[Freesurfer] Freeview screenshot automation questions

[Eric Xiuming ZHANG]

Dear FreeSurfer experts,

I understand that
> freeview -v brain.nii.gz -ss screenshot
takes the screenshots and quits the freeview.

Regarding this, I have the following two questions.

(1) Is it possible to suppress the redundant GUI flashing?

It is really a pain when many images are batch-processed, because the GUI keeps 
flashing up and closing.

(2) Is it possible to take multiple screenshots with one session?

I wish to screenshot multiple slices of one image. I have tried 
> freeview -v brain.nii.gz\
> -viewport sagittal -slice 80 127 127  -ss sag1 \
> -viewport sagittal -slice 127 127 127 -ss sag2 \
> -viewport sagittal -slice 156 127 127 -ss sag3 \
However, the session ends right after the first -ss, producing only one 
screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to get 
these 3 screenshots, but that is very inefficient.

Thank you very much for your help in advance!

Best regards,
Xiuming ZHANG (Eric)

Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) :: 
National University of Singapore (NUS)___
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[Freesurfer] exporting QDEC results

[elisa veronese]

Dear FreeSurfers,

can anybody tell me if there is a way to export results in form of table
(or text file) from the QDEC GUI after having performed analysis on
thickness, area, volume, etc etc... ?
I mean, is the infomation regarding the significant clusters saved in table
format?

Thank you.

Best,
Elisa

-- 
Elisa Veronese - PhD

*Research Unit on Brain Imaging and Neuropsychology (RUBIN)*


*Inter-University Center for Behavioral Neurosciences (ICBN)University of
Udine and University of Verona, ItalyICBN
Website: http://icbn.uniud.it/tiki-index.php
*
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[Freesurfer] mri_vol2surf

[Nicholas Heugel]

I looked over the documentation but can;t seem to find what I am looking
for.  How exactly does the function project the mdi data onto the surface?
 What method is it using to accomplish this, is it just projecting to the
nearest neighbor or is there something more complex occurring.  I ask
because I just want to make sure I completely understand what every step in
my analysis is doing and not have it be a blackbox that I put data in and
it gives me stuff out.  Thanks for your help.

Nicholas
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[Freesurfer] quick quality assessment for MPRAGE images

[Wegbreit, Ezra]

Dear Freesurfer Users,

I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio
scanner that I would like to run through recon-all to get cortical
thickness values.  However, some of the MPRAGE scans are contaminated by
subject motion, but the extent of this varies from scan to scan.   Is there
a quick automated way to assess whether each MPRAGE is high-quality enough
to bother with running through recon-all?

Thanks!
Ezra
*___*
*Ezra Wegbreit, PhD*
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org

*___*
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[Freesurfer] DWI questions

[Gabriel Gonzalez Escamilla]

Dear Freesurfer and DTI experts,I will start some analyses with DWI data, but I have some doubts about it:1) I have data with 5 different acquisition protocols, so, I'm not sure if the standard pre-processing protocol (like eddy-current compensations the reorientation of the vectors and the intra-subject registration) can be applied to all images equally or if I do need to set any specific parameters for each acquisition protocol?2) Does your method have any tool to check that the vectors are good, before or after fitting the tensors?Many thanks in advanced,Gabriel
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Re: [Freesurfer] mri_vol2surf

[Bruce Fischl]

Hi Nicholas

mri_vol2surf has options that lets you control its behavior. It can do 
various types of sampling (e.g. averaging within the cortical ribbon, point 
sampling at a specified distance or percentage, etc)


cheers
Bruce

On Thu, 18 Sep 
2014, Nicholas Heugel wrote:



I looked over the documentation but can;t seem to find what I am looking
for.  How exactly does the function project the mdi data onto the surface?
 What method is it using to accomplish this, is it just projecting to the
nearest neighbor or is there something more complex occurring.  I ask
because I just want to make sure I completely understand what every step in
my analysis is doing and not have it be a blackbox that I put data in and it
gives me stuff out.  Thanks for your help.
Nicholas

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[Freesurfer] problem with mris_preproc

[Lars M. Rimol]

Hi,

I get the following error message when running mris_preproc, and I'm
wondering what file is it looking for?:

Reading curvature file
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
MRISreadCurvature: could not open
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
No such file or directory
ERROR: reading curvature file

This subject, 007, seems to have all the files it should:

