Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

[Douglas Greve]

On 9/29/15 10:59 AM, chenhf_uestc wrote:

Dear Freesurfer experts,
In the stats folder of subject in the SUBJECTS_DIR, I found the files 
of lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical 
results belong to two different atlas? *Because the values and brain 
regions are different in these two files.*
In these two files, I found the command "mris_anatomical_stats -mgz 
-cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a 
../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" 
*_and_* "mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label 
-f ../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab NC058 lh white".
So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats, 
respectively. Right?

Correct.
However, when I open these two atlas (attached aparc.annot.ctab and 
aparc.annot.DKTatlas40.ctab), I found the contents are same. In 
addition, I would really want to know that the value in the 
aparc.annot.ctab. For ex.   1  bankssts 25 100 400; what does the 
values mean? 25 100 40 0
You are looking at the color table. 25 100 40 is the red-green-blue 
values for when it is displayed. The .stats file should be different

Best,
Feng


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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

[andrea cristina Lima]

Em 30/09/2015 11:30, "andrea cristina Lima" 
escreveu:

> I got the error below. Could you help me? I've already check the dti file
> and it seems Ok. Tks
>
> macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
> /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt
>
> INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer
>
> INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
> -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd
>
> #-
>
> /Applications/freesurfer/bin/trac-preproc
>
> #-
>
> #@# Image corrections Wed Sep 30 11:27:28 BRT 2015
>
> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>
> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>
> niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...
>
> Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
> 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015
>
> --
> Andrea Cristina de Lima Pardini
> CV: http://lattes.cnpq.br/0921194840474573
>
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[Freesurfer] selxavg3-sess outputs

[Jiahe Zhang]

Dear Freesurfer experts,

The freesurfer command 'selxavg3-sess' outputs many files in the contrast
folder in addition to the three documented on the Wiki (ces, cesvar, sig).
Is there more detailed documentation on what each output is and how they're
computed? In particular, I was wondering if the t.nii.gz and z.nii.gz maps
contain standard t and standard z scores.

Thanks,
Jiahe


-- 
Jiahe Zhang
Ph.D. Candidate
Department of Psychology
Northeastern University
617-373-4789
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Re: [Freesurfer] Sulc value of given Tal coordinates

[Bunday, Karen]

Rudolph

Could you possibly tell me or point in the direction of a tutorial on how to 
map tal coordinates to the vertex mesh?

Many thanks

Karen

Karen Bunday, PhD
Honorary Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 29 September 2015 14:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulc value of given Tal coordinates

when you load the fsaverage surface into freeview or tksurfer you will see some 
coordinates, those coordinates will be MNI305 coords. If you map the individual 
sulc or curv into fsaverage space and load is as an overlay, then you can see 
what the sulc/curv value is at a given coordinate.

On 9/29/15 4:44 AM, Bunday, Karen wrote:
> Rudolph
> That's great, so as I understand I should be able to get the sulc value for a 
> given vertex.
>
> Forgive my naivety, but how do I map the tal coordinates to the vertex mesh? 
> Is there also a function for this? I'm very new to this!
>
> I just need the nearest vertex for a given tal coordinates (I do also have 
> these in MNI, but converted then as I thought freesurfer worked in tal), then 
> I should be able to get the sulc value.
>
> Doug, I'm also not sure what this mean exactly, could you elaborate?
>
> Karen Bunday, PhD
> Honorary Research Associate
> Sobell Department of Motor Neuroscience and Movement Disorders 
> Institute of Neurology, University College London
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 28 September 2015 23:15
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
>
> You can also map the sulc or curv to fsaverage. The coordinates (in freeview 
> or tksurfer) are in MNI305 coordinates which are pretty close to Tal.
>
> doug
>
> On 09/28/2015 05:26 PM, Rudolph Pienaar wrote:
>> Hi Karen --
>>
>> A given FreeSurfer surface can be thought of as a triangular mesh.
>> This mesh contains many "points" (i.e. the vertex points of the 
>> constituent triangles).
>>
>> Each of these mesh vertex points contains many internal values, i.e.
>> the x, y, z position of the point, the normal to the surface at this 
>> point, some curvature values at this point, and many more.
>>
>> Each of these mesh points is also referenced by a single number, its 
>> ID if you will. If there are 100,000 mesh points, this ID will range 
>> in value from 0 (the arbitrary first point) to 99,999 (the last point 
>> on the mesh).
>>
>> A sulc or curvature file, is simply a long array of sulc or curvature 
>> values. The index of the array corresponds to the ID of the same 
>> indexed point on the FreeSurfer surface (there is slightly confusing 
>> change in that in MatLAB counting of arrays starts at 1, while in 
>> FreeSurfer the counting starts at 0). So, for example, a file 
>> "lh.sulc", is simply a long list of values, in order, corresponding 
>> to the sulc value at each corresponding index location of the surface.
>>
>> So, in MatLAB, a line like:
>>
>>  [curv, fnum] = read_curv(fname);
>>
>> and assuming that
>>
>>  fname = '/some/path/to/lh.sulc';
>>
>> will read the lh.sulc located at the directory spec '/some/path/to/'
>> and will return two bits of data. The 'fnum' you can ignore. The 
>> 'curv' is what you are interested in. It is a MatLAB array (or 
>> vector) of, in this case, the sulc values.
>>
>> curv[1]  corresponds to the sulc value at the first mesh point (which is
>> actually index 0 of the mesh).
>>
>> curv[2] corresponds to the sulc value at the second mesh point (which 
>> is actually index 1 of the mesh).
>>
>> and so on and so forth.
>>
>> If you set fname to
>>
>>  fname = '/some/path/to/lh.curv';
>>
>> then the lh.curv file and its values are read and returned as the 
>> indexed MatLAB vector.
>>
>> In order to get the sulc and curv at a given tal coordinate, you'd 
>> have to map the tal coordinate to the index of the point on the FreeSurfer 
>> mesh.
>>
>> HTH
>> -=R
>>
>> On 9/28/15 12:31 , Bunday, Karen wrote:
>>> Hi
>>>
>>> I am not a Freesurfer expert or Matlab connoisseur. I am trying to 
>>> find out how to get the Sulc and Curv value for a given  tal 
>>> coordinate.  I was told that you load it in Matlab using read_curv, 
>>> but how exactly do I do this, what does they syntax look like?
>>>
>>> I can see in the help this: [curv, fnum] = read_curv(fname)
>>>
>>> But I don't know what I'm supposed to out in here more explicitly.
>>>
>>> Thanks
>>>
>>> Karen
>>>
>>> Karen Bunday, PhD
>>>
>>> Honorary Research Associate
>>>
>>> Sobell Department of Motor Neuroscience and Movement Disorders
>>>
>>> Institute of Neurology, University College London
>>>
>>> 33 Queen Square
>>>
>>> 

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

[Matthieu Vanhoutte]

Hi Martin,

Thank you for helping !

1) What should I use for the parameter estimation: "mass univariate" or Novel
mass-univariate tools (spatiotemporal models)" ?

2) I have one group of subjects with different timepoints (non equally
spaced and different numbers of timepoints), and would like to see the
significant change of FA according to time. Will LME study allow me to get
this change and how to define contrast to assess it ? Are the results of
this longitudinal study directionals, i.e. is it possible to establish an
increase or decrease of FA in significant regions according to time ?

3) Should the covariates (age, gender...) be demeaned or centered ?

4) Has the accurate time variable to be in years absolutely or could it be
also in days ?


Best regards,

Matthieu


2015-09-29 17:11 GMT+02:00 Martin Reuter :

> Hi Matthieu,
>
> use lme_mass_fit_vw and the y is a simple vector. I would mask the image
> before doing this and only pass the brain voxels (to increase speed and
> reduce comparisons).
>
> Best, Martin
>
>
> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote:
>
> Hi Martin,
>
> I understand for the multiple comparisons problem. But if I consider a
> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for
> estimation), how could I consider a correction for multiple comparisons in
> this univariate case ?
>
> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass
> univariate case ? If yes, how do I have to format my 3D FA volume as input
> of the LME toolbox ?
>
> Best regards,
>
> Matthieu
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-09-29 16:34 GMT+02:00 Martin Reuter :
>
>> Hi Matthieu,
>>
>> yes, multiple comparisons are a problem for any mass univariate approach.
>> You can use the FDR2 correction (in the lme matlab tools) which is less
>> conservative than standard FDR. You can also work in specific ROI's and
>> average there, to reduce the number of comparisons.
>>
>> Best, Martin
>>
>>
>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote:
>>
>> Hi Martin,
>>
>> Thank you for your answer.
>>
>> However, I would like to consider FA maps as a mass-univariate problem
>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my
>> voxels aren't independant, are they ? So, how to correct for multiple
>> comparisons then ?
>>
>> Best regards,
>>
>> Matthieu
>>
>> 2015-09-29 15:04 GMT+02:00 Martin Reuter :
>>
>>> Hi Matthieu,
>>>
>>> if all your images are perfectly registered, you can do LME on a
>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other
>>> ROI measure.
>>>
>>> Best, Martin
>>>
>>>
>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote:
>>>
>>> Dear experts,
>>>
>>> I would like to know if it is possible to make a longitudinal study with
>>> LME toolbox from volume FA maps registered in a common space ?
>>>
>>> I don't have T1 images so the recon-all process couldn't be processed.
>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels
>>> format, could it be in good way for LME ?
>>>
>>> Thanks for helping !
>>>
>>> Best regards,
>>>
>>> Matthieu
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> --
>>> Martin Reuter, PhD
>>> Assistant Professor of Radiology, Harvard Medical School
>>> Assistant Professor of Neurology, Harvard Medical School
>>> A.A.Martinos Center for Biomedical Imaging
>>> Massachusetts General Hospital
>>> Research Affiliate, CSAIL, MIT
>>> Phone: +1-617-724-5652
>>> Web  : http://reuter.mit.edu
>>>
>>>
>>> ___
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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.
>>>
>>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  

[Freesurfer] mri_vol2surf

[Martin Tisdall]

I am trying to produce a scalar overlay from PET data to overlay onto the pial 
surface. 
I have coregistered the pet with T1.mgz and then used the transform from 
mri_info --scanner2tkr to co-localise with orig.mgz. I then do:
mri_vol2surf --src  --out  --out_type paint 
--regheader  --hemi lh --surf pial --projfrac 0.5. 

