Re: [Freesurfer] error of color bar in freeview

[Ruopeng Wang]

If you are running freeview on a Mac, you can ignore those “Invalid drawable” 
messages. Can you post a screenshot of the whole freeview window with the color 
bar issue?

Best,
Ruopeng

On Jul 20, 2014, at 11:34 PM, 郝磊  wrote:

> Dear experts
> 
> when I open freeview, it report that "2014-07-21 11:22:28.453 
> Freeview[10414:303] invalid drawable". Afterwards, when I click on Show Color 
> Scale, the color bar was in black alternating with white. How should I solve 
> this problem?
> 
> Thank you 
> 
> Hao Lei (new learner of freesurfer) 
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[Freesurfer] Tools for FreeSurfer group analysis in R

[Andreas Berger]

Hello FreeSurfers,

during the course of my diploma thesis i wrote a few R functions around
FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I
thought i'd just contribute the code here, on the off chance that
someone may find it useful, and despite the code quality (i wrote this
as part of me learning R, so it may actually set your house on fire and
so on). It could be of use for someone already working in R and looking
to bring FreeSurfer data into it, or someone looking for an alternative
to QDEC and the plots created by QDEC. Hardware requirement is not
entirely modest unfortunately; it eats up about 8G of memory and takes
about 15 minutes around here.


Here's an example of how it is used:


 BEGIN R CODE ##
# Presupposing that you have a dataframe 'data' containing your group
# description and that all subjects have been processed in ~/subjects

### Group analysis with lm ###
# Run the model. This takes some time and memory.
lm <- freesurfer.group.analysis.lm(data = data, formula = thickness ~ 
Age + Gender + Diagnosis, hemi = "lh", fwhm = 10, template = 
"fsaverage", freesurfer_subjects_dir = "~/subjects")

# Extract t values from the model, do FDR correction
t <- freesurfer.group.analysis.lm.stats(lm, type.of.value = "t", 
correction="fdr")

# Write the t values to mgh files and open them in FreeSurfer's freeview
freesurfer.group.analysis.lm.stats.to.mgh(t, hemi = "lh", template = 
"fsaverage", freesurfer_subjects_dir = "~/subjects", launch.freeview = TRUE)

# Write the t values to .dset ASCII files and open them in AFNI's SUMA
freesurfer.group.analysis.lm.stats.to.suma(t, hemi = "lh", template = 
"fsaverage", freesurfer_subjects_dir = "~/subjects", launch.suma = TRUE)

# Make nice plots for vertex #1000
freesurfer.group.analysis.lm.plot(lm, vertex = 1000, interactive = TRUE)


### Group analysis with QDEC ###
# Call QDEC
freesurfer.group.analysis.QDEC(data = data, freesurfer_subjects_dir = 
"~/subjects")


### Extract stats ###
# Get segmentation stats
segstats <- freesurfer.get.segstats(subjects = data$ID, 
freesurfer_subjects_dir = "~/subjects")
## END R CODE ##


i uploaded the R package here, i called it freesurfR:
https://www.nitrc.org/projects/freesurf_r/

thanks also goes to Heath Pardoe, whose code for reading and writing MGH
files (also posted on this list) i was allowed to include.


regards,
Andreas
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Re: [Freesurfer] Tools for FreeSurfer group analysis in R

[Alan Francis]

Hi Andreas:

Very kind of you to share your code. I am sure many of us will benefit from
this.

thanks,

Alan Francis


On Mon, Jul 21, 2014 at 9:12 AM, Andreas Berger <
n0642...@students.meduniwien.ac.at> wrote:

> Hello FreeSurfers,
>
> during the course of my diploma thesis i wrote a few R functions around
> FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I
> thought i'd just contribute the code here, on the off chance that
> someone may find it useful, and despite the code quality (i wrote this
> as part of me learning R, so it may actually set your house on fire and
> so on). It could be of use for someone already working in R and looking
> to bring FreeSurfer data into it, or someone looking for an alternative
> to QDEC and the plots created by QDEC. Hardware requirement is not
> entirely modest unfortunately; it eats up about 8G of memory and takes
> about 15 minutes around here.
>
>
> Here's an example of how it is used:
>
>
>  BEGIN R CODE ##
> # Presupposing that you have a dataframe 'data' containing your group
> # description and that all subjects have been processed in ~/subjects
>
> ### Group analysis with lm ###
> # Run the model. This takes some time and memory.
> lm <- freesurfer.group.analysis.lm(data = data, formula = thickness ~
> Age + Gender + Diagnosis, hemi = "lh", fwhm = 10, template =
> "fsaverage", freesurfer_subjects_dir = "~/subjects")
>
> # Extract t values from the model, do FDR correction
> t <- freesurfer.group.analysis.lm.stats(lm, type.of.value = "t",
> correction="fdr")
>
> # Write the t values to mgh files and open them in FreeSurfer's freeview
> freesurfer.group.analysis.lm.stats.to.mgh(t, hemi = "lh", template =
> "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.freeview =
> TRUE)
>
> # Write the t values to .dset ASCII files and open them in AFNI's SUMA
> freesurfer.group.analysis.lm.stats.to.suma(t, hemi = "lh", template =
> "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.suma = TRUE)
>
> # Make nice plots for vertex #1000
> freesurfer.group.analysis.lm.plot(lm, vertex = 1000, interactive = TRUE)
>
>
> ### Group analysis with QDEC ###
> # Call QDEC
> freesurfer.group.analysis.QDEC(data = data, freesurfer_subjects_dir =
> "~/subjects")
>
>
> ### Extract stats ###
> # Get segmentation stats
> segstats <- freesurfer.get.segstats(subjects = data$ID,
> freesurfer_subjects_dir = "~/subjects")
> ## END R CODE ##
>
>
> i uploaded the R package here, i called it freesurfR:
> https://www.nitrc.org/projects/freesurf_r/
>
> thanks also goes to Heath Pardoe, whose code for reading and writing MGH
> files (also posted on this list) i was allowed to include.
>
>
> regards,
> Andreas
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Re: [Freesurfer] freeview brush value problem