[rimol @ ~/subjects/long/long_v0v2_amd]$ ls
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf
lh.area   lh.inflated.H  lh.pial_lgi
lh.smoothwm.K1.crv  lh.thicknessrh.avg_curv
rh.orig rh.smoothwm.BE.crv  rh.smoothwm.S.crv  rh.white
lh.area.mid   lh.inflated.K  lh.pial-outer-smoothed
lh.smoothwm.K2.crv  lh.volume   rh.curv
rh.orig_pialrh.smoothwm.C.crv   rh.sphere
lh.area.pial  lh.jacobian_white  lh.smoothwm
lh.smoothwm.K.crv   lh.w-g.pct.mgh  rh.curv.pial
rh.orig_white   rh.smoothwm.FI.crv  rh.sphere.reg
lh.avg_curv   lh.origlh.smoothwm.BE.crv
lh.smoothwm.S.crv   lh.whiterh.inflated
rh.pial rh.smoothwm.H.crv   rh.sulc
lh.curv   lh.orig_pial   lh.smoothwm.C.crv
lh.sphere   rh.area rh.inflated.H
rh.pial_lgi rh.smoothwm.K1.crv  rh.thickness
lh.curv.pial  lh.orig_white  lh.smoothwm.FI.crv
lh.sphere.reg   rh.area.mid rh.inflated.K
rh.pial-outer-smoothed  rh.smoothwm.K2.crv  rh.volume
lh.inflated   lh.piallh.smoothwm.H.crv
lh.sulc rh.area.pialrh.jacobian_white
rh.smoothwm rh.smoothwm.K.crv   rh.w-g.pct.mgh


Here's the entire output:
--
 [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long
~/long_qdec_FINAL2_w33_model1.dat  --target fsaverage --hemi lh --meas area
--area pial --out test_pial.mgh
nsubjects = 172
INFO: turning on jacobican correction
tmpdir is ./tmp.mris_preproc.11745
/cluster/home/rimol/subjects/long/long_v0v2_amd
Log file is test_pial.mris_preproc.log
Thu Sep 18 17:23:19 CEST 2014
setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd
cd /cluster/home/rimol/subjects/long/long_v0v2_amd
/cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long
/usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage
--hemi lh --meas area --area pial --out test_pial.mgh

Linux login-0-1.local 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
$Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
tmpdir is ./tmp.mris_preproc.11745
Src lh sphere.reg
Trg lh sphere.reg



---
#@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 --
---
mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg
sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
--tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial
--jac --sfmt curv --noreshape --no-cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = 007v2.long.007_base
srcval = (null)
srctype= curv
trgsubject = fsaverage
trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg
Loading source data
Reading curvature file
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
MRISreadCurvature: could not open
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
No such file or directory
ERROR: reading curvature file


-- 
yours,

Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
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Re: [Freesurfer] quick quality assessment for MPRAGE images

[Harms, Michael]

Hi Ezra,
I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion.  It is time consuming, but you have to put eyes on the
 data.


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: , Ezra 
Reply-To: Freesurfer support list 
Date: Thursday, September 18, 2014 9:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] quick quality assessment for MPRAGE images






Dear Freesurfer Users,


I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values.  However, some of the MPRAGE scans are
 contaminated by subject motion, but the extent of this varies from scan to scan.   Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?  


Thanks!
Ezra


___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital 
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org                                                          
                                                                 
___














 



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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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[Freesurfer] Scatter plot from mri_glmfit analyses

[Celine Louapre]

Hi Doug and FS team

I did glm analyses using mri_glmfit, and I was trying to plot the
individual values in the population for a specific significant cluster.
However I am not sure how to extract individual values from the entire
cluster. (note that the concatenated surface used as input for the glm
contains some 0 values that I want to exclude from the mean value of the
cluster).
Is there a way to build a label from a specific significant cluster?

Then, I was thinking about using mri_segstats --avgwf on the 4D
concatenated file to get the average of the region but is there a way to
not include 0 values?

And then I was also interested in getting the correlation coefficient from
that same cluster, so maybe the script below would be helpful for that but
I could not open it.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m

Thanks so much for your help
Best
Celine

On 05/31/2012 06:09 AM, Knut J Bjuland wrote:
> Hi
>
> I am trying to calculate correlation coefficient using freesurfer GLM
> for associations between volumes and IQ. I found this ealier answar,
> but the matlab script but the link appear to be dead.
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html
>
> Best regards
>
> Knut J
>
>
>
>
> ___
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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
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Re: [Freesurfer] quick quality assessment for MPRAGE images

[Chris Watson]

Try out Freesurfer's QAtools. It still isn't "automatic", but you can 
get a bunch of screenshots and view them all on an html page.