The output doesn't seem quite right as seems to be some areas of signal drop 
out. 
Can anyone tell me if my options look right or am I missing something. 
Thank you
Martin
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[Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

[andrea cristina Lima]

I got the error below. Could you help me? I've already check the dti file
and it seems Ok. Tks

macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
/Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt

INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer

INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
-log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-

#@# Image corrections Wed Sep 30 11:27:28 BRT 2015

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...

Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015

-- 
Andrea Cristina de Lima Pardini
CV: http://lattes.cnpq.br/0921194840474573
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Re: [Freesurfer] Freesurfer methods and reviewer queries

[Bruce Fischl]

Hi Mahinda

1. The subvoxel accuracy has been verified experimentally in Dianas Rosas' 
paper:


http://www.ncbi.nlm.nih.gov/pubmed/11889230

where she measured the thickness under a microscope (ex vivo) and compared 
it to our results and found they agreed within a couple of hundred microns.


It's easy to see why this would work. Imagine you have a voxel that is all 
gray matter and the next voxel is all csf, so the pial boundary is between 
them. Now imagine that there is some atrophy and the boundary moves into 
the voxel. The voxel intensity will decline (on a T1) giving us the 
information we need to detect this type of effect.


2. No we can't really distinguish loss of tissue from changes in tissue 
properties. This is true of most of MRI.


3. You mean manually measuring the thickness? This is very very difficult 
to do, an IMO would result in a significantly less accurate result. The 
thickness has to be measured in 3D and not necessarily along any of the 
cardinal viewing planes


cheers
Bruce


 On Tue, 29 Sep 2015, 
Mahinda Yogarajah wrote:



Dear Freesurfer team,

I have a manuscript under review which has used Freesurfer to compare
cortical thickness differences between groups, controls and patients with a
specific genetic mutation. There are robust, statistically significant group
differences in biologically plausible regions. However one of the reviewers
has taken offence at aspects of the methods, and before I put together a
response I was hoping for help from the Freesurfer team.

(1) In my methods I have stated that “the maps produced are not restricted
to the voxel resolution of the original data and thus are capable of
detecting sub-millimetre differences between groups,”

The reviewer takes umbrage with the fact that partial volume effects prevent
an MRI acquired with 1.1x1.1x1.1 mm3 voxel size from providing a metric
measuring sub-millimetric changes.

I was wondering how the Freesurfer team might compose a response to this  ?

(2) The reviewer also asks the question as to how one can differentiate loss
of cortical volume (thickness in this case) from alterations in the contents
of the volume: changes in cell type, cell shape or cell volume. He/she asks
how one defines the tissue classes across which the spatial intensity
gradients are applied.

The first part of this question seems slightly circular to me (!). I would
answer the second part by pointing out that the initial surface is refined
to follow the intensity gradients between the white and gray matter (this is
referred to as the white surface). The white surface is then nudged to
follow the intensity gradients between the gray matter and CSF (this is the
pial surface). The cortical thickness is the distance in between them.

(3) Finally he/she suggests that one might confirm cortical thickness
differences by measuring sulcal thickness or subarachnoid space volumes over
those areas where I see significant results. This seems like over kill to me
- any suggestions as how to make a firm rebuttal ?

Thanks, 

Mo 

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Re: [Freesurfer] Question about the negative value of surface area

[Bruce Fischl]

Hi Feng

the area of the triangls is oriented to detected changes in the jacobian. 
That said, they should be positive definite (you can verify 
thismris_remove_intersection on the ?h.sphere.reg to make sure that this is 
the case. Perhaps Anderson or Doug can comment?


cheers
Bruce
On Tue, 29 Sep 2015, chenhf_uestc wrote:


Dear Freesurfer experts,
 
I read the raw area file and the area resampled to the fsaverage space and
found several interesting things.
 
raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the
area value is [-0.0471 6.2118]
raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); % the range of the
area value is [0 6.8963]
raw59l = read_curv('E:\fs_result\NC059\surf\lh.area'); % the range of the
area value is [-0.3347 5.4892]
raw59r = read_curv('E:\fs_result\NC059\surf\rh.area'); % the range of the
area value is [-1818 5.4269]
 
The first question, what is the unit of the area file in the surf folder
(such as lh.area), mm2? Why the minimal value of the area can be less than
zero?
 
Subsequently, I perform further experiments, reading the resampled area
file.
 
resamp_58l = load_mgh('E:\fs_result\NC058\surf\lh.area.fsaverage.mgh'); %
the range of the area value is [-0.0118 7.4073]
resamp_58r = load_mgh('E:\fs_result\NC058\surf\rh.area.fsaverage.mgh'); %
the range of the area value is [0 19.0191]
resamp_59l = load_mgh('E:\fs_result\NC059\surf\lh.area.fsaverage.mgh'); %
the range of the area value is [-0.3937 9.9084]
resamp_59r = load_mgh('E:\fs_result\NC059\surf\rh.area.fsaverage.mgh'); %
the range of the area value is -0.0909 8.2306[]
 
The second question, why the value of some area file change a lot? For
example, the maximum value of raw58r is 6.8963, but 19.0191 of resampled
one.
 
Next,
resamp_smooth5_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm5.fsaverage.mgh');  % the
range of the area value is [0 1.7293]
resamp_smooth5_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm5.fsaverage.mgh');  % the
range of the area value is [0 2.1877]
resamp_smooth5_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm5.fsaverage.mgh');  % the
range of the area value is [0 1.2875]
resamp_smooth5_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm5.fsaverage.mgh');  % the
range of the area value is [0 1.3542]
 
The third question, why all the minimal values after smooth was zero? Why
all the maximal values after smooth reduce a lot?
 
Finally,
resamp_smooth25_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm25.fsaverage.mgh');  % the
range of the area value is [0 1.2014]
resamp_smooth25_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm25.fsaverage.mgh');  % the
range of the area value is [0 1.2611]
resamp_smooth25_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm25.fsaverage.mgh');  % the
range of the area value is [0 0.9730]
resamp_smooth25_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm25.fsaverage.mgh');  % the
range of the area value is [0 1.0119]
 
The final question, why all the maximal values  of fwhm25 smooth are less
than the values  of fwhm5 smooth?
 
How can I get the area value in the recon-all analyses? The cortical
thickness is the distance betwwen the white matter and the pial, but what is
the procedures the area value obtained? If there any reference? My
freesurfer version is stable v5.3.0.
 
Any help would be greatly appreciately!
 
Best,
Feng
 
 
 
 
 

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Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

[Bruce Fischl]

Hi Feng

it depends on where the tumor is

cheers
Bruce
On Wed, 30 Sep 2015, chenhf_uestc wrote:


Hi, freesurfer experts,
 
If my data came from the patients with brain tumors, could I perform
recon-all analyses to calculate cortical thickness, surface area and so on.
If not, could I mask the brain region with tumor and then conduct such
analyses? I think the tumor might lead to the inaccuracy of cortical
reconstruction
 
Best,
Feng

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[Freesurfer] WM segmentation error longitudinal stream

[Adam, Ruth]

Hi all,

We have run longitudinal analysis on two time points.
The resulting longitudinal WM surface for both time points excludes large parts 
of the cortex.
The cross sectional surfaces and the wm.mgz are correct. 
The base wm.mgz also seems to be fine, however, the base white and pial 
surfaces do not follow the wm volume properly.

We have rerun the longitudinal anlaysis (recon-all -long) according to the 
cheat sheet:
1. marking the base wm.mgz border with 255 voxel value (instead of 110)
2. adding control points to the base wm.mgz
but it did not change the original result.

Any idea how this can be fixed?
Thank you very much in advance!

Best,
ruthi
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Re: [Freesurfer] warping surface label to volume space

[Jacobs H (NP)]

Hi Doug,

Just as a reminder: I uploaded the data yesterday.

Best
Heidi

From: Douglas Greve 
>
Reply-To: Freesurfer support list 
>
Date: Tuesday 29 September 2015 17:01
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: Re: [Freesurfer] warping surface label to volume space

filedrop2 url at the end of this email

On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
Sure, where should I upload it to?
Thanks!
Heidi

From: Douglas Greve 
>
Reply-To: Freesurfer support list 
>
Date: Tuesday 29 September 2015 16:28
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: Re: [Freesurfer] warping surface label to volume space

Can you upload the subject so I can look at it?

On 9/29/15 9:05 AM, Jacobs H (NP) wrote:

Hi Doug,

The label looks actually ok and the surface as well. I attached the images to 
this email, Not sure where it went wrong?

Best
Heidi


Van: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 28 september 2015 23:58
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] warping surface label to volume space

Something is definitely going wrong. Can you load the label as well and
verify that the label itself looks ok?

On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:


Yes, here it is!
Thanks! Heidi



Yes, here it is!
Thanks! Heidi


image1.png



ATT1.txt





Op 28 sep. 2015 om 17:26 heeft Douglas N 
Greve  het 
volgende geschreven:

Can you send a picture?