[Ruopeng Wang]

What date type is your volume? Is it uchar? If so, a value of 570 would 
overflow.


Ruopeng

On 07/20/2014 12:25 PM, Tracy Riggins wrote:


Hello Freesurfer experts

I am trying to edit an aseg file.  I want to set my brush value to a 
value that does not exist in the default lookup table (e.g,. 570).  
So, I edited the lookup table, saved this , and loaded it in 
freeview.  My new label and brush value is now visible.  However when 
I set the brush value to this value/label (both the main GUI window 
and edit voxel window say "Brush value = 570") and draw on the aseg 
file it does not use this brush value.  It uses a different value (eg 
48).  I can't seem to figure out why.  Any thoughts?


Thanks in advance,

Tracy

Tracy Riggins, Ph.D.

Assistant Professor
Department of Psychology

BPS 2147J
University of Maryland

College Park, MD 20742
Office: (301) 405-5905

Fax: (301) 314-9566

http://ncdl.umd.edu 

rigg...@umd.edu 



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[Freesurfer] dwi_motion Tracula

[Cat Chong]

Hello Anastasia,

 I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I 
would like to use the command "dwi_motion" on my data. I have installed the 
updates, but will I have to completely reprocess my data inducing steps 
trac-all -prep, trace-all -bedp, and trac-all path in order to use dwi_motion? 

cheers,
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[Freesurfer] Edits to Pial and CP at the same time?

[Mark Fletcher]

Dear FreeSurfers,

In the training that I attended in May, I believe it was demonstrated by
Allison that you could fix multiple problems at the same time.   I
understand how to make the edits at the same time, but am unsure what
command to run to integrate all of these changes concurrently.

Since I currently do not know how to do this, it is taking me multiple days
to fix some problems on subjects with multiple types of errors.  Currently
I first manually delete some dura on the brainmask.mgz (thus I would run
recon-all -autorecon-pial -subjid ).  After examining the output the
next day, I then add control points in the anterior temporal lobe or other
places if needed on the same subject ( recon-all -autorecon2-cp -autorecon3
-subjid  ).

I was wondering how to both manually delete the dura, and add cp at the
same time for one processing event (thus saving me a lot of time)?  Would
the correct command line be:

recon-all -autorecon-pial autorecon2-cp -autorecon3 -subjid   ?

Also, is it possible to edit the pial, add white matter, and control points
all at the same time for one recon-all processing event?  Would the correct
command line be

recon-all -autorecon-pial autorecon2*-cp-wm* -autorecon3 -subjid 

or

recon-all -autorecon-pial *autorecon2-cp* *autorecon2-wm* -autorecon3
-subjid 

Thanks for your help :)


Sincerely,
Mark Fletcher
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Re: [Freesurfer] [Fwd: LGI recon problem]

[Marie Schaer]

Hi Angela,

Have you tried that: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?

You can look also in the release notes 
(http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using Matlab 
2013.

The issue will be corrected in the next FreeSurfer release.

Let mw know if it doesn't work,

Marie



On Jul 19, 2014, at 1:56 AM, angela.fav...@unipd.it wrote:

> Dear FS experts,
> I had no answer to my question below (log was attached in my previous mail)
> The error repeated in different subjects and I do not know how to
> overcome. Can anyone give me some help?
> 
> Angela
> 
> 
> 
> Hi all,
> I had an error message while running LGI recon
> I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with
> the Image processing toolbox
> 
> Any help is welcome. Thank you!
> Angela
> 
> 
> the error is:
> 
> mesh_outer =
> 
> vertices: [61278x3 double]
>faces: [122552x3 double]
>facesOfVertex: [61278x1 struct]
> 
> preparing pial mesh structure ...
> ...searching for mesh edges...done (315.30 sec).
> ... creating path file for vertex 1 / 61278
> area file for outer ROIs saved at 1
> {Improper assignment with rectangular empty matrix.
> 
> Error in dsearchn (line 79)
>[d(i),t(i)] = min(sum((x-yi).^2,2));
> 
> Error in mesh_vertex_nearest (line 29)
> nearestIndex = dsearchn(vertices,points);
> 
> Error in reorganize_verticeslist (line 28)
>
> [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
> 
> Error in make_roi_paths (line 93)
>reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
>verticeslist, step);
> }
>>> 
> ERROR:  make_roi_paths did not complete successfully!
> Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug
> 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
> 
> recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
> 
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] lobes gyrification

[Marie Schaer]

Hi Melly,

The LGI has the same format as the thickness files, so you can extract them 
using mris_anatomical_stats (providing you have your own annotation). The 
command will look something like:

mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT  -t $SUBJ/surf/?h.pial_lgi  -f 
$SUBJ/stats/OUTPUT_FILE  $SUBJ  ?h

Hope it helps,

Marie


On Jul 19, 2014, at 7:29 AM, melinda dora 
mailto:mellyd...@outlook.com>> wrote:

Dear freesurfer group, is there a command to extract lobar gyrification values 
for each subject? If so please what are the steps? if Ive already created the 
lobar annotation labels, can I extract gyrifaction with these if I have already 
passed the gyrification command?

