> I still wasnt quite able to get the freeview GUI to build. But If you
> change the "--disable-GUI-build" flag to "--without-qt" then you will
> get all the tktool GUIs except freeview. Im working on getting freeview
> to build at the moment and will update the wiki page once I figure it out.
>
> -Zeke
>
>
>
>
> On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
>> Gotcha, thanks!
>>
>> On February 18, 2016 3:27:21 PM EST, Z K  
>> wrote:
>>>
 I would be infinitely grateful if freesurfer could build natively on
>>> Debian
 stable! ;)  Thanks for trying.  In my case I am trying the build
>>> under jessie
 chroot (using schroot helper), so I could quickly setup/enter such
>>> environment
 while maintaining user/directory.  I will do the same now for 14.04.
>>> If you
 would like more -- let me know I could give a bit more detailed
 instructions.

>>>
>>> I have a debian jessie system just setup, but I have a high priority
>>> project due Monday, so I would be able to begin determining the exact
>>> build procedure on Debian jessie until beginning of next week. It is
>>> something I have been meaning to do so I plan on getting to it. If you
>>> dont hear from me by Tuesday/Wedensday feel free to shoot me an email
>>> for an update. Thanks.
>>>
>>> -Zeke
>>>
>>>
>>> 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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>


-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] Building from source -- autoconf error

2016-02-19 Thread Z K

Ive discovered that if you add the following line to the 
freeview/Makefile.am file then it will build succcessfully.

  freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS)
  freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS)
-freeview_LDFLAGS   = $(QT_LDFLAGS) $(OS_LDFLAGS)
+freeview_LDFLAGS   = $(QT_LDFLAGS) $(OS_LDFLAGS) \
+   -Wl,--allow-multiple-definition 
  freeview_LDADD= $(QT_LIBS)\
$(addprefix $(top_builddir)/, $(LIBS_MGH)) \
$(top_builddir)/vtkfsio/libvtkfsio.a \

Turns out the issue is with the build of LAPACK provided by Ubuntu, as 
it contains a duplicate function. (https://cmake.org/Bug/view.php?id=12912)

I will be committing the change and pushing to the git repo after some 
testing, probably later this evening.

-Zeke

On 02/19/2016 02:29 PM, Rudolph Pienaar wrote:
> I have been able to build the FS GUI tools succesfully on Ubuntu in the
> past... Admittedly this was a long time ago (pre 14.04 days). I can dig
> through my notes and see if they are still applicable. We no longer have
> any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose
> in a few weeks will be superseded by 16.04's release.
>
>
> On 2/19/16 12:45 , Z K wrote:
>> Hello Yaroslav,
>>
>> Ive built freesurfer on Debian "Jessie" platform. It was just a matter
>> of adding "libtool-bin" and "tcsh" to the list of packages that need to
>> be installed. Ive update the wiki page:
>>
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>>
>> I still wasnt quite able to get the freeview GUI to build. But If you
>> change the "--disable-GUI-build" flag to "--without-qt" then you will
>> get all the tktool GUIs except freeview. Im working on getting freeview
>> to build at the moment and will update the wiki page once I figure it out.
>>
>> -Zeke
>>
>>
>>
>>
>> On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
>>> Gotcha, thanks!
>>>
>>> On February 18, 2016 3:27:21 PM EST, Z K  
>>> wrote:

> I would be infinitely grateful if freesurfer could build natively on
 Debian
> stable! ;)  Thanks for trying.  In my case I am trying the build
 under jessie
> chroot (using schroot helper), so I could quickly setup/enter such
 environment
> while maintaining user/directory.  I will do the same now for 14.04.
 If you
> would like more -- let me know I could give a bit more detailed
> instructions.
>

 I have a debian jessie system just setup, but I have a high priority
 project due Monday, so I would be able to begin determining the exact
 build procedure on Debian jessie until beginning of next week. It is
 something I have been meaning to do so I plan on getting to it. If you
 dont hear from me by Tuesday/Wedensday feel free to shoot me an email
 for an update. Thanks.