On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
Dear Doug,

By looking at it in Freeview. Anatomically, I would expect that the entorhinal 
cortex would not be localized so laterally? And some voxels are not in the 
temporal lobe.

Best
Heidi


Van:freesurfer-boun...@nmr.mgh.harvard.edu
  
[freesurfer-boun...@nmr.mgh.harvard.edu]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 28 september 2015 23:00
Aan:freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] warping surface label to volume space

how are you determining that it is not in the right place? When I run
this it works.



On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
Hi,

Bringing this to the FS list:
I am trying to warp the entorhinal cortex label (ex vivo) to volume
space, so that I can see and use the full ROI. Using the command
stated below doesn’t seem to work, as it is not in the right location
of the subject’s brain. Any thoughts?

I used this command:
mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
--regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l

This was the output on the terminal:
subject S_3RSPPP --hemi lh
INFO: subject not needed, igorning.
Number of labels: 1
S_3RSPPP/label/lh.entorhinal_exvivo.label
Annot File:  (null)
Template Volume: (null)
Outut Volume: lh.entorhinal_exvivo_vol.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType: (null)
ProjTypeId: 0
ProjStart:  0
ProjStop: 0
ProjDelta:  0.1
Subject:  S_3RSPPP
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
  INFO: loading
surface  
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white

nvertices = 120130
Reading thickness
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness
nlabels = 1
Loading
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz
Loading S_3RSPPP/label/lh.entorhinal_exvivo.label
Mapping

Any suggestions how I can improve this?
Thanks
Heidi


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--
Douglas N. Greve, Ph.D.
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 

Re: [Freesurfer] dt_recon

[Alshikho, Mohamad J.]

Hi Doug,
Thank you very much for your answers!

Kindly I have one more question:
At the end of DTI analysis using the tool "dt_recon" we will have  " stats" 
file including the FA value for every segment and parcellate in the brain. 
Depending on this output can we use the term " DTI morphometry" to describe the 
analysis?


Thanks
Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon


On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals 
f.bvecs --s M87102113 --o dti  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment 
in aseg and wmparc atlases) using the command "mri_segstats"

In order to do so I need to move "fa.nii" to anatomical space using the command:

mri_vol2vol -mov fa.nii -lta register.lta -fstarg -o fa.anat.mgh
  <<< source:   Freesurfer wiki>>>


My questions are about the file "register.lta" :

1.   What is the difference between this file and the file "register.dat" ( 
which I can see it as an output of  the command " bbregister" in the final 
analysis using the command "dt_recon")
They hold the same basic registration information just in different formats. We 
are trying to move to the LTA as it is a much better format for these things.


2.   How can I generate the file " register.lta"?
Use lta_convert, something like
   lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz 
--trg $SUBJECTS_DIR/$subject/mri/orig.mgz


3.   Can I feed the file " register.dat" instead of the file " 
register.lta" into the command "mri_vol2vol "  (in order to move the ''fa.nii" 
to anatomical space). If so which flag I should use instead of the flag "--lta" 
in the command mri_vol2vol?
Yes, pass it with --reg flag.



Many thanks
Mohamad




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Re: [Freesurfer] 3_group_comparison

[Dusan Hirjak]

Thank you very much for your suggestion. Now it has worked well. 
However, I am having trouble running the simulation via:
mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces
ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
Where can I set up the EN language with "setenv LANG en_US.UTF-8"?
I am getting this message: 
bash-3.2$ setenv LANG en_US.UTF-8
bash: setenv: command not found 
How can I change the language? 

Many thanks! 
Dusan
From: rpw...@nmr.mgh.harvard.edu
Date: Mon, 28 Sep 2015 19:35:12 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3_group_comparison

Was the path of the overlay file correct? It looks like it can’t find the file. 
Try providing the full path of the overlay file in the freeview command.
Best,Ruopeng
On Sep 28, 2015, at 6:46 PM, Dusan Hirjak  wrote:Many 
thanks!!!, yes, freeview has opened, but I am still not seeing any results, 
just the "lh.inflated"
It says: "Failed to load surface overlay" 
and than I got the following message: 
bash-3.2$ freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5
 -viewport 3d2015-09-29 00:41:53.887 Freeview[22049:303] invalid 
drawable2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable2015-09-29 
00:41:53.905 Freeview[22049:303] invalid drawable2015-09-29 00:41:53.906 
Freeview[22049:303] invalid drawable2015-09-29 00:41:53.921 Freeview[22049:303] 
invalid drawable2015-09-29 00:41:53.922 Freeview[22049:303] invalid 
drawable2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable2015-09-29 
00:41:53.939 Freeview[22049:303] invalid drawableDid not find any volume 
geometry information in the surfaceø;C 8Íÿ¿ø;C È+’Àá
reading colortable from annotation file...colortable with 36 entries read 
(originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)colortable
 with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
 -1): could not open 
filemghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
 -1): could not open filecould not read overlay data from 
/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mghmghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh,
 -1): could not open file2015-09-29 00:42:02.445 Freeview[22049:303] 
modalSession has been exited prematurely - check for a reentrant call to 
endModalSession:
I dont understand the problem. Do you have any ideas???
Thank you! 
Dusan


> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Mon, 28 Sep 2015 18:33:50 -0400
> Subject: Re: [Freesurfer] 3_group_comparison
> 
> I think it needs a -f before the surface
> 
> On 09/28/2015 06:27 PM, Dusan Hirjak wrote:
> > Many thanks, yes, it did work well.
> >
> > But, than I ran "freeview 
> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
> >  
> > -viewport 3d"
> >
> > and got the following message:
> >
> > bash-3.2$ freeview 
> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
> >  
> > -viewport 3d
> >
> > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable
> >
> > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable
> >
> > Unrecognized sub-option flag 'annot=aparc.annot'.
> >
> >
> > Freeview has opened, but it showed no results at all:-(
> >
> >
> > What should I do? I read that one has to upgrade the newest 
> > freeview-version? Is it possible to get the newest version without 
> > installing freesurfer again?
> >
> > Many thanks!
> >
> > Dusan
> >
> >
> > 
> > Date: Mon, 28 Sep 2015 11:35:50 -0400
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] 3_group_comparison
> >
> > Did you include the back slashes in your command? If so, remove them 
> > and retry.
> >
> > On 9/25/15 7:11 PM, Dusan Hirjak wrote:
> >
> > Dear Freesurfer experts,
> >
> > I am trying to compare 3 groups (aut, sch, ges) according to
> > thickness, area and LGI at once 

[Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

[Nam, Kie Woo]

Dear experts,

I'm trying to calculate local gyrifcation index using CIVET's surface file 
('.obj').




First, I've successfully done 'CIVET --> FreeSurfer' conversion and created a 
'.pial' file - below are the commands that worked for 'CIVET --> FreeSurfer' 
and 'FreeSurfer --> CIVET' conversions.
CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big Endian)): 
"ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj -o_fs lh.pial; 
mris_convert lh.pial.asc lh.pial"
FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): "ConvertSurface -i_fs 
lh.pial -o_mni lh.pial"





Then, I ran "recon-all -s Subject -localGI", but it keeps crashing with the 
following message.

lGI for vertex number 5501 of the outer mesh is 4.1122
lGI for vertex number 5601 of the outer mesh is 0.86156
lGI for vertex number 5701 of the outer mesh is 3.8343
... remeasuring lGI value for vertex iV = 5801. It may take a few minutes.
WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high 
(lGI=62.3205)...
...lGI computation will be stopped. This may be caused by topological defects, 
check mris_euler_number on the pial surface.


The link below suggests rerunning "recon-all -autorecon2-wm -randomness", but 
it's not an option for me because I have no other FreeSurfer compatible files 
except ".pial".
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html



So, could there be any solution for this?



Best wishes,

Kie Woo
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[Freesurfer] Calculate the cortical thickness in patients with brain tumor

[chenhf_uestc]

Hi, freesurfer experts,

If my data came from the patients with brain tumors, could I perform recon-all 
analyses to calculate cortical thickness, surface area and so on. If not, could 
I mask the brain region with tumor and then conduct such analyses? I think the 
tumor might lead to the inaccuracy of cortical reconstruction 

Best,
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Re: [Freesurfer] problem fast_selxavg3b

[Silvia Désirée Thielemann]

Dear freesurfer experts,

I included the new function but I got another problem:

First error:

/opt/freesurfer/bin/mris_fwhm --mask  
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
 --i 
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
 --o 
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
 --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd  
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
/opt/freesurfer/bin/mris_fwhm: symbol lookup error:  
/opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr

ERROR: /opt/freesurfer/bin/mris_fwhm --mask  
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
 --i 
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
 --o 
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
 --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd  
/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann

ans =

127

Second error with another server running the analyses:

/opt/freesurfer/bin/mris_fwhm:  
/opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version  
`GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm)
/opt/freesurfer/bin/mris_fwhm:  
/opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version  
`GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)


The problem seems to be the version of matlab. Which version would you  
suggest to use while using the function fast_selxavg3b? And why is  
there an undefined symbol?

Do you have any suggestions how to solve the problem?

Best regard,
Desiree


>> --
ERROR: fast_selxavg3() failed\n

Zitat von Douglas Greve :

> oops, sorry, that did not make it into the distribution. You can get it here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
>
> thanks
> doug
>
>
> On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
>> Dear members of the freesurfer mailing list,
>>
>> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to
>> analyse mri data with fs-fast. I did the preprocessing and used the
>> function mkanalysis-sess and mkcontrast-sess without any problems. I
>> tried to run the function selxavg3-sess next and it stopped with the
>> error message:
>>
>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /opt/freesurfer/matlab/MRIread.m
 ??? Undefined function or method 'fast_selxavg3b' for input
 arguments of type
>> 'char'.
>>
 --
>> ERROR: fast_selxavg3() failed\n
>>
>> I looked for the function fast_selxavg3b in matlab. Unfortunatly only
>> the function fast_selxavg3 is included in the fsfast/toolbox. By
>> trying to use the function fast_selxavg3, it recommand me to use
>> fast_selxavg3b. I could not find the function in the internet.
>>
>> Do you have any suggestions what to do?
>>
>> Best regards,
>> Desiree
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> ___
> 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  
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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

[andrea cristina Lima]

Ok! Thank you! I will try again!