On 09/18/2014 11:42 AM, Harms, Michael wrote:


Hi Ezra,
I'd love to hear otherwise if someone has established some robust 
signal processing approaches to do this automatically, but I'm not 
aware of any good reliable ways to do this in a automated fashion.  It 
is time consuming, but you have to put eyes on the data.


cheers,
-MH

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

From: , Ezra >
Reply-To: Freesurfer support list >

Date: Thursday, September 18, 2014 9:56 AM
To: "freesurfer@nmr.mgh.harvard.edu 
" 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Subject: [Freesurfer] quick quality assessment for MPRAGE images

Dear Freesurfer Users,

I have a large number of T1 MPRAGE scans collected on a 3T Siemens 
Trio scanner that I would like to run through recon-all to get 
cortical thickness values.  However, some of the MPRAGE scans are 
contaminated by subject motion, but the extent of this varies from 
scan to scan.   Is there a quick automated way to assess whether each 
MPRAGE is high-quality enough to bother with running through recon-all?


Thanks!
Ezra
*___*
*Ezra Wegbreit, PhD*
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org 
*___*



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the contents of this information is strictly prohibited. If you have 
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Re: [Freesurfer] quick quality assessment for MPRAGE images

[Harms, Michael]

Yes, that can be helpful.  As a caution though, the overall quality may appear fine, but things like topology correction errors can still occur and will be quite local.  Thus, they would easily be missed if the density of your screenshots isn't high enough.
  Personally, I find it only marginally more time consuming to navigate through the entire set of slices in 'tkmedit', and the quality of your QA will be better.


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: Chris Watson 
Reply-To: Freesurfer support list 
Date: Thursday, September 18, 2014 2:00 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] quick quality assessment for MPRAGE images




Try out Freesurfer's QAtools. It still isn't "automatic", but you can get a bunch of screenshots and view them all on an html page.


On 09/18/2014 11:42 AM, Harms, Michael wrote:





Hi Ezra,
I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion.  It is time consuming, but you have to put eyes on the
 data.


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: , Ezra 
Reply-To: Freesurfer support list 
Date: Thursday, September 18, 2014 9:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] quick quality assessment for MPRAGE images






Dear Freesurfer Users,


I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values.  However, some of the MPRAGE scans are
 contaminated by subject motion, but the extent of this varies from scan to scan.   Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?  


Thanks!
Ezra


___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital 
Department of Psychiatry and Human Behavior
Brown University Medical School
(401) 432-1615
ezra_wegbr...@brown.edu  (preferred)
ewegbr...@lifespan.org                                  
                                                                                         
___












 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.

 
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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

[Douglas N Greve]

When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? 
Does it overlay correctly on the T1.mgz?
doug