Best,

Melly
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[Freesurfer] Diffusion analysis qs - gradient matrix

[Rotem Saar]

Dear freesurfer experts,

For diffusion analysis in freesurfer - I want to know which gradient matrix
freesurfer expects.

The thing is - when I look at the gradient matrix created using a MATLAB
script that reads the directions from the dicom header - I get one table,
but the bvecs file created in MRIconvert (for converting dicoms to nifti)
looks different.

This is the situation when an angle is applied during the acquisition of
the dMRI scans, which means that each subject has its own gradient matrix.

So my question is which table should I use for diffusion analysis in
freesurfer? The one that was created from the dicom header or the one
created for NIFTI format using MRIconvert ?

Thanks

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211

Israel
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Re: [Freesurfer] Diffusion analysis qs - gradient matrix

[Harms, Michael]

FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan.


cheers,
-MH




-- 
Michael Harms, Ph.D.

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






From: Rotem Saar 
Reply-To: Freesurfer support list 
Date: Monday, July 21, 2014 1:54 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Diffusion analysis qs - gradient matrix






Dear freesurfer experts,


For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects.


The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for
 converting dicoms to nifti) looks different.


This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix.


So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? 


Thanks




Rotem Saar-Ashkenazy


Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105



School of Social Work
Ashkelon Academic College, Ashkelon, 78211 



Israel








 



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[Freesurfer] Repost | Re: mni152reg error

[jaco...@nmr.mgh.harvard.edu]

Hello Doug,

Ideally, I am trying to take subject tstat maps from FsFast (stable3
environment) and register these native structural space maps to the
MNI152_2mm standard brain.

The t_000.bfloat file is what was generated relative to my contrast that
was set up in FsFast stable3. There are a series of these files ranging
from t_000.bfloat to t_029.bfloat and there are also these same named
files with a .hdr extension. t_000.bfloat is the file I designate when I
select an overlay within tkmedit.

Your help sorting out this registration is very appreciated.

Thank you,
Jacob



>> I'm not sure what you are trying to do, but that command line looks
like
>> things are not set up properly. What is t_000.bfloat? (And why are you
using bfloats?)
>> doug
>> On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
>>> Hello again Doug,
>>> Thank you for sending the updated version of mri152reg. It ran without
error and generated the reg.mni152.2mm.dat registration matrix.
Unfortunately though, when I tried to apply the transformation to the
same
>>> subject's t_000.bfloat, the registration is not correct (command below).
>>> mri_vol2vol --inv --targ /.../t_000.bfloat --mov
>>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
>>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
/.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a
positive note, I was able to load the output image and
>>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be
>>> shifted too far anterior.
>>> With my next attempt, I used mri_convert to make the t_000.bfloat into a
>>> .mgz and than ran mri_vol2vol, but the same misalignment occurred (see
attached photo).
>>> Using tkmedit, I have confirmed that this file aligns properly on this
subject's native structural image, so I am not quite sure why the
registration matrix may be off. Given that the reg.mni152.2mm.dat file
reflects the transformation of the native struc to MNI, I wonder if I
need
>>> to account for the reg file between the func data and the native
struc?
>>> Can you please let me know what I may be doing incorrectly?
>>> As always, your help is very appreciated.
>>> Jacob
 Yea, i fixed this problem. I've attached a new version with the fix.
doug
 On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote:
> Hello Freesurfer Experts,
> I am trying to view stats generated with FsFast in fslview/MNIspace,
>>> and
> in doing so I have run mni152reg to generate the registration
matrix.
>>> That said, mni152reg did not complete correctly and below I have
pasted
>>> the terminal output:
> Thu Jul 17 09:58:10 EDT 2014
> setenv SUBJECTS_DIR
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
> CD_cerv_pat4_sess1_recon
> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
>>> UTC
> 2014 x86_64 x86_64 x86_64 GNU/Linux
> fslregister --mov
> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
>>> --s CD_cerv_pat4_sess1_recon --reg
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>>> --dof 12
> mkdir: cannot create directory
> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
>>> Permission denied
> Log file is
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
>>> Thu Jul 17 09:58:11 EDT 2014
> --mov
> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
>>> --s CD_cerv_pat4_sess1_recon --reg
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>>> --dof 12
> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
> purkinje
> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
>>> UTC
> 2014 x86_64 x86_64 x86_64 GNU/Linux
> nIters 1
> --
> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
mri_convert
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
mri_convert
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
niiWrite(): error opening file
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz...
>>> TR=2530.00, TE=3.25, TI=1100.