 -Zeke


 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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>>
>
>
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Re: [Freesurfer] qdec

2016-02-19 Thread levi solomyak

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 <
>> gr...@nmr.mgh.harvard.edu> 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 appreciated!
>>> >
>>> >
>>> > Here are the details of the errors:
>>> >
>>> > 1) machine being used: Linux localhost.localdomain
>>> > 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64
>>> > x86_64 x86_64 GNU/Linux
>>> > 2) Freesurfer version:
>>> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
>>> > 3) Current working directory:
>>> /projects/IndivRITL/data/leviDiff/Subjects
>>> > 4) which qdec :  /usr/local/freesurfer/bin/qdec
>>> > 5) After loading the gui, I attempted to generate a qdec stats table.
>>> > This is the error that was returned:
>>> >
>>> >
>>> ---
>>> > 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

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

2016-02-19 Thread Bruce Fischl

Hi Thomas

the seed sets the random number generator to the same starting point so 
that the algorithm is repeateable.

Maybe Doug can comment on the second question. How are you visualizing it?

cheers
Bruce

On Fri, 19 Feb 2016, 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?
>
> 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...
>
> Thank you for your help,
>
> Yours faithfully,
>
> Thomas
>
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Re: [Freesurfer] Building from source -- autoconf error

2016-02-19 Thread Yaroslav Halchenko

On Fri, 19 Feb 2016, Z K wrote:

> Hello Yaroslav,

> Ive built freesurfer on Debian "Jessie" platform. It was just a matter 
> of adding "libtool-bin" and "tcsh" to the list of packages that need to 
> be installed. 

I had tcsh but not libtool-bin installed in that chroot... heh

> Ive update the wiki page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

> I still wasnt quite able to get the freeview GUI to build. But If you 
> change the "--disable-GUI-build" flag to "--without-qt" then you will 
> get all the tktool GUIs except freeview. Im working on getting freeview 
> to build at the moment and will update the wiki page once I figure it out.

sweet! thanks.  I will give it a shot!

in my case I have got stuck still on 14.04 trying to build with GUI but
./configure failed to find xawplus rightfully so since even
centos6-x86_64-packages provides only a static build of it while
configure sensing for a dynamic library.  (and debian/ubuntus do
not provide this antiquity) 

I just wondered how do you guys build against it then? ;) 

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] Building from source -- autoconf error

2016-02-19 Thread Yaroslav Halchenko

On Fri, 19 Feb 2016, Yaroslav Halchenko wrote:

> On Fri, 19 Feb 2016, Z K wrote:

> > I still wasnt quite able to get the freeview GUI to build. But If you 
> > change the "--disable-GUI-build" flag to "--without-qt" then you will 
> > get all the tktool GUIs except freeview. Im working on getting freeview 
> > to build at the moment and will update the wiki page once I figure it out.

> sweet! thanks.  I will give it a shot!

> in my case I have got stuck still on 14.04 trying to build with GUI but
> ./configure failed to find xawplus rightfully so since even
> centos6-x86_64-packages provides only a static build of it while
> configure sensing for a dynamic library.  (and debian/ubuntus do
> not provide this antiquity) 

> I just wondered how do you guys build against it then? ;) 

Hi Z K,

and I guess it didn't even matter somehow while building under jessie
with GUI enabled (after your patch for lapack multiple definitions
and my patch for DESTDIR).  FWIW -- success, I have managed to build the
beast and it seems even to work ;) hip hip hoorray!

next question:  I see some test files spread out through the
code-base.  Is there some centralized/uniform way to run them???

Thanks in advance!
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] Entorhinal thickness

[Freesurfer] R: Re: FS-FAST using MRS voxel or .label as seed

Re: [Freesurfer] Building from source -- autoconf error

[Freesurfer] comparison between two hemisphere in single

Re: [Freesurfer] comparison between two hemisphere in single

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

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

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

[Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

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

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

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

Re: [Freesurfer] R: Re: FS-FAST using MRS voxel or .label as seed

Re: [Freesurfer] R: Re: R: FS-FAST using MRS voxel or .label as seed

Re: [Freesurfer] Building from source -- autoconf error

Re: [Freesurfer] Building from source -- autoconf error

Re: [Freesurfer] Building from source -- autoconf error

Re: [Freesurfer] qdec

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

Re: [Freesurfer] Building from source -- autoconf error

Re: [Freesurfer] Building from source -- autoconf error

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