On 09/14/2014 11:40 PM, Salil Soman wrote:
> Thank you Doug.  I am having trouble with extracting statistics using 
> this method.
>
> I am able to use bbregister to get a transformation that registers the 
> PD image of the ASL to the T1. I then used this transformation matrix 
> to register the CBF map for the ASL study into the T1.mgz space. 
> Checking the images, the registration looked reasonable. However, when 
> I try to extract the values from the registered image using the vois 
> from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values.
>
> *The command I ran is:*
>
> mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab 
> $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz 
> --sum SUBJECT_ID_ASL.stats --seg-erode 1
>
> *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:*
>
> mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest 
> --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg
>
> (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same 
> folder).
>
> *for which SUBJECT_ID.dat was generated by running the code:*
>
> bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg 
> SUBJECT_ID.dat --t1 --init-fsl
>
> Thank you for your consideration of this question.
>
> Best wishes,
>
> Salil Soman, MD, MS
>
>
>
>
> On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> yep, you can use it for anything.
> doug
>
>
> On 9/14/14 12:52 PM, Salil Soman wrote:
>> Dear Doug,
>>
>> Thank you again for this email. Do you think it is possible to
>> use this method for ASL images as well? If so, how would you
>> change the options?
>>
>> Best wishes,
>>
>> Salil Soman, MD, MS
>>
>> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> On 5/25/13 1:39 PM, Salil Soman wrote:
>>> Thank you Doug.
>>>
>>>  Just so I am clear - is the anatomical the nifti T1.mgz or
>>> is it a different file. From your email I gather should do
>>> the following:
>>>
>>> *1)  Use bbregister to register the lowb image to the
>>> anatomical. This creates a registration matrix.*
>>>
>>> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg
>>> register.dat
>> That is right, but add --t2 (since it is t2 weighted).
>>>
>>> *2) Use mri_vol2vol and the registration to map the ADC map
>>> to the anatomical*
>>> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o 
>>> $vol2diff --reg $outdir/register.dat --no-save-reg
>> Use the ADC as the moveable (not lowb, but use the lowb for
>> bbregister). The target volume should be the T1.mgz (or any
>> conformed volume). The output will be the adc in the
>> anatomical space (not sure why you call it vol2diff).
>>> *3) use mri_segstats to extract the values*
>>> *mri_segstats*  --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz 
>>> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats
>> The input would be the adc volume mapped the anatomical
>> space. I would use WMParcStatsLUT.txt or else you'll get a
>> billion different areas not represented in wmparc. You may
>> also want to add "--seg-erode 1" to erode the segmentations
>> by a voxel. This helps to prevent partial voluming.
>>
>> doug
>>
>>
>>> Where lowb.nii is the other MRI tissue sequence I am
>>> analyzing (e.g. ADC), $vol2diff is the output image of the
>>> registration, and fa.stats will be my output stats table?
>>>
>>> I suspect there is part of the syntax for these tools I do
>>> not understand. Also, what input would $vol be?
>>>
>>> Best wishes,
>>>
>>> Sal
>>>
>>>
>>> On Sat, May 25, 2013 at 10:06 AM, Douglas Greve
>>> >> > wrote:
>>>
>>>
>>> Hi Sal, yes you can. Use bbregister to register the lowb
>>> image to the anatomical. This creates a registration
>>> matrix. Use mri_vol2vol and the registration to map the
>>> ADC map to the anatomical, then use mri_segstats to
>>> extract the values
>>> doug
>>>
>>> ps. Please post questions to the FS list instead of us
>>> directly so that others can benefit and it gets
>>> archived. thanks!
>>>
>>>
>>>
>>> On 5/25/13 1:03 PM, Salil Soman wrote:
>>>
>>> Dear Dr. Greve,
>>>
>>> Is it possible to register a nonstructural MR
>>> sequences (e.g. an ADC map) with the aseg.mgz file
>>> (or aparc+aseg.mgz file, etc) and then, 

Re: [Freesurfer] mincost bb_register

[Douglas N Greve]

0.5 is pretty good for fMRI. If it looks good visually, then I would not 
worry about it further
doug

On 09/17/2014 09:25 AM, lorenzo pasquini wrote:
> Dear Freesurfer users,
> I have used the command bb_register to automatically register raw fMRI 
> data on the anatomy. The output looks visually fine, however the 
> mincost file gives me values around 0.5 for my subjects. Is this range 
> acceptable? Does anybody has a hint on how the registration could be 
> optimized?
> I use init-fsl and --bold as contrast in my bbregister command.
> Best,
>
> Lorenzo
>
>
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gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Pial Surface Incorrect For Native T1

[Douglas N Greve]

Can you get it to display correctly on the pial surface in conformed space?

On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
> Hello Freesurfer experts,
>
> I am having a tough time getting my pial surfaces into the correct 
> anatomical space. I work with ECoG Patients, so we have pre-implant 
> high resolution T1s (GE SPGR), and post-implant high resolution CTs 
> that show the location of ECoG electrodes within the patient's skull. 
> Our goal: display ECoG electrodes in their correct positions on the 
> patient's native pial surface.
>
> Right now, my pipeline works like this:
> -ACPC align the T1, leave it in LAS orientation.
> -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu
> -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 space
> -plot the electrodes on the resultant .pial surface from freesurfer
>
> The problem is, I can definitely tell that the position of the pial 
> mesh is off (probably by 10 millimeters or so), as the electrodes 
> (which have the correct coordinates from the T1 correg, confirmed 
> visually by overlaying the CT on T1) are not in their correct 
> positions on the mesh. Likewise, DTI fibers reconstructed from EPIs 
> correctly corregistered to the T1 also appear off position within the 
> .pial mesh.
>
> Here is what I have tried:
>
> compute the transform from .pial to .pial.native as suggested on 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>
> tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat 
> --noedit --regheader
> mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval 
> lh.pial.native --tval-xyz --hemi lh --s subjectname
> This results in a mesh that is flipped (left is right) and rotated 
> such that anterior is inferior (frontal cortex is pointing downward). 
> The mesh appears this way when plotted in any viewer besides 
> freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation 
> in freeview. Replacing orig.mgz with the original T1.nii in the 
> command above produces the opposite effect, freeview plots the 
> orientation wrong, and any other viewer plots the Mesh oriented 
> correctly, and the mesh appears to be identical to the originally 
> output .pial mesh (electrodes are still wrong).
>
> Any help in pin pointing what is going wrong here would be greatly 
> appreciated. I have a feeling it has something to do with the mesh 
> being in surface RAS and the original T1 being in LAS.
>
> Thanks a bunch,
> -Zack
>
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] exporting QDEC results