2015-09-30 19:16 GMT-03:00 andrea cristina Lima :

> Em 30/09/2015 11:30, "andrea cristina Lima" 
> escreveu:
>
>> I got the error below. Could you help me? I've already check the dti file
>> and it seems Ok. Tks
>>
>> macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
>> /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt
>>
>> INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer
>>
>> INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1
>>
>> Actual FREESURFER_HOME /Applications/freesurfer
>>
>> trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
>> -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd
>>
>> #-
>>
>> /Applications/freesurfer/bin/trac-preproc
>>
>> #-
>>
>> #@# Image corrections Wed Sep 30 11:27:28 BRT 2015
>>
>> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>>
>> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>>
>> niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
>>
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>
>> reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...
>>
>> Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
>> 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>>
>>
>> trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015
>>
>> --
>> Andrea Cristina de Lima Pardini
>> CV: http://lattes.cnpq.br/0921194840474573
>>
>


-- 
Andrea Cristina de Lima Pardini
CV: http://lattes.cnpq.br/0921194840474573
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Re: [Freesurfer] Sulc value of given Tal coordinates

[Bunday, Karen]

Hi Doug

Thank you. Could you point me in the direction of some tutorials that might 
help me do this?

BW
Karen

Karen Bunday, PhD
Honorary Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 29 September 2015 14:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulc value of given Tal coordinates

when you load the fsaverage surface into freeview or tksurfer you will see some 
coordinates, those coordinates will be MNI305 coords. If you map the individual 
sulc or curv into fsaverage space and load is as an overlay, then you can see 
what the sulc/curv value is at a given coordinate.

On 9/29/15 4:44 AM, Bunday, Karen wrote:
> Rudolph
> That's great, so as I understand I should be able to get the sulc value for a 
> given vertex.
>
> Forgive my naivety, but how do I map the tal coordinates to the vertex mesh? 
> Is there also a function for this? I'm very new to this!
>
> I just need the nearest vertex for a given tal coordinates (I do also have 
> these in MNI, but converted then as I thought freesurfer worked in tal), then 
> I should be able to get the sulc value.
>
> Doug, I'm also not sure what this mean exactly, could you elaborate?
>
> Karen Bunday, PhD
> Honorary Research Associate
> Sobell Department of Motor Neuroscience and Movement Disorders 
> Institute of Neurology, University College London
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 28 September 2015 23:15
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Sulc value of given Tal coordinates
>
> You can also map the sulc or curv to fsaverage. The coordinates (in freeview 
> or tksurfer) are in MNI305 coordinates which are pretty close to Tal.
>
> doug
>
> On 09/28/2015 05:26 PM, Rudolph Pienaar wrote:
>> Hi Karen --
>>
>> A given FreeSurfer surface can be thought of as a triangular mesh.
>> This mesh contains many "points" (i.e. the vertex points of the 
>> constituent triangles).
>>
>> Each of these mesh vertex points contains many internal values, i.e.
>> the x, y, z position of the point, the normal to the surface at this 
>> point, some curvature values at this point, and many more.
>>
>> Each of these mesh points is also referenced by a single number, its 
>> ID if you will. If there are 100,000 mesh points, this ID will range 
>> in value from 0 (the arbitrary first point) to 99,999 (the last point 
>> on the mesh).
>>
>> A sulc or curvature file, is simply a long array of sulc or curvature 
>> values. The index of the array corresponds to the ID of the same 
>> indexed point on the FreeSurfer surface (there is slightly confusing 
>> change in that in MatLAB counting of arrays starts at 1, while in 
>> FreeSurfer the counting starts at 0). So, for example, a file 
>> "lh.sulc", is simply a long list of values, in order, corresponding 
>> to the sulc value at each corresponding index location of the surface.
>>
>> So, in MatLAB, a line like:
>>
>>  [curv, fnum] = read_curv(fname);
>>
>> and assuming that
>>
>>  fname = '/some/path/to/lh.sulc';
>>
>> will read the lh.sulc located at the directory spec '/some/path/to/'
>> and will return two bits of data. The 'fnum' you can ignore. The 
>> 'curv' is what you are interested in. It is a MatLAB array (or 
>> vector) of, in this case, the sulc values.
>>
>> curv[1]  corresponds to the sulc value at the first mesh point (which is
>> actually index 0 of the mesh).
>>
>> curv[2] corresponds to the sulc value at the second mesh point (which 
>> is actually index 1 of the mesh).
>>
>> and so on and so forth.
>>
>> If you set fname to
>>
>>  fname = '/some/path/to/lh.curv';
>>
>> then the lh.curv file and its values are read and returned as the 
>> indexed MatLAB vector.
>>
>> In order to get the sulc and curv at a given tal coordinate, you'd 
>> have to map the tal coordinate to the index of the point on the FreeSurfer 
>> mesh.
>>
>> HTH
>> -=R
>>
>> On 9/28/15 12:31 , Bunday, Karen wrote:
>>> Hi
>>>
>>> I am not a Freesurfer expert or Matlab connoisseur. I am trying to 
>>> find out how to get the Sulc and Curv value for a given  tal 
>>> coordinate.  I was told that you load it in Matlab using read_curv, 
>>> but how exactly do I do this, what does they syntax look like?
>>>
>>> I can see in the help this: [curv, fnum] = read_curv(fname)
>>>
>>> But I don't know what I'm supposed to out in here more explicitly.
>>>
>>> Thanks
>>>
>>> Karen
>>>
>>> Karen Bunday, PhD
>>>
>>> Honorary Research Associate
>>>
>>> Sobell Department of Motor Neuroscience and Movement Disorders
>>>
>>> Institute of Neurology, University College London
>>>
>>> 33 Queen Square
>>>
>>> London
>>>
>>> WC1N 3BG
>>>
>>>
>>>

Re: [Freesurfer] problem fast_selxavg3b

[Desiree Thielemann]

Thanks Doug!

I have another question: We did the fsfast analysis some time ago before 
we updated freesurfer version with fast_selxavg3. Now we want to analyse 
additional persons. Do you think it is comparable or is it better to 
re-do the analysis for all persons with fast_selxavg3b instead of 13 
persons with fast_selxavg3 and 2 persons with fast_selxavg3b?

Thanks in advance,
Desiree

Am 29.09.2015 um 15:34 schrieb Douglas Greve:
> oops, sorry, that did not make it into the distribution. You can get it here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
>
> thanks
> doug
>
>
> On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
>> Dear members of the freesurfer mailing list,
>>
>> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to
>> analyse mri data with fs-fast. I did the preprocessing and used the
>> function mkanalysis-sess and mkcontrast-sess without any problems. I
>> tried to run the function selxavg3-sess next and it stopped with the
>> error message:
>>
>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /opt/freesurfer/matlab/MRIread.m
 ??? Undefined function or method 'fast_selxavg3b' for input
 arguments of type
>> 'char'.
>>
 --
>> ERROR: fast_selxavg3() failed\n
>>
>> I looked for the function fast_selxavg3b in matlab. Unfortunatly only
>> the function fast_selxavg3 is included in the fsfast/toolbox. By
>> trying to use the function fast_selxavg3, it recommand me to use
>> fast_selxavg3b. I could not find the function in the internet.
>>
>> Do you have any suggestions what to do?
>>
>> Best regards,
>> Desiree
>>
>> ___
>> 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 
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[Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

> Hello,
> When I run the command "sFSstart" on version 5.0.0, I am receiving the
> messages below. Would you please explain to me what the problem is? It
> seems like there is trouble accessing the bin.
> Thank you
>
>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/tle7/freesurfer
> FSFAST_HOME   /home/tle7/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii
> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
> MNI_DIR   /home/tle7/freesurfer/mni
> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
> H 0
> checking sid number 00152-DT2
> 1 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
> Actual FREESURFER_HOME /home/tle7/freesurfer
> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP Wed
> Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary file
> not executable.
> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. Binary
> file not executable.
> /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not
> executable.
> /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error.
> Binary file not executable.
> /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file not
> executable.
> -cw256 option is now persistent (remove with -clean-cw256)
> /home/tle7/freesurfer/subjects/00152-DT2_v5
>
>  mri_convert
> 

Re: [Freesurfer] Parcellation stats

[Bruce Fischl]

that will generate a parcellation on the individual subject surface of 
Thomas Yeo's 17-network clustering. It won't do anything with the thickness 
though. What are you trying to do?


On Tue, 29 Sep 2015, Ali Radaideh wrote:


mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
--tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve 
wrote:
  what is your surf2surf command?

  On 9/28/15 5:11 PM, Ali Radaideh wrote:
  Dear Douglas,

Thanks for your email. I meant to say that after running the
recon-all, i ran the sur2surf command to get the cortical
parcellation using Thomas Yeo Atlas.

I thought that the extracted cortical thickness after running
the surf2surf command will be different from the one extracted
before running the command. But, Bruce kindly replied to my
email saying that it is the same if it is calculated on
vertex-wise basis. 

Thanks,
Ali

On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
 wrote:
  I can't understand what you are asking. Can you
  elaborate?