Re: [Freesurfer] Repost | Re: mni152reg error

[Bruce Fischl]

Hi Jacob

Doug is on vacation for a couple of weeks, so you should probably repost 
in early August.

cheers
Bruce
On Mon, 21 Jul 2014, jaco...@nmr.mgh.harvard.edu wrote:

> Hello Doug,
>
> Ideally, I am trying to take subject tstat maps from FsFast (stable3
> environment) and register these native structural space maps to the
> MNI152_2mm standard brain.
>
> The t_000.bfloat file is what was generated relative to my contrast that
> was set up in FsFast stable3. There are a series of these files ranging
> from t_000.bfloat to t_029.bfloat and there are also these same named
> files with a .hdr extension. t_000.bfloat is the file I designate when I
> select an overlay within tkmedit.
>
> Your help sorting out this registration is very appreciated.
>
> Thank you,
> Jacob
>
>
>
>>> I'm not sure what you are trying to do, but that command line looks
> like
>>> things are not set up properly. What is t_000.bfloat? (And why are you
> using bfloats?)
>>> doug
>>> On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
 Hello again Doug,
 Thank you for sending the updated version of mri152reg. It ran without
> error and generated the reg.mni152.2mm.dat registration matrix.
> Unfortunately though, when I tried to apply the transformation to the
> same
 subject's t_000.bfloat, the registration is not correct (command below).
 mri_vol2vol --inv --targ /.../t_000.bfloat --mov
 $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
 CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
> /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a
> positive note, I was able to load the output image and
 MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be
 shifted too far anterior.
 With my next attempt, I used mri_convert to make the t_000.bfloat into a
 .mgz and than ran mri_vol2vol, but the same misalignment occurred (see
> attached photo).
 Using tkmedit, I have confirmed that this file aligns properly on this
> subject's native structural image, so I am not quite sure why the
> registration matrix may be off. Given that the reg.mni152.2mm.dat file
> reflects the transformation of the native struc to MNI, I wonder if I
> need
 to account for the reg file between the func data and the native
> struc?
 Can you please let me know what I may be doing incorrectly?
 As always, your help is very appreciated.
 Jacob
> Yea, i fixed this problem. I've attached a new version with the fix.
> doug
> On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Freesurfer Experts,
>> I am trying to view stats generated with FsFast in fslview/MNIspace,
 and
>> in doing so I have run mni152reg to generate the registration
> matrix.
 That said, mni152reg did not complete correctly and below I have
> pasted
 the terminal output:
>> Thu Jul 17 09:58:10 EDT 2014
>> setenv SUBJECTS_DIR
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
 /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
>> CD_cerv_pat4_sess1_recon
>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
 UTC
>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>> fslregister --mov
>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
 --s CD_cerv_pat4_sess1_recon --reg
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
 --dof 12
>> mkdir: cannot create directory
>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
 Permission denied
>> Log file is
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
 Thu Jul 17 09:58:11 EDT 2014
>> --mov
>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
 --s CD_cerv_pat4_sess1_recon --reg
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
 --dof 12
>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>> purkinje
>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
 UTC
>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>> nIters 1
>> --
>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
> mri_convert
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
 /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> mri_convert
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
 /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> niiWrite(): error opening file
>> /usr/pub

[Freesurfer] ERROR: dimension mismatch between input volume and seg

[Jon Wieser]

hi freesurfer experts

I am compiling the FA segment stats for several subject

I used
 mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp 
nearest --o fa.anat.mgh

then I used:

 mri_segstats --seg mri/wmparc.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stats


for some of my subjects, Iam getting the following error: 



 mri_segstats --seg mri/wmparc.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg mri/wmparc.mgz --ctab 
/Applications/freesurfer/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum 
dti/fa.stat 
sysname  Darwin
hostname psy-blackbird.ad.uwm.edu
machine  x86_64
user wieser
UseRobust  0
Loading mri/wmparc.mgz
Loading dti/fa.anat.mgh
ERROR: dimension mismatch between input volume and seg
  input 256 256 192
  seg   256 256 256



can you tell me how to fix this?

thanks
Jon


-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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Re: [Freesurfer] dwi_motion Tracula

[Anastasia Yendiki]

Hi Cat - Just install the update and run trac-all -qa. This will produce 
the motion measures. Check the tutorial for where to find the output.


a.y

On Mon, 21 Jul 2014, Cat Chong wrote:


Hello Anastasia,

 I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now,
I would like to use the command "dwi_motion" on my data. I have installed
the updates, but will I have to completely reprocess my data inducing steps
trac-all -prep, trace-all -bedp, and trac-all path in order to use
dwi_motion? 

cheers,
Cat

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Re: [Freesurfer] Repost | Re: mni152reg error

[jaco...@nmr.mgh.harvard.edu]

Thank you for the heads up Bruce.