[Douglas N Greve]

The easiest way is to run mri_glmfit-sim from the command line on the 
QDEC output folder. It will automatically correct for multiple 
comparisons and create tables. See the tutorial (and other posts along 
this line).
doug

On 09/18/2014 05:56 AM, elisa veronese wrote:
> Dear FreeSurfers,
>
> can anybody tell me if there is a way to export results in form of 
> table (or text file) from the QDEC GUI after having performed analysis 
> on thickness, area, volume, etc etc... ?
> I mean, is the infomation regarding the significant clusters saved in 
> table format?
>
> Thank you.
>
> Best,
> Elisa
>
> -- 
> Elisa Veronese - PhD
>
> /
> Research Unit on Brain Imaging and Neuropsychology (RUBIN)
> /
> /
> Inter-University Center for Behavioral Neurosciences (ICBN)
> University of Udine and University of Verona, Italy
> /
> ICBN Website:Â http://icbn.uniud.it/tiki-index.php
> /
>
> /
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

For each vertex, the col, row, slice in the mdi is computed based on the 
registration. The value from this voxel is extracted; the default is 
nearest neighbor but this can be changed with --interp trilin
doug

On 09/18/2014 10:52 AM, Nicholas Heugel wrote:
> I looked over the documentation but can;t seem to find what I am 
> looking for.  How exactly does the function project the mdi data onto 
> the surface?  What method is it using to accomplish this, is it just 
> projecting to the nearest neighbor or is there something more complex 
> occurring.  I ask because I just want to make sure I completely 
> understand what every step in my analysis is doing and not have it be 
> a blackbox that I put data in and it gives me stuff out.  Thanks for 
> your help.
>
> Nicholas
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] problem with mris_preproc

[Douglas N Greve]

This is a bug in mris_preproc. A work-around is to add --srcfmt mgh as 
the last argument. In the mean time I'll fix mris_preproc