  On 09/28/2015 01:51 PM, Ali Radaideh wrote:
  > Thanks alot Douglas,
  >
  > Yes it is there but after checking it many time I
  found it corrupted
  > for some subjects due to copying them many times
  between machines.
  >
  > But May I ask you some thing related. I have just
  posted a question
  > regarding getting the cortical thickness after
  running the surf2surf
  > command (17 networks cortical parcellation). Now I
  found the stats
  > file not updated after running this command only
  the annotation files
  > in label folder.
  [rh.Yeo2011_17Networks_N1000.annot]. We thought that
  > using Yeo Atlas will give slightly different
  cortical thickness, are
  > we correct?
  >
  > Thanks,
  > Ali
  >
  > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
  > > wrote:
  >
  >     does that file exist?
  >
  >     On 09/28/2015 01:05 PM, Ali Radaideh wrote:
  >     > Dear FreeSurfer experts,
  >     > After finishing the recon-all, I am trying
  to extract the cortical
  >     > thickness for each subject and group them
  into one table but
  >     > unfortunately i keep getting the following
  error:
  >     >
  >     > ​rh.aparc.DKTatlas40.stats is not found or is
  too small to be a
  >     valid
  >     > statsfile
  >     > Use --skip flag to automatically skip bad
  stats files​
  >     >
  >     > i tried to change the stats file (e.g I used
  aparc.a2009s) but I got
  >     > the same error.
  >     >
  >     > I tried each brain alone and also got the
  same error.
  >     >
  >     > Any ideas please
  >     > ​Thanks,
  >     > Ali​
  >     >
  >     > --
  >     > /Ali M. Al-Radaideh. PhD
  >     > Head of Department of Medical Imaging
  >     > Vice Dean of the Faculty of Allied Health
  Sciences
  >     > The Hashemite University,
  >     > Zarqa, Jordan
  >     > W.phone +962 5 390 ext.5422, 5355, 5364
  >     > Email: ali.radai...@hu.edu.jo
  
  >     >
  >     > /
  >     > /webpage:
  http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
  >     >
  >     >
  >     >
  >     >
  ___
  >     > Freesurfer mailing list
  >     > Freesurfer@nmr.mgh.harvard.edu
  >     
  >     >
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >     --
  >     Douglas N. Greve, Ph.D.
  >     MGH-NMR Center
  >     gr...@nmr.mgh.harvard.edu
  
  >     Phone Number: 617-724-2358
  >     Fax: 617-726-7422
  >
  >     Bugs:
  surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  >   
   
  >     FileDrop:
  https://gate.nmr.mgh.harvard.edu/filedrop2
  >   
   www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  >   
   
  >     Outgoing:
  >   
   ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
  >
  >   
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  >   
   

Re: [Freesurfer] R: import FS-FAST results in FSL

[Douglas N Greve]

Do you mean surface-based analysis? You'd have to put them back into the 
volume using mri_surf2vol, write them out as nifti and then run fslview 
on them

On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>
> Hi list,
>
> I would like to import FS-FAST results (conjunction maps) in FSL,
> opening them by fslview.
> Could you provide me any suggestion?
>
> Thank you very much
> Best regards,
>
>
> Stefano
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Isxconcat-sess error

[Rodriguez-Thompson, Anais]

Hi Freesurfer experts,

I'm trying to concatenate subjects using the command

isxconcat-sess -d $SUBJECTS_DIR -sf 
/cluster/roffman/users/Stable5_PerRun/Subject_Files/TEST -analysis 
SIRP_LoadRegression_Stable5_072915 -c Cond2vFix -hemis -o 
/cluster/roffman/users/STable5_PerRun/Analyses_GDD/GDD_All/100_GDD_92Adults_8Adolescents/TEST

I'm receiving the error

ERROR: cannot find 
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA147/bold/register.dof6.dat

I have register.dof6.dat in my run folders, but not in the general bold folder. 
I know that I can create a register.dof6.dat file in my bold folder if I run 
registration on my subjects -per-session. However, I want my subjects to stay 
preprocessed and registered -per-run. 

The analysis used in the isxconcat-sess command is also specified to be 
-per-run. The command I used to make it was 

mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm 
slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
-native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
-fwhm 5 -per-run

Is there a way to specify in the concatenation command that my subjects are 
registered -per-run, and that the command should not look in the bold folder 
for the register.dof6.dat file, but instead in the run folders?

Thanks,
Anais

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Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

[Eugenio Iglesias]

This is really weird.
Can you please confirm that the file
/Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib
exists?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
Sent: Tuesday, September 29, 2015 11:39:00 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Eugenio,

Thanks for the response. I just tried that and it still didn't work (same error 
message).

Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 lab  wheel  638418 Sep 29 08:37 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#
#@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left 
\n
See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
  Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
  Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 90075 Trace/BPT trap: 5   
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args
#
#@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT 
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right 
\n
See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
  Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
  Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 90112 Trace/BPT trap: 5   
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args




Thanks,

Aarthi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Monday, September 21, 2015 1:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH 
environment variable, and the run the hippocampal subfield module. You can do 
that as follows:

In bash:
unset DYLD_LIBRARY_PATH

In (t)csh:
unsetenv DYLD_LIBRARY_PATH

Let us know if this helps

Cheers,

Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Aarthi Padmanabhan" 
To: "Freesurfer support list" 
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi, I had posted this earlier and am still having issues.




Thank you,










I tried running the Hippocampal Segmentation using the Dev version, I get the 
following error (running on a mac os x Yosemite):

I just downloaded the dev version a couple of days ago. Recon-all -all runs 
fine, but it's unable to run the hippocampals segmentation component.






recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1




Subject Stamp: freesurfer-Darwin-OSX-dev-20150826

Current Stamp: freesurfer-Darwin-OSX-dev-20150826

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56 

Re: [Freesurfer] PVE correction tool within the V 6 beta

[m . bahri]

Dear Greve,

Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some 
unclear options (e.g. --mgx .01) 
Could you please explain which method is used for the pve correction and how 
can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of 
all regions?

Many thanks for your help,

Best,

Mohamed

- Mail original -
De: "Douglas Greve" 
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 28 Septembre 2015 17:49:49
Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta

I'm still putting all the documentation together, but you can start with the 
instructions below. They are assuming you will use kinetic modeling. If you 
have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 
not needed. Let me know and I can give you further instructions.
doug


1. To start, run

gtmseg --s subject

This will take a couple of hours and produces some files needed for GTM PVC 
(which is used for GTM, MG, RBV).

2. You'd then register the PET to the anatomical with bbregister (with --t2 
weighting). Make sure to save the output as an LTA (--lta). I usually use the 
mean TAC as the input. You can do this in parallel with #1.

3. You'd then run mri_gtmpvc, something like

mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg gtmseg.mgz 
--reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 
50 51 52 --km-ref 8 47 --no-rescale

PSF is the point-spread FWHM of the scanner; reg.lta is the registration from 
#2.  --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the 
reference region.  --mgx specifies to output a muller-gartner map (not 
necessary for GTM ROI analysis).

4. For the GTM (ROI) MRTM1 KM analysis, you would then run

  mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 
--no-est-fwhm --nii.gz

where time.dat is a text file withe acquisition time of each time point in the 
tac.

5. For the MRTM2 analysis

set k2p = `cat mrtm1/k2prime.dat`
mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 
--no-est-fwhm --nii.gz

If you want to run a voxel-wise analysis, then you can use the mgx
volume as input (--y). Probably you'll want to sample this to the
surface using mri_vol2surf and the registration file aux/anat2pet.lta,
then smooth on the surface



On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote:
> Dear Expert,
>
> Are there any explanation (steps to follow) about the use of FreeSurfer
> (version 6 beta) to correct for the partial volume effect (PET dynamic
> data)?
>
> Many thanks in advance,
>
> Best,
>
> Mohamed
>

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Re: [Freesurfer] Error Messages for Accessing Bin

[Bruce Fischl]

can you try chmod a+x on one of them and see if it can then be executed? 
e.g.:


chmod a+x  /home/tle7/freesurfer/bin/mri_convert
 /home/tle7/freesurfer/bin/mri_convert

and see if you get an error. If not, you probably downloaded the wrong 
hardware version

cheers
Bruce


On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:



  Hello,
When I run the command "sFSstart" on version 5.0.0, I am receiving the
messages below. Would you please explain to me what the problem is? It
seems like there is trouble accessing the bin.
Thank you

 freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/tle7/freesurfer
FSFAST_HOME   /home/tle7/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR  /home/tle7/freesurfer/subjects
MNI_DIR   /home/tle7/freesurfer/mni
tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
H 0
checking sid number 00152-DT2
1
00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
Actual FREESURFER_HOME /home/tle7/freesurfer
Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mris_register: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_robust_register: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mri_robust_template: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error.
Binary file not executable.
/home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file
not executable.
-cw256 option is now persistent (remove with -clean-cw256)

[Freesurfer] Test incoming emails -

[pablo najt]

I am sending this message as a test since my income emails from FS stopped 
working on the 29 of September.Regards
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[Freesurfer] mri_convert doubles file size when changing TR header information

[Shaun Patel]

I noticed after running slice-time correction with SPM, the resulting Nifti 
files do not have TR information in the header. This breaks the Freesurfer 
pipeline. To get around this, I attempted to use the mir_convert function with 
the “tr” flag to set the TR. However, in doing so, I noticed that the resulting 
nifti file doubles in size. I used the following command: mri_convert f.nii 
f.nii -tr 2000, to set the TR to 2s. Any suggestions as to what is happening to 
the file size and how to prevent it? 