> Hi Jacob
>
> Doug is on vacation for a couple of weeks, so you should probably repost
> in early August.
>
> cheers
> Bruce
> On Mon, 21 Jul 2014, jaco...@nmr.mgh.harvard.edu wrote:
>
>> Hello Doug,
>>
>> Ideally, I am trying to take subject tstat maps from FsFast (stable3
>> environment) and register these native structural space maps to the
>> MNI152_2mm standard brain.
>>
>> The t_000.bfloat file is what was generated relative to my contrast that
>> was set up in FsFast stable3. There are a series of these files ranging
>> from t_000.bfloat to t_029.bfloat and there are also these same named
>> files with a .hdr extension. t_000.bfloat is the file I designate when I
>> select an overlay within tkmedit.
>>
>> Your help sorting out this registration is very appreciated.
>>
>> Thank you,
>> Jacob
>>
>>
>>
 I'm not sure what you are trying to do, but that command line looks
>> like
 things are not set up properly. What is t_000.bfloat? (And why are you
>> using bfloats?)
 doug
 On 7/17/14 1:14 PM, jaco...@nmr.mgh.harvard.edu wrote:
> Hello again Doug,
> Thank you for sending the updated version of mri152reg. It ran
> without
>> error and generated the reg.mni152.2mm.dat registration matrix.
>> Unfortunately though, when I tried to apply the transformation to the
>> same
> subject's t_000.bfloat, the registration is not correct (command
> below).
> mri_vol2vol --inv --targ /.../t_000.bfloat --mov
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
>> /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a
>> positive note, I was able to load the output image and
> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed
> to be
> shifted too far anterior.
> With my next attempt, I used mri_convert to make the t_000.bfloat
> into a
> .mgz and than ran mri_vol2vol, but the same misalignment occurred
> (see
>> attached photo).
> Using tkmedit, I have confirmed that this file aligns properly on
> this
>> subject's native structural image, so I am not quite sure why the
>> registration matrix may be off. Given that the reg.mni152.2mm.dat file
>> reflects the transformation of the native struc to MNI, I wonder if I
>> need
> to account for the reg file between the func data and the native
>> struc?
> Can you please let me know what I may be doing incorrectly?
> As always, your help is very appreciated.
> Jacob
>> Yea, i fixed this problem. I've attached a new version with the fix.
>> doug
>> On 07/17/2014 10:35 AM, jaco...@nmr.mgh.harvard.edu wrote:
>>> Hello Freesurfer Experts,
>>> I am trying to view stats generated with FsFast in
>>> fslview/MNIspace,
> and
>>> in doing so I have run mni152reg to generate the registration
>> matrix.
> That said, mni152reg did not complete correctly and below I have
>> pasted
> the terminal output:
>>> Thu Jul 17 09:58:10 EDT 2014
>>> setenv SUBJECTS_DIR
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
>>> CD_cerv_pat4_sess1_recon
>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19
>>> 21:14:45
> UTC
>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>> fslregister --mov
>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
> --s CD_cerv_pat4_sess1_recon --reg
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
> --dof 12
>>> mkdir: cannot create directory
>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
> Permission denied
>>> Log file is
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
> Thu Jul 17 09:58:11 EDT 2014
>>> --mov
>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
> --s CD_cerv_pat4_sess1_recon --reg
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
> --dof 12
>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>>> purkinje
>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19
>>> 21:14:45
> UTC
>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>> nIters 1
>>> --
>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>> mri_convert
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>> mri_convert
>>> /cluster/ablood/1/AdjustedParadigm

[Freesurfer] Save-the-Date: Feb 12-13, 2015, Real-time Functional Imaging and Neurofeedback Conference, Gainesville, Florida

[Frank Scharnowski]

Dear Real-Time Functional Neuroimaging Community,

It is our pleasure to announce the conference on real-time Functional
Imaging and Neurofeedback (rtFIN) in Gainesville, Florida on February
12-13, 2015 at the University of Florida, hosted by Prof. Ranganatha
(Ranga) Sitaram.
This conference is the second iteration following the first conference on
rtfMRI neurofeedback held in Zurich in 2012.  We currently have four
keynote speakers:

Niels Birbaumer, University of Tuebingen
Eberhard Fetz, University of Washington
John Gabrieli, MIT
Mitsuo Kawato, ATR Japan

Please fill out the survey below if you're interested.  Website, venue,
registration and abstract submission information will be announced at a
later date on the rtfMRI email list.  Please sign up at the link below if
you'd like to be kept updated.

Survey link: https://www.surveymonkey.com/s/7NVVQZH

Best regards, your co-organizers,

Ranganatha Sitaram, University of Florida
Sven Haller, University of Geneva
Jarrod Lewis-Peacock, University of Texas at Austin
Frank Scharnowski, University of Geneva
Luke Stoeckel, Harvard University / National Institutes of Health
James Sulzer, University of Texas at Austin
Nikolaus Weiskopf, University College London


--
Dr. Frank Scharnowski, Lecturer
Swiss Institute of Technology Lausanne &
University of Geneva, Switzerland
+41 78 76 76 749
www.neurofeedback-research.org
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Re: [Freesurfer] [Fwd: LGI recon problem]

[angela . favaro]

thank you Marie!