doug

On 09/18/2014 11:32 AM, Lars M. Rimol wrote:
> Hi,
>
> I get the following error message when running mris_preproc, and I'm 
> wondering what file is it looking for?:
>
> Reading curvature file 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
> MRISreadCurvature: could not open 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
> No such file or directory
> ERROR: reading curvature file
>
> This subject, 007, seems to have all the files it should:
>
> [rimol @ ~/subjects/long/long_v0v2_amd]$ ls 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf
> lh.area   lh.inflated.H  lh.pial_lgi lh.smoothwm.K1.crv  
> lh.thicknessrh.avg_curv rh.orig 
> rh.smoothwm.BE.crv  rh.smoothwm.S.crv rh.white
> lh.area.mid   lh.inflated.K  lh.pial-outer-smoothed 
> lh.smoothwm.K2.crv  lh.volume   rh.curv rh.orig_pial
> rh.smoothwm.C.crv   rh.sphere
> lh.area.pial  lh.jacobian_white  lh.smoothwm lh.smoothwm.K.crv   
> lh.w-g.pct.mgh  rh.curv.pial rh.orig_white   
> rh.smoothwm.FI.crv  rh.sphere.reg
> lh.avg_curv   lh.origlh.smoothwm.BE.crv 
> lh.smoothwm.S.crv   lh.whiterh.inflated 
> rh.pial rh.smoothwm.H.crv   rh.sulc
> lh.curv   lh.orig_pial   lh.smoothwm.C.crv lh.sphere   
> rh.area rh.inflated.H rh.pial_lgi 
> rh.smoothwm.K1.crv  rh.thickness
> lh.curv.pial  lh.orig_white  lh.smoothwm.FI.crv 
> lh.sphere.reg   rh.area.mid rh.inflated.K 
> rh.pial-outer-smoothed  rh.smoothwm.K2.crv  rh.volume
> lh.inflated   lh.piallh.smoothwm.H.crv lh.sulc 
> rh.area.pialrh.jacobian_white rh.smoothwm 
> rh.smoothwm.K.crv   rh.w-g.pct.mgh
>
>
> Here's the entire output:
> --
>  [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long 
> ~/long_qdec_FINAL2_w33_model1.dat  --target fsaverage --hemi lh --meas 
> area --area pial --out test_pial.mgh
> nsubjects = 172
> INFO: turning on jacobican correction
> tmpdir is ./tmp.mris_preproc.11745
> /cluster/home/rimol/subjects/long/long_v0v2_amd
> Log file is test_pial.mris_preproc.log
> Thu Sep 18 17:23:19 CEST 2014
> setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd
> cd /cluster/home/rimol/subjects/long/long_v0v2_amd
> /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc 
> --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat 
> --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh
>
> Linux login-0-1.local 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
> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> tmpdir is ./tmp.mris_preproc.11745
> Src lh sphere.reg
> Trg lh sphere.reg
>
>
>
> ---
> #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 --
> ---
> mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh 
> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh 
> --trgsurfreg sphere.reg --tval 
> ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial 
> --jac --sfmt curv --noreshape --no-cortex
> Source registration surface changed to sphere.reg
> Target registration surface changed to sphere.reg
> srcsubject = 007v2.long.007_base
> srcval = (null)
> srctype= curv
> trgsubject = fsaverage
> trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg
> Loading source data
> Reading curvature file 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
> MRISreadCurvature: could not open 
> /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
> No such file or directory
> ERROR: reading curvature file
>
>
> -- 
> yours,
>
> Lars M. Rimol, PhD
> St. Olavs Hospital
> Trondheim,
> Norway
>
>
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Phone Number: 61

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

[Douglas N Greve]

Have you run mri_glmfit-sim? It will create labels (ie, annotations) of 
the clusters as well as run mri_segstats to get means in each cluster 
for each subject. Try that link now
doug

On 09/18/2014 12:15 PM, Celine Louapre wrote:
> Hi Doug and FS team
>
> I did glm analyses using mri_glmfit, and I was trying to plot the
> individual values in the population for a specific significant cluster.
> However I am not sure how to extract individual values from the entire
> cluster. (note that the concatenated surface used as input for the glm
> contains some 0 values that I want to exclude from the mean value of the
> cluster).
> Is there a way to build a label from a specific significant cluster?
>
> Then, I was thinking about using mri_segstats --avgwf on the 4D
> concatenated file to get the average of the region but is there a way to
> not include 0 values?
>
> And then I was also interested in getting the correlation coefficient from
> that same cluster, so maybe the script below would be helpful for that but
> I could not open it.
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m
>
> Thanks so much for your help
> Best
> Celine
>
> On 05/31/2012 06:09 AM, Knut J Bjuland wrote:
>> Hi
>>
>> I am trying to calculate correlation coefficient using freesurfer GLM
>> for associations between volumes and IQ. I found this ealier answar,
>> but the matlab script but the link appear to be dead.
>>
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html
>>
>> Best regards
>>
>> Knut J
>>
>>
>>
>>
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] displaying a single label from aparc in tksurfer

[Douglas N Greve]

The only way I know is to break the annotation into labels 
(mri_annotation2label), then creating a new annotation with only the 
labels you want (mris_label2annot). If you only want one label, then you 
don't need to create a new annotation
doug

On 09/18/2014 03:11 PM, Maria Kharitonova wrote:
> Hi all,
>
> I would like make a figure where only 1 or 2 regions (labels from the 
> aparc.a2009s atlas are displayed). I know how to turn on/off all 
> labels, but how do I only display 1? (e.g. rh_G_and_S_cingul-Mid-Ant). 
> Turning off all but the one I need is tedious and I was wondering if 
> there was a better way.
>
> I was able to change the color of the ACC region I needed to make it 
> more apparent (see attached), but was looking for a way that the white 
> region is only label that is shown. I looked through the archives 
> but could not find anything.
>
> Thanks in advance for the help!
> Best,
>
> Maria
>
> --
> Maria Kharitonova, PhD
> Research Assistant Professor
> Department of Medical Social Sciences
> Northwestern University Feinberg School of Medicine
> 625 N. Michigan Ave, Suite 2700
> Chicago, IL 60611
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> Email: maria.khariton...@northwestern.edu 
> 
>
>
>
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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

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

[Salil Soman]

Dear Doug,

Thank you for your email.