Many Thanks,

Shaun

--
Shaun Patel, Ph.D.
Research Fellow
Department of Neurosurgery
Massachusetts General Hospital
Harvard Medical School
e. shaun.pa...@me.com
w. http://shaunpatel.com
c. 317.340.7260


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Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

[Bruce Fischl]

Hi Feng

they are different atlases made up of a different set of manually labeled 
subjects but they share the same colortable


cheers
Bruce
On Tue, 29 Sep 2015, 
chenhf_uestc wrote:



Dear Freesurfer experts,
 
In the stats folder of subject in the SUBJECTS_DIR, I found the files of
lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results
belong to two different atlas? Because the values and brain regions are
different in these two files.
 
In these two files, I found the command "mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a
../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" and
"mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot
-c ../label/aparc.annot.DKTatlas40.ctab NC058 lh white".
 
So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats,
respectively. Right?
However, when I open these two atlas (attached aparc.annot.ctab and
aparc.annot.DKTatlas40.ctab), I found the contents are same. In addition, I
would really want to know that the value in the aparc.annot.ctab. For ex.  
1  bankssts 25 100  40    0; what does the values mean? 25 100 40 0
 
Best,
Feng

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[Freesurfer] qdec errors

[Lim, Lena]

Dear Doug/Experts,

I tried to compare the right area between 2 groups (A, PC) with Age, Gender and 
total right surface area as covariates using Qdec but encountered the following 
errors. Please kindly help?

Many thanks,

Lena

---

Reading /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl

Using /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl

Loading data table 
/home/spjwker/PAC/Lena/CT_SA/FSL/APC_TA/qdec.table_APC_RA.dat...
Number of columns:  5
fsid column:1
Number of factors:  4
Number of subjects: 41

Data table /home/spjwker/PAC/Lena/CT_SA/FSL/APC_TA/qdec.table_APC_RA.dat 
loaded.Verifying subject data.Subject 
verification complete.
Input table: /home/spjwker/PAC/Lena/CT_SA/FSL/APC_TA/qdec.table_APC_RA.dat
Subj#, SubjID, Data...
1 PAC07 Abused Male 19.50 104641.00
2 PAC08 Abused Male 20.83 84314.40
3 PAC10 Abused Female 15.00 76115.00
4 PAC11 Abused Male 18.08 86775.30
5 PAC13B Abused Male 18.83 6.40
6 PAC15 Abused Male 17.75 87943.80
7 PAC16B Abused Male 18.67 80553.90
8 PAC17 Abused Male 17.75 88693.90
9 PAC20 Abused Female 17.92 85204.00
   10 PAC21B Abused Female 19.67 74220.20
   11 PAC22 Abused Male 18.67 77872.20
   12 PAC25 Abused Male 20.08 85559.00
   13 PAC29 Abused Male 13.67 100163.00
   14 PAC30 Abused Female 15.92 94218.20
   15 PAC31 Abused Male 18.67 94218.20
   16 PAC32 Abused Female 16.92 92242.40
   17 PAC34 Abused Male 18.08 89322.50
   18 PAC35 Abused Male 12.92 74837.10
   19 PAC36 Abused Male 20.83 89709.30
   20 PAC50 Abused Female 13.50 93759.10
   21 PAC55B Abused Female 15.42 72894.70
   22 PAC57 Abused Male 19.08 90090.00
   23 PAC24 PC Female 20.33 76837.10
   24 PAC26B PC Female 14.50 84698.40
   25 PAC27 PC Male 17.75 86312.70
   26 PAC28 PC Male 17.08 89002.50
   27 PAC33 PC Female 13.92 95946.90
   28 PAC37 PC Female 17.42 74634.80
   29 PAC39 PC Male 19.50 86479.80
   30 PAC41 PC Male 18.42 85007.50
   31 PAC42 PC Female 13.17 63154.40
   32 PAC43 PC Male 19.25 94902.40
   33 PAC44 PC Male 15.00 84676.50
   34 PAC45 PC Female 17.92 73046.70
   35 PAC48 PC Female 20.50 81855.30
   36 PAC52 PC Female 12.42 73954.70
   37 PAC59 PC Male 17.75 85728.90
   38 PAC63 PC Male 12.42 80241.70
   39 PAC66 PC Male 18.92 86695.20
   40 PAC69 PC Female 15.83 79890.00
   41 PAC70 PC Female 17.92 79619.60
1  Group  discrete 2
1  Abused
2  PC
2  Gender  discrete 2
1  Male
2  Female
3  Age  continuous 0
4  RH_TotalArea  continuous 0
Continuous Factors: Mean:   StdDev:
--- -   ---
Age17.263 2.442
   RH_TotalArea 84483.139  8381.281

Number of subjects:   41
Number of factors:4 (2 discrete, 2 continuous)
Number of classes:4
Number of regressors: 12

Data table loading completed successfully.
SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL'
rh-Avg-Intercept-area ---
Does the average area differ from zero?
Nuisance factors: Age RH_TotalArea
1.000   1.000   1.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
0.000   0.000;

rh-Diff-Abused-PC-Intercept-area ---
Does the average area, accounting for Gender, differ between Abused and PC?
Nuisance factors: Age RH_TotalArea
1.000  -1.000   1.000  -1.000   0.000   0.000   0.000   0.000   0.000   0.000  
0.000   0.000;

rh-Diff-Male-Female-Intercept-area ---
Does the average area, accounting for Group, differ between Male and Female?
Nuisance factors: Age RH_TotalArea
1.000   1.000  -1.000  -1.000   0.000   0.000   0.000   0.000   0.000   0.000  
0.000   0.000;

rh-X-Group-Gender-Intercept-area ---
Is there a Group--Gender interaction in the mean area?
Nuisance factors: Age RH_TotalArea
1.000  -1.000  -1.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
0.000   0.000;

ninputs = 41
Checking inputs
nframestot = 41
Allocing output
Done allocing
nframes = 41
Writing to 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/rh-area-APC_covAgeGenderRA/y.mgh
gdfReadHeader: reading 
/home/spjwker_PAC/Lena/CT_SA/FSL/qdec/rh-area-APC_covAgeGenderRA/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 

[Freesurfer] Error using selexavg3-sess

[Morenikeji Adebayo]

Hi there,

I’m running into difficulty executing the “selexavg3-sess” command for a few 
participants. For example, when I run the command:

foreach c(lh rh mni305)
selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d . 
-no-preproc
end


I get the following error:


Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);

Any help on this error would be much appreciated!

Thanks,
Keji

---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

[Watson, Christopher]

Yes, they are 2 separate atlases. The references are on the FS wiki.

The "ctab" files are colortable files, so I believe the "25 100 40 0" are the 
RGB + transparency/opacity


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of chenhf_uestc 
[chenhf_ue...@163.com]
Sent: Tuesday, September 29, 2015 10:59
To: freesurfer
Subject: [Freesurfer] Questions about the files of lh.aparc.stats and   
lh.aparc.DKTatlas40.stats

Dear Freesurfer experts,

In the stats folder of subject in the SUBJECTS_DIR, I found the files of 
lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results 
belong to two different atlas? Because the values and brain regions are 
different in these two files.

In these two files, I found the command "mris_anatomical_stats -mgz -cortex 
../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a 
../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" and 
"mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab NC058 lh white".

So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats, 
respectively. Right?
However, when I open these two atlas (attached aparc.annot.ctab and 
aparc.annot.DKTatlas40.ctab), I found the contents are same. In addition, I 
would really want to know that the value in the aparc.annot.ctab. For ex.   1  
bankssts 25 100  400; what does the values mean? 25 100 40 0

Best,
Feng

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[Freesurfer] Calculate the cortical thickness in patients with brain tumor

[chenhf_uestc]

Hi, freesurfer experts,

If my data came from the patients with brain tumors, could I perform recon-all 
analyses to calculate cortical thickness, surface area and so on. If not, could 
I mask the brain region with tumor and then conduct such analyses? I think the 
tumor might lead to the inaccuracy of cortical reconstruction 

Best,
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Re: [Freesurfer] GRF correction in mri_glmfit-sim

[Douglas Greve]

On 9/29/15 11:32 AM, chenhf_uestc wrote:
I am also very interested in these questions, but I do not find the 
response. Could anyone provide the answers?

Thanks,
Feng


*发件人：*"Meiling Li" 
*发送时间：*2015-09-22 22:09
*主题：*[Freesurfer] GRF correction in mri_glmfit-sim
*收件人：*"freesurfer-help"
*抄送：*
Dear FS experts
I do GRF correction using mri_glmfit-sim --grf in volume. I find
--grf pos and --grf neg, but not --grf abs.
My first question is, is the --grf just used for ONE-side
correction? For instance,  we can test, are the FCs of patients
larger than that of healthy controls or smaller than the healthy
controls? If I want to test the difference of FCs between patients
and healthy controls, how do i do that?

We don't have anything specifically to do this (though it is 
theoretically possible).



Please help me to check the following commands i used to do the
TWO-sides correction (for example. voxel-wise p: 0.05,
cluster-wise p: 0.05):
  mri_glmfit-sim --glmdir g2v0 --grf 1.3 pos --cwp .05
  mri_glmfit-sim --glmdir g2v0 --grf 1.3 neg --cwp .05


Those look correct.


Then  i use the following commands to combine the 'pos' and 'neg'
results together
mri_convert grf.th1.3.neg.sig.cluster.mgh
grf.th1.3.neg.sig.cluster.nii.gz
mri_convert grf.th1.3.pos.sig.cluster.mgh
grf.th1.3.pos.sig.cluster.nii.gz
fslmaths grf.th1.3.pos.sig.cluster.nii.gz -add
grf.th1.3.neg.sig.cluster.nii.gz grf.th1.3.sig.cluster.nii.gz
Finally, i think the result  grf.th1.3.sig.cluster.nii.gz is what
i want, which is the difference between patients and healthy
controls with GRF corrected, with vertex-wise p< 0.05 and
cluster-wise p<0.05. Is it right?