>
> Hi Angela,
>
> Have you tried that:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
>
> You can look also in the release notes
> (http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using
> Matlab 2013.
>
> The issue will be corrected in the next FreeSurfer release.
>
> Let mw know if it doesn't work,
>
> Marie
>
>
>
> On Jul 19, 2014, at 1:56 AM, angela.fav...@unipd.it wrote:
>
>> Dear FS experts,
>> I had no answer to my question below (log was attached in my previous
>> mail)
>> The error repeated in different subjects and I do not know how to
>> overcome. Can anyone give me some help?
>>
>> Angela
>>
>>
>>
>> Hi all,
>> I had an error message while running LGI recon
>> I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with
>> the Image processing toolbox
>>
>> Any help is welcome. Thank you!
>> Angela
>>
>>
>> the error is:
>>
>> mesh_outer =
>>
>> vertices: [61278x3 double]
>>faces: [122552x3 double]
>>facesOfVertex: [61278x1 struct]
>>
>> preparing pial mesh structure ...
>> ...searching for mesh edges...done (315.30 sec).
>> ... creating path file for vertex 1 / 61278
>> area file for outer ROIs saved at 1
>> {Improper assignment with rectangular empty matrix.
>>
>> Error in dsearchn (line 79)
>>[d(i),t(i)] = min(sum((x-yi).^2,2));
>>
>> Error in mesh_vertex_nearest (line 29)
>> nearestIndex = dsearchn(vertices,points);
>>
>> Error in reorganize_verticeslist (line 28)
>>
>> [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
>>
>> Error in make_roi_paths (line 93)
>>reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer,
>> perim,
>>verticeslist, step);
>> }

>> ERROR:  make_roi_paths did not complete successfully!
>> Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug
>> 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
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>
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>



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Re: [Freesurfer] Diffusion analysis qs - gradient matrix

[Anastasia Yendiki]

It'd be nice if things were that simple, but!

Although the pre-processing is done with FSL tools, tractography is done 
with locally written code. Some gradient sets may appear to work with FSL, 
but they won't work for us. For example, some dicom converters may perform 
a L-R flip as preparation for feeding the gradient vectors into FSL. We 
need the unflipped vectors because, instead of flipping vectors, we 
convert both vectors and images to LAS orientation. This ensures that they 
work both for FSL and for us, and that you can view things correctly in 
both freeview and fslview, without the subject looking like it's hanging 
upside down from its bat cave or some such awkward arrangement.


In the end, the best way of knowing that the gradient table is correct is 
to run one example subject through and view the eigenvectors of the 
tensors as lines to see if they're pointing in the right direction. (Even 
though the tensors themselves aren't used for tractography, they're good 
for troubleshooting.)


On Mon, 21 Jul 2014, Harms, Michael wrote:



FS uses FSL tools under the hood, so you want to use the bvecs that are
rotated into the axes of the scan.

cheers,
-MH

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

From: Rotem Saar 
Reply-To: Freesurfer support list 
Date: Monday, July 21, 2014 1:54 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Diffusion analysis qs - gradient matrix

Dear freesurfer experts,

For diffusion analysis in freesurfer - I want to know which gradient matrix
freesurfer expects.

The thing is - when I look at the gradient matrix created using a MATLAB
script that reads the directions from the dicom header - I get one table,
but the bvecs file created in MRIconvert (for converting dicoms to nifti)
looks different.

This is the situation when an angle is applied during the acquisition of the
dMRI scans, which means that each subject has its own gradient matrix.

So my question is which table should I use for diffusion analysis in
freesurfer? The one that was created from the dicom header or the one
created for NIFTI format using MRIconvert ? 

Thanks

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211 

Israel

 





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[Freesurfer] DTImap

[Shantanu Ghosh]

Hi FS experts,

Is the DtiMap software (www.kennedykrieger.org) compatible with
Freesurfer/Tracula?

Thanks
Shantanu


-- 
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is stranger than we
can think. -Werner Heisenberg

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Re: [Freesurfer] Thickness measurements on longitudinal data set

[Martin Reuter]

Hi Bastian,

yes, lta are the (here rigid) transformations (dat files are deprecated).

you can use mri_convert -at 

or mri_vol2vol for mapping images.

I think, however, you are not interested in mapping images, but in ROI's 
on the surface.
You can do the following:

- draw/create the ROI in the base and use it on all the tp1.long.base 
etc.  (surfaces are in alignment).
- draw/create the ROI in the tp1.long.base and use it on all ohter time 
points directly (again this works as surfaces are in alignment)
- map things non-linearly with mri_surf2surf

You won't need the lta files for any of this.