The registration overlap looks reasonable. Thank you for considering this
question.

Best wishes,

Sal

On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve  wrote:

>
> When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does
> it overlay correctly on the T1.mgz?
> doug
>
> On 09/14/2014 11:40 PM, Salil Soman wrote:
>
>> Thank you Doug.  I am having trouble with extracting statistics using
>> this method.
>>
>> I am able to use bbregister to get a transformation that registers the PD
>> image of the ASL to the T1. I then used this transformation matrix to
>> register the CBF map for the ASL study into the T1.mgz space. Checking the
>> images, the registration looked reasonable. However, when I try to extract
>> the values from the registered image using the vois from aparc+aseg.mgz,
>> and the FreeSurferColorLUT I get all 0 values.
>>
>> *The command I ran is:*
>>
>> mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab
>> $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz
>> --sum SUBJECT_ID_ASL.stats --seg-erode 1
>>
>> *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:*
>>
>> mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest
>> --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg
>>
>> (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same
>> folder).
>>
>> *for which SUBJECT_ID.dat was generated by running the code:*
>>
>> bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg
>> SUBJECT_ID.dat --t1 --init-fsl
>>
>> Thank you for your consideration of this question.
>>
>> Best wishes,
>>
>> Salil Soman, MD, MS
>>
>>
>>
>>
>> On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve > > wrote:
>>
>> yep, you can use it for anything.
>> doug
>>
>>
>> On 9/14/14 12:52 PM, Salil Soman wrote:
>>
>>> Dear Doug,
>>>
>>> Thank you again for this email. Do you think it is possible to
>>> use this method for ASL images as well? If so, how would you
>>> change the options?
>>>
>>> Best wishes,
>>>
>>> Salil Soman, MD, MS
>>>
>>> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve
>>> mailto:gr...@nmr.mgh.harvard.edu>>
>>> wrote:
>>>
>>>
>>> On 5/25/13 1:39 PM, Salil Soman wrote:
>>>
 Thank you Doug.

  Just so I am clear - is the anatomical the nifti T1.mgz or
 is it a different file. From your email I gather should do
 the following:

 *1)  Use bbregister to register the lowb image to the
 anatomical. This creates a registration matrix.*

 bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg
 register.dat

>>> That is right, but add --t2 (since it is t2 weighted).
>>>

 *2) Use mri_vol2vol and the registration to map the ADC map
 to the anatomical*
 mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest
 --o $vol2diff --reg $outdir/register.dat --no-save-reg

>>> Use the ADC as the moveable (not lowb, but use the lowb for
>>> bbregister). The target volume should be the T1.mgz (or any
>>> conformed volume). The output will be the adc in the
>>> anatomical space (not sure why you call it vol2diff).
>>>
 *3) use mri_segstats to extract the values*
 *mri_segstats*  --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz
 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum
 fa.stats

>>> The input would be the adc volume mapped the anatomical
>>> space. I would use WMParcStatsLUT.txt or else you'll get a
>>> billion different areas not represented in wmparc. You may
>>> also want to add "--seg-erode 1" to erode the segmentations
>>> by a voxel. This helps to prevent partial voluming.
>>>
>>> doug
>>>
>>>
>>>  Where lowb.nii is the other MRI tissue sequence I am
 analyzing (e.g. ADC), $vol2diff is the output image of the
 registration, and fa.stats will be my output stats table?

 I suspect there is part of the syntax for these tools I do
 not understand. Also, what input would $vol be?

 Best wishes,

 Sal


 On Sat, May 25, 2013 at 10:06 AM, Douglas Greve
 >>> > wrote:


 Hi Sal, yes you can. Use bbregister to register the lowb
 image to the anatomical. This creates a registration
 matrix. Use mri_vol2vol and the registration to map the
 ADC map to the anatomical, then use mri_segstats to
 extract the values
 doug

 ps. Please post questions to the FS list instead of us
 directly so that others can bene

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

[Douglas N Greve]

Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you 
force it to report hundreds (or thousands) of ROIs which are not 
represented in the aparc+aseg.mgz. Also, try removing --seg-erode.