I'm not sure about this. The glmfit-sim commands above will give you 
cluster tables. You will need to multiply the p-value in the table by 2 
to account for both pos and neg. The map you create could be used to 
display the results.


2. The other question is, If i  do the two-sides GRF
correction(vertex-wise p<0.05 and cluster-wise p<0.05) with 'pos'
or 'neg', should the vertex-wise or cluster-wise be 0.05/2 and
0.05/2? or 0.05 and 0.05?
for example, we should write like this
  mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) pos --cwp 0.05/2
  mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) neg --cwp 0.05/2

It should be .05 (though this is a bit liberal for GRF, .01 would be 
better).



3. If i want to do cluster-based FDR correction, is there any FS
command to do it? is it right if i load the statistic p map into
MATLAB and do the FDR correction, then i use 'mri_volcluster
--minsizevox'  to threshold it to remove voxels smaller than the
cluster size i set.



There is not a command to do this. You can do it in matlab with 
fast_fdrthresh.m. I don't understand the question about the voxel size 
and FDR.



Thank you very much for any help!

All the best,
Meiling












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[Freesurfer] Error Message when Accessing Bin

[Timothy Quang-Tin Le]

Hello,
When I run the command "sFSstart" on version 5.0.0, I am receiving the
messages below. Would you please explain to me what the problem is? It
seems like there is trouble accessing the bin.
Thank you

 freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/tle7/freesurfer
FSFAST_HOME   /home/tle7/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR  /home/tle7/freesurfer/subjects
MNI_DIR   /home/tle7/freesurfer/mni
tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
H 0
checking sid number 00152-DT2
1 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
Actual FREESURFER_HOME /home/tle7/freesurfer
Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP Wed Jul
29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary file
not executable.
/home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_register: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_robust_register: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_robust_template: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not
executable.
/home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. Binary
file not executable.
/home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file not
executable.
-cw256 option is now persistent (remove with -clean-cw256)
/home/tle7/freesurfer/subjects/00152-DT2_v5

 mri_convert /home/tle7/freesurfer/subjects/practicemotherdaughter/
rawdata/00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
/home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz

/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not
executable.
Linux 

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

[Marie Schaer]

Hi Kie Woo,

The other thing that you might want to check is that the pial-outer-smoothed 
surface and the pial surface match, in case the transformation from the CIVET 
format induced any strange translation in space and they don't line up. Just 
open them both on a volume using tkmedit or freeview.

Best,

Marie

On Oct 1, 2015, at 8:54 AM, Bruce Fischl 
 wrote:

> Hi Kie Woo
> 
> can you run mris_euler_number on those surfaces to see if they are 
> topologically correct?
> 
> cheers
> Bruce
> 
> 
> On Thu, 1 Oct 2015, Nam, Kie Woo wrote:
> 
>> Dear experts,
>>  
>> I’m trying to calculate local gyrifcation index using CIVET’s surface file
>> (‘.obj’).
>>  
>>  
>>  
>>  
>> First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created
>> a ‘.pial’ file - below are the commands that worked for ‘CIVET -->
>> FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions.
>> CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big
>> Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj
>> -o_fs lh.pial; mris_convert lh.pial.asc lh.pial”
>> FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface
>> -i_fs lh.pial -o_mni lh.pial”
>>  
>>  
>>  
>>  
>> Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the
>> following message.
>> 
>> lGI for vertex number 5501 of the outer mesh is 4.1122
>> lGI for vertex number 5601 of the outer mesh is 0.86156
>> lGI for vertex number 5701 of the outer mesh is 3.8343
>> ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes.
>> WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high
>> (lGI=62.3205)...
>> ...lGI computation will be stopped. This may be caused by topological
>> defects, check mris_euler_number on the pial surface.
>> 
>>  
>> The link below suggests rerunning “recon-all -autorecon2-wm -randomness”,
>> but it’s not an option for me because I have no other FreeSurfer compatible
>> files except “.pial”.
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html
>>  
>>  
>>  
>> So, could there be any solution for this?
>>  
>>  
>>  
>> Best wishes,
>>  
>> Kie Woo
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> 
> 
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> 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] Freesurfer Dev 6.0 Hippocampal Segmentation

[Aarthi Padmanabhan]

Hi Eugenio

the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/

Should I reinstall freesurfer?

thanks!



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Tuesday, September 29, 2015 10:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

This is really weird.
Can you please confirm that the file
/Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib
exists?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
Sent: Tuesday, September 29, 2015 11:39:00 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Eugenio,

Thanks for the response. I just tried that and it still didn't work (same error 
message).

Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 lab  wheel  638418 Sep 29 08:37 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#
#@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left 
\n
See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
  Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
  Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 90075 Trace/BPT trap: 5   
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args
#
#@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT 
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right 
\n
See log file: 
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
  Referenced from: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
  Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40: 90112 Trace/BPT trap: 5   
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args




Thanks,

Aarthi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Monday, September 21, 2015 1:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH 
environment variable, and the run the hippocampal subfield module. You can do 
that as follows:

In bash:
unset DYLD_LIBRARY_PATH

In (t)csh:
unsetenv DYLD_LIBRARY_PATH

Let us know if this helps

Cheers,

Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Aarthi Padmanabhan" 
To: "Freesurfer support list" 
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi, I had posted this earlier and am still having issues.




Thank you,










I tried running the Hippocampal Segmentation using the Dev version, I get the 
following error (running on a mac os x Yosemite):

I just downloaded the dev version a 

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

[Bruce Fischl]

Hi Kie Woo

can you run mris_euler_number on those surfaces to see if they are 
topologically correct?


cheers
Bruce


On Thu, 1 Oct 2015, Nam, Kie Woo wrote:



Dear experts,

 

I’m trying to calculate local gyrifcation index using CIVET’s surface file
(‘.obj’).

 

 

 

 

First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created
a ‘.pial’ file - below are the commands that worked for ‘CIVET -->
FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions.

CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big
Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj
-o_fs lh.pial; mris_convert lh.pial.asc lh.pial”

FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface
-i_fs lh.pial -o_mni lh.pial”

 

 

 

 

Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the
following message.



lGI for vertex number 5501 of the outer mesh is 4.1122

lGI for vertex number 5601 of the outer mesh is 0.86156

lGI for vertex number 5701 of the outer mesh is 3.8343

... remeasuring lGI value for vertex iV = 5801. It may take a few minutes.

WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high
(lGI=62.3205)...

...lGI computation will be stopped. This may be caused by topological
defects, check mris_euler_number on the pial surface.



 

The link below suggests rerunning “recon-all -autorecon2-wm -randomness”,
but it’s not an option for me because I have no other FreeSurfer compatible
files except “.pial”.

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html

 

 

 

So, could there be any solution for this?

 

 

 

Best wishes,

 

Kie Woo


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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

[Anastasia Yendiki]

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This 
is a relative path, i.e., it's trying to find it under the directory where 
you are currently cd'd.


This seems like a problem with defining paths properly for unix, rather 
than a tracula problem per se.


On Wed, 30 Sep 2015, andrea cristina Lima wrote:


I got the error below. Could you help me? I've already check the dti file and 
it seems Ok. Tks 

macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
/Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt

INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer

INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc 

#-

#@# Image corrections Wed Sep 30 11:27:28 BRT 2015

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz 

niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...

Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 
02:26:53 PDT 2015;
root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015


--
Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573

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Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

Hi,
I tried the chmod command, but it did not work. How I check that I've
downloaded the correct version?
Thank you very much
Timothy

On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl 
wrote:

> can you try chmod a+x on one of them and see if it can then be executed?
> e.g.:
>
> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>  /home/tle7/freesurfer/bin/mri_convert
>
> and see if you get an error. If not, you probably downloaded the wrong
> hardware version
> cheers
> Bruce
>
>
>
> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>
>
>>   Hello,
>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>> messages below. Would you please explain to me what the problem is? It
>> seems like there is trouble accessing the bin.
>> Thank you
>>
>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/tle7/freesurfer
>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii
>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>> MNI_DIR   /home/tle7/freesurfer/mni
>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>> H 0
>> checking sid number 00152-DT2
>> 1
>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>> Actual FREESURFER_HOME /home/tle7/freesurfer
>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_robust_register: Exec format error.
>> Binary file not executable.
>> 

Re: [Freesurfer] Registering set of extracted hippocampus

[Chester Dolph]

Hello,

Rewording to clarify in case the wording was confusing.  What I would like to 
do is to use each registered ROI for intensity based analysis. I am confused 
how to use Freesurfer to register and align about three axis.  I understand 
there is variability with positioning the head within the scanner of MRI. I am 
guessing one solution might be to align each ROI centroid to the same location. 
This seems to be a trivial concept, but I was hoping there was a simple way of 
doing this using Freesurfer tools.  I appreciate your time and help.

Thanks,
Chester


> On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH  wrote:
> 
> Dear experts,
> 
> I look like to register a set of extracted hippocampus to a common atlas.  
> Here is my workflow:
> 
> I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then 
> used mri_mask to mask the norm.mgz to get a volume of intensities.  After 
> this process, I noticed that hippocampus do not seem aligned in terms of the 
> axial axis.  
> 
> I have been looking at the registration tools at:
> 
>  https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration 
> 
> 
> Would someone please make a recommendation of a freesurfer tool well suited 
> to registering a set of extracted left or right hippocampus to a common 
> atlas?  Also is there a flag to indicate the region, for instance from the 
> look up table: $FREESURFER_HOME/FreeSurferColorLUT.txt
> 
> Thanks,
> Chester

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Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.


Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl 
wrote:

> that will generate a parcellation on the individual subject surface of
> Thomas Yeo's 17-network clustering. It won't do anything with the thickness
> though. What are you trying to do?
>
> On Tue, 29 Sep 2015, Ali Radaideh wrote:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
>>
>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
>> --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>
>> scz10 is my subject name
>>
>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve > >
>> wrote:
>>   what is your surf2surf command?
>>
>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>   Dear Douglas,
>>
>> Thanks for your email. I meant to say that after running the
>> recon-all, i ran the sur2surf command to get the cortical
>> parcellation using Thomas Yeo Atlas.
>>
>> I thought that the extracted cortical thickness after running
>> the surf2surf command will be different from the one extracted
>> before running the command. But, Bruce kindly replied to my
>> email saying that it is the same if it is calculated on
>> vertex-wise basis.
>>
>> Thanks,
>> Ali
>>
>> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
>>  wrote:
>>   I can't understand what you are asking. Can you
>>   elaborate?
>>
>>   On 09/28/2015 01:51 PM, Ali Radaideh wrote:
>>   > Thanks alot Douglas,
>>   >
>>   > Yes it is there but after checking it many time I
>>   found it corrupted
>>   > for some subjects due to copying them many times
>>   between machines.
>>   >
>>   > But May I ask you some thing related. I have just
>>   posted a question
>>   > regarding getting the cortical thickness after
>>   running the surf2surf
>>   > command (17 networks cortical parcellation). Now I
>>   found the stats
>>   > file not updated after running this command only
>>   the annotation files
>>   > in label folder.
>>   [rh.Yeo2011_17Networks_N1000.annot]. We thought that
>>   > using Yeo Atlas will give slightly different
>>   cortical thickness, are
>>   > we correct?
>>   >
>>   > Thanks,
>>   > Ali
>>   >
>>   > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
>>   > >   > wrote:
>>   >
>>   > does that file exist?
>>   >
>>   > On 09/28/2015 01:05 PM, Ali Radaideh wrote:
>>   > > Dear FreeSurfer experts,
>>   > > After finishing the recon-all, I am trying
>>   to extract the cortical
>>   > > thickness for each subject and group them
>>   into one table but
>>   > > unfortunately i keep getting the following
>>   error:
>>   > >
>>   > > ​rh.aparc.DKTatlas40.stats is not found or is
>>   too small to be a
>>   > valid
>>   > > statsfile
>>   > > Use --skip flag to automatically skip bad
>>   stats files​
>>   > >
>>   > > i tried to change the stats file (e.g I used
>>   aparc.a2009s) but I got
>>   > > the same error.
>>   > >
>>   > > I tried each brain alone and also got the
>>   same error.
>>   > >
>>   > > Any ideas please
>>   > > ​Thanks,
>>   > > Ali​
>>   > >
>>   > > --
>>   > > /Ali M. Al-Radaideh. PhD
>>   > > Head of Department of Medical Imaging
>>   > > Vice Dean of the Faculty of Allied Health
>>   Sciences
>>   > > The Hashemite University,
>>   > > Zarqa, Jordan
>>   > > W.phone +962 5 390 ext.5422, 5355, 5364
>>   > > Email: ali.radai...@hu.edu.jo
>>   
>>   > >   >
>>   > > /
>>   > > /webpage:
>>   http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>>   > >
>>   > >
>>   > >
>>   > >
>>   ___
>>   > > Freesurfer mailing list
>>   > > Freesurfer@nmr.mgh.harvard.edu
>>   > 
>>   > >
>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>   >
>>   > --
>>   > Douglas N. Greve, Ph.D.
>>   > MGH-NMR Center
>>   > gr...@nmr.mgh.harvard.edu
>>   
>>   > Phone Number: 617-724-2358
>>   > Fax: 617-726-7422
>>   >
>>   > Bugs:
>>   surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>  

Re: [Freesurfer] Registering set of extracted hippocampus

[Bruce Fischl]

Hi Chester

you can use the talairach.m3z to map to a common space (which is our 
nonlinear atlas space). The easiest thing is probably to do (e.g.)


mri_extract_label -t transforms/talairach.m3z aseg.mgz 17 lh.hippo.mgz

this will extract the lh hippo label and transform it into our common atlas 
space.


cheers
Bruce




On Thu, 1 Oct 2015, Chester Dolph wrote:


Hello,
Rewording to clarify in case the wording was confusing.  What I would like
to do is to use each registered ROI for intensity based analysis. I am
confused how to use Freesurfer to register and align about three axis.  I
understand there is variability with positioning the head within the scanner
of MRI. I am guessing one solution might be to align each ROI centroid to
the same location. This seems to be a trivial concept, but I was hoping
there was a simple way of doing this using Freesurfer tools.  I appreciate
your time and help.

Thanks,
Chester


  On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH 
  wrote:

Dear experts,
I look like to register a set of extracted hippocampus to a common
atlas.  Here is my workflow:

I used mri_binarize to get a mask of the hippocampus from aseg.mgz and
then used mri_mask to mask the norm.mgz to get a volume of
intensities.  After this process, I noticed that hippocampus do not
seem aligned in terms of the axial axis.  

I have been looking at the registration tools at:

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

Would someone please make a recommendation of a freesurfer tool well
suited to registering a set of extracted left or right hippocampus to
a common atlas?  Also is there a flag to indicate the region, for
instance from the look up
table: $FREESURFER_HOME/FreeSurferColorLUT.txt

Thanks,
Chester



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Re: [Freesurfer] Parcellation stats

[Bruce Fischl]

sure, you can use mri_segstats to get stats from it
Bruce
On Thu, 1 Oct 2015, Ali 
Radaideh wrote:



Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be
loaded tksurfer as an overlay.


Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl 
wrote:
  that will generate a parcellation on the individual subject
  surface of Thomas Yeo's 17-network clustering. It won't do
  anything with the thickness though. What are you trying to do?

  On Tue, 29 Sep 2015, Ali Radaideh wrote:

mri_surf2surf --srcsubject fsaverage --trgsubject
scz10 --hemi rh
--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
_N1000.annot
--tval
$SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve

wrote:
      what is your surf2surf command?

      On 9/28/15 5:11 PM, Ali Radaideh wrote:
      Dear Douglas,

Thanks for your email. I meant to say that after
running the
recon-all, i ran the sur2surf command to get the
cortical
parcellation using Thomas Yeo Atlas.

I thought that the extracted cortical thickness
after running
the surf2surf command will be different from the one
extracted
before running the command. But, Bruce kindly
replied to my
email saying that it is the same if it is calculated
on
vertex-wise basis. 

Thanks,
Ali

On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
 wrote:
      I can't understand what you are asking. Can
you
      elaborate?

      On 09/28/2015 01:51 PM, Ali Radaideh wrote:
      > Thanks alot Douglas,
      >
      > Yes it is there but after checking it many
time I
      found it corrupted
      > for some subjects due to copying them many
times
      between machines.
      >
      > But May I ask you some thing related. I have
just
      posted a question
      > regarding getting the cortical thickness
after
      running the surf2surf
      > command (17 networks cortical parcellation).
Now I
      found the stats
      > file not updated after running this command
only
      the annotation files
      > in label folder.
      [rh.Yeo2011_17Networks_N1000.annot]. We
thought that
      > using Yeo Atlas will give slightly different
      cortical thickness, are
      > we correct?
      >
      > Thanks,
      > Ali
      >
      > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N
Greve
      > > wrote:
      >
      >     does that file exist?
      >
      >     On 09/28/2015 01:05 PM, Ali Radaideh
wrote:
      >     > Dear FreeSurfer experts,
      >     > After finishing the recon-all, I am
trying
      to extract the cortical
      >     > thickness for each subject and group
them
      into one table but
      >     > unfortunately i keep getting the
following
      error:
      >     >
      >     > ​rh.aparc.DKTatlas40.stats is not found
or is
      too small to be a
      >     valid
      >     > statsfile
      >     > Use --skip flag to automatically skip
bad
      stats files​
      >     >
      >     > i tried to change the stats file (e.g
I used
      aparc.a2009s) but I got
      >     > the same error.
      >     >
      >     > I tried each brain alone and also got
the
      same error.
      >     >
      >     > Any ideas please
      >     > ​Thanks,
      >     > Ali​
      >     >
      >     > --
      >     > /Ali M. Al-Radaideh. PhD
      >     > Head of Department of Medical Imaging
      >     > Vice Dean 

[Freesurfer] FreeSurfer Ubuntu Server

[Bruno LAD]

Hi, could you help me please, because a couldn't find the answer for my
question in the wiki.

Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if
it's possible?


Thank you.

-- 
Best Regards
Bruno Bragança Mendes
Laboratório de Alto Desempenho LAD/PUCRS
Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120
+55 51 33538001
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[Freesurfer] freeview and ?h.cortex.patch.flat

[Xiaomin Yue]

Hi,
Can the developmental freeview display ?h.cortex.patch.flat?  I can't find 
answers in the mail list.  If not, is there any way to convert the patch.flat 
to a format freeview can display?
Thanks,Xiaomin___
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[Freesurfer] Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School

[Poornima Kumar]

Two post-doctoral positions are available within the Laboratory for
Affective and Translational Neuroscience at McLean Hospital/Harvard Medical
School, directed by Diego A. Pizzagalli, Ph.D.



The laboratory is part of the Center for Depression, Anxiety and Stress
Research (CDASR), a vibrant research center that embraces a
multi-disciplinary approach to improve our understanding of the
psychological, environmental, and neurobiological factors associated with
depression, anxiety and related disorders across the lifespan (
http://cdasr.mclean.harvard.edu/).



Currently ongoing studies in Dr. Pizzagalli’s laboratory focus on reward
processing, stress responsivity, and executive functioning in a range of
populations including individuals with major depression, mood spectrum
disorders, as well as at-risk samples (