Best, Martin

On 07/19/2014 01:45 AM, Bastian Cheng wrote:
> Thank you for clarification, Martin!
>
> Will do so and also try registration of  base >> TP1.long etc.
>
> Does FS create registration files (.dat) for this purpose
> automatically? I found some *.lta files in the /mri/transfers folder
> of the base image but am not sure how to apply them (maybe
> tkregister2?)
>
> best regards,
> Bastian
>
> On 18 July 2014 23:00, Martin Reuter  wrote:
>> Hi Bastian,
>>
>> use the longitudinal base for it. Also, once your ROI is in that space
>> you can simply apply it in each long as they are in the same space as
>> the base. The registration of base >> TP1.long etc. probably only
>> changes results very little.
>>
>> Best, Martin
>>
>>
>> On 07/18/2014 10:45 AM, Bastian Cheng wrote:
>>> Dear Freesurfer-Experts,
>>>
>>> I am currently trying to measure Cortical Thickness of a
>>> Volume-defined ROI in a patient measured at 4 timepoints.
>>>
>>> Basically, I am interested in a ROI resulting from fMRI activation
>>> measured on Timepoint 1.
>>> I would then like to get thickness values in the same ROI for all
>>> Timepoints 1-4.
>>>
>>> I have read the instructions here:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>>> this works.
>>>
>>> now, my idea is:
>>>
>>> ROI from TP1 >> register to base image of longit. recon. ("base")
>>> ROI from base >> TP1.long (from long recon)
>>> ROI from base >> TP2.long (from long recon)
>>> ROI from base >> TP3 long (from long recon)
>>> ROI from base >> TP4.long (from long recon)
>>>
>>> OR should I simpy map my ROI to fsaverage and project it back all
>>> individual timepoints?
>>> ROI from TP1 >> register to fsaverage
>>> ROI from fsaverage >> TP1 (not from long recon)
>>> ROI from fsaverage >> TP2 (not from long recon)
>>> etc.
>>>
>>> I understand that registration using the long. recon is more robust...
>>>
>>> Best regards,
>>> Bastian
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Martin Reuter, Ph.D.
>>
>> Instructor in Neurology
>> Harvard Medical School
>> Assistant in Neuroscience
>> Dept. of Radiology, Massachusetts General Hospital
>> Dept. of Neurology, Massachusetts General Hospital
>> Research Affiliate
>> Computer Science and Artificial Intelligence Lab,
>> Dept. of Electrical Engineering and Computer Science,
>> Massachusetts Institute of Technology
>>
>> A.A.Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, MA 02129
>>
>> Phone: +1-617-724-5652
>> Email:
>>  mreu...@nmr.mgh.harvard.edu
>>  reu...@mit.edu
>> Web  : http://reuter.mit.edu
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, Ph.D.

Instructor in Neurology
   Harvard Medical School
Assistant in Neuroscience
   Dept. of Radiology, Massachusetts General Hospital
   Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
   Computer Science and Artificial Intelligence Lab,
   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Freesurfer longitudinal GLM Design question

[Martin Reuter]

Hi Sal,

(please send to freesurfer list).

Take a look at the cross sectional qdec file. Years will be the average 
of 0 and 0.1 (= 0.05) for all subjects, so that may be the reason why it 
fails as a co-variate.
Age is also not time-varying, it is the average age per subject. The 
analysis at this point is completely cross sectional. You compare the 
atrophy rates (which were created in the first step with 
long_mris_slopes) across subjects. So everything is exactly the same as 
if you were running a cross sectional thickness analysis (except you 
look at thickness change instead of thickness now).


I don't know qdec so well. I am not sure if it can do a 
one-sample-group-mean. If not use mri_glmfit -osgm directly (there is 
also a wiki tutorial on how to run glmfit).


Best, Martin

On 07/21/2014 06:34 PM, Salil Soman wrote:

Thank you Martin.

I created a minimal longitudinal table (fsid, sid-base, age, and 
years). Years is either 0 (timepoint 1) or 0.1 (timepooint2).  I ran 
mri_slopes using this table, and made the cross table. I load qdec 
using the cross table, and have 2 continuous variables (years and 
age). I try to run an analysis using long.thickness-rate as the 
measure, with years as the covariate, and I keep getting an error 
screen "Error in Analyze: command failed: mri_glmfit --y "


If I use age as the covariate, the analysis works and I find no 
signficant differences (i.e. no relationship between thickness 
differences and age). Is there a way I can simply see if there are any 
thickness differences without using any covariates (so look at any 
areas of significant difference in thickness-rate) while correcting 
for multiple comparisons using fdr?


Thank you all your help.

Best wishes,

Sal


On Wed, Jul 9, 2014 at 6:13 AM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Sal,

it looks like you have everything together then. You can run your
QDEC analysis on the long.thickness-rate (or one of the percent
change files) to see where the rate is significantly different
from zero. Negative rate means thickness decrease.

You could also use glmfit with the one sample group mean (-osgm)
to test the same thing. There is a tutorial about that and also
about multiple comparison correction.

After you create your within subject rate (or percent change)
files. The whole thing turns into a simple cross-sectional
analysis (as if you are analyzing thickness in a cross sectional
design). Instead of thickness you now look at the 'change of
thickness'. If you are unsure how to use qdec or glmfit, look at
those tutorials first.

Best, Martin

On Jul 8, 2014, at 11:19 PM, Salil Soman mailto:salso...@stanford.edu>> wrote:


Hi,

I have been following the tutorial from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
and here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

And I believe I am running into problems with my GLM design.

I have a set of subjects with 2 time points each (all about 0.1
years apart).

All I wish to do is see what areas are significantly changed in
volume, after correcting for multiple comparisons (fdr or
montecarlo).

Could anyone suggest how I should setup the Design in QDEC?. I
have included years and age in my cross.qdec.table.dat file (made
from my long.qdec.table.dat file as described the tutorial, and
have the measures of long.thickness-avg, long.thickness-rate,
long.thickness-pc1 and long.thickness-spc avaialble (again from
the tutorial).

Any advice would be greatly appreciated.

Sal


-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652 
Email:
mreu...@nmr.mgh.harvard.edu 
reu...@mit.edu 
Web  : http://reuter.mit.edu 

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.




--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care 
System


--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical Sc

Re: [Freesurfer] error of color bar in freeview

[郝磊]

Dear Wang

   Ok. The sceenshot of the whole freeeview window was in the attachment. I
cann't send the screenshot to  freesurferATnmr.mgh.harvard.edu.