On 09/18/2014 04:43 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email.
>
> The registration overlap looks reasonable. Thank you for considering 
> this question.
>
> Best wishes,
>
> Sal
>
> On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look
> reasonable? Does it overlay correctly on the T1.mgz?
> doug
>
> On 09/14/2014 11:40 PM, Salil Soman wrote:
>
> Thank you Doug.  I am having trouble with extracting
> statistics using this method.
>
> I am able to use bbregister to get a transformation that
> registers the PD image of the ASL to the T1. I then used this
> transformation matrix to register the CBF map for the ASL
> study into the T1.mgz space. Checking the images, the
> registration looked reasonable. However, when I try to extract
> the values from the registered image using the vois from
> aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values.
>
> *The command I ran is:*
>
> mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz
> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1
>
> *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:*
>
> mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp
> nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat
> --no-save-reg
>
> (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the
> same folder).
>
> *for which SUBJECT_ID.dat was generated by running the code:*
>
> bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg
> SUBJECT_ID.dat --t1 --init-fsl
>
> Thank you for your consideration of this question.
>
> Best wishes,
>
> Salil Soman, MD, MS
>
>
>
>
> On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> yep, you can use it for anything.
> doug
>
>
> On 9/14/14 12:52 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you again for this email. Do you think it is
> possible to
> use this method for ASL images as well? If so, how
> would you
> change the options?
>
> Best wishes,
>
> Salil Soman, MD, MS
>
> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve
>  
>  >> wrote:
>
>
> On 5/25/13 1:39 PM, Salil Soman wrote:
>
> Thank you Doug.
>
>  Just so I am clear - is the anatomical the
> nifti T1.mgz or
> is it a different file. From your email I
> gather should do
> the following:
>
> *1)  Use bbregister to register the lowb image
> to the
> anatomical. This creates a registration matrix.*
>
> bbregister -s SUBJECTNAME --mov lowb.nii
> --initfsl --reg
> register.dat
>
> That is right, but add --t2 (since it is t2 weighted).
>
>
> *2) Use mri_vol2vol and the registration to
> map the ADC map
> to the anatomical*
> mri_vol2vol --mov lowb.nii --targ $vol --inv
> --interp nearest --o $vol2diff --reg
> $outdir/register.dat --no-save-reg
>
> Use the ADC as the moveable (not lowb, but use the
> lowb for
> bbregister). The target volume should be the
> T1.mgz (or any
> conformed volume). The output will be the adc in the
> anatomical space (not sure why you call it vol2diff).
>
> *3) use mri_segstats to extract the values*
> *mri_segstats*  --seg
> $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab
> $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii
> --sum fa.stats
>
> The input would be the adc volume mapped the
> anatomical
> space. I would use WMParcStatsLUT.txt or else
> you'll g

Re: [Freesurfer] displaying a single label from aparc in tksurfer

[Daniel Carey]

Hi Maria,

You can display a single label (or labels) in tksurfer by loading the aparc 
annotation onto fsaverage; then, simply click on the label you're interested 
in, and click File, then Label, and Save Selected Label. This will let you save 
out a single label from aparc, which can these easily be loaded onto fsaverage 
on its own. You can of course also overlay multiple labels in tksurfer that 
you've saved out in this way (and naturally change colour schemes if you're so 
inclined).

Best,
Dan

---


On 18 Sep 2014, at 22:03, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

> displaying a single label from aparc in tksurfer

Daniel Carey
Marie Curie Ph.D. Fellow,
Centre for Brain and Cognitive Development,
32 Torrington Sq.,
London WC1E 7HX

email: d.ca...@bbk.ac.uk
web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey



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[Freesurfer] Map both hemisphere to lh of fsaverage_sym

[ting xu]

Dear FreeSurfers,

I have data has been recon-all analyzed. I would like to compare the
symmetry of function/structure property between LH and RH, such as cortical
thickness. I already know that the vertices in the left hemisphere are not
correspond to vertices in the right hemisphere. I would like to know the
exactly symmetric vertex for both hemisphere. Thus the question is, how can
I register both hemisphere to one hemisphere of fsaverage_sym, then compare
them?

I followed the instruction:

xhemireg --s sub001
surfreg --s sub001--t fsaverage_sym --lh
surfreg --s sub001/xhemi --t fsaverage_sym --lh --xhemi

then here is the error:


MRISread(/data/sub001/xhemi/xhemi/surf/lh.sphere): could not open file

No such file or directory

mris_register: could not read surface file
/data/sub001/xhemi/xhemi/surf/lh.sphere

No such file or directory

Thank you in advance for any suggestion!
Regards,

Ting
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