Thank you


2014-07-21 20:36 GMT+08:00 Ruopeng Wang :

> If you are running freeview on a Mac, you can ignore those “Invalid
> drawable” messages. Can you post a screenshot of the whole freeview window
> with the color bar issue?
>
> Best,
> Ruopeng
>
> On Jul 20, 2014, at 11:34 PM, 郝磊  wrote:
>
> > Dear experts
> >
> > when I open freeview, it report that "2014-07-21 11:22:28.453
> Freeview[10414:303] invalid drawable". Afterwards, when I click on Show
> Color Scale, the color bar was in black alternating with white. How should
> I solve this problem?
> >
> > Thank you
> >
> > Hao Lei (new learner of freesurfer)
> > ___
> > 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
> 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] DTImap

[Anastasia Yendiki]

Hi Shantanu - What do you mean by compatible? Are you trying to import an 
output from the other software into tracula or vice versa?

a.y

On Mon, 21 Jul 2014, Shantanu Ghosh wrote:

> Hi FS experts,
>
> Is the DtiMap software (www.kennedykrieger.org) compatible with
> Freesurfer/Tracula?
>
> Thanks
> Shantanu
>
>
>
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Re: [Freesurfer] Thickness measurements on longitudinal data set

[Bastian Cheng]

Sounds great, will try that!
Again, thank you very much for your help!
Bastian.

On 22 July 2014 01:53, Martin Reuter  wrote:
> Hi Bastian,
>
> yes, lta are the (here rigid) transformations (dat files are deprecated).
>
> you can use mri_convert -at 
>
> or mri_vol2vol for mapping images.
>
> I think, however, you are not interested in mapping images, but in ROI's
> on the surface.
> You can do the following:
>
> - draw/create the ROI in the base and use it on all the tp1.long.base
> etc.  (surfaces are in alignment).
> - draw/create the ROI in the tp1.long.base and use it on all ohter time
> points directly (again this works as surfaces are in alignment)
> - map things non-linearly with mri_surf2surf
>
> You won't need the lta files for any of this.
>
> Best, Martin
>
> On 07/19/2014 01:45 AM, Bastian Cheng wrote:
>> Thank you for clarification, Martin!
>>
>> Will do so and also try registration of  base >> TP1.long etc.
>>
>> Does FS create registration files (.dat) for this purpose
>> automatically? I found some *.lta files in the /mri/transfers folder
>> of the base image but am not sure how to apply them (maybe
>> tkregister2?)
>>
>> best regards,
>> Bastian
>>
>> On 18 July 2014 23:00, Martin Reuter  wrote:
>>> Hi Bastian,
>>>
>>> use the longitudinal base for it. Also, once your ROI is in that space
>>> you can simply apply it in each long as they are in the same space as
>>> the base. The registration of base >> TP1.long etc. probably only
>>> changes results very little.
>>>
>>> Best, Martin
>>>
>>>
>>> On 07/18/2014 10:45 AM, Bastian Cheng wrote:
 Dear Freesurfer-Experts,

 I am currently trying to measure Cortical Thickness of a
 Volume-defined ROI in a patient measured at 4 timepoints.

 Basically, I am interested in a ROI resulting from fMRI activation
 measured on Timepoint 1.
 I would then like to get thickness values in the same ROI for all
 Timepoints 1-4.

 I have read the instructions here:
 https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
 this works.

 now, my idea is:

 ROI from TP1 >> register to base image of longit. recon. ("base")
 ROI from base >> TP1.long (from long recon)
 ROI from base >> TP2.long (from long recon)
 ROI from base >> TP3 long (from long recon)
 ROI from base >> TP4.long (from long recon)

 OR should I simpy map my ROI to fsaverage and project it back all
 individual timepoints?
 ROI from TP1 >> register to fsaverage
 ROI from fsaverage >> TP1 (not from long recon)
 ROI from fsaverage >> TP2 (not from long recon)
 etc.

 I understand that registration using the long. recon is more robust...

 Best regards,
 Bastian
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> --
>>> Martin Reuter, Ph.D.
>>>
>>> Instructor in Neurology
>>> Harvard Medical School
>>> Assistant in Neuroscience
>>> Dept. of Radiology, Massachusetts General Hospital
>>> Dept. of Neurology, Massachusetts General Hospital
>>> Research Affiliate
>>> Computer Science and Artificial Intelligence Lab,
>>> Dept. of Electrical Engineering and Computer Science,
>>> Massachusetts Institute of Technology
>>>
>>> A.A.Martinos Center for Biomedical Imaging
>>> 149 Thirteenth Street, Suite 2301
>>> Charlestown, MA 02129
>>>
>>> Phone: +1-617-724-5652
>>> Email:
>>>  mreu...@nmr.mgh.harvard.edu
>>>  reu...@mit.edu
>>> Web  : http://reuter.mit.edu
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Martin Reuter, Ph.D.
>
> Instructor in Neurology
>Harvard Medical School
> Assistant in Neuroscience
>Dept. of Radiology, Massachusetts General Hospital
>Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>Computer Science and Artificial Intelligence Lab,
>Dept. of Electrical Engineering and Computer Science,
>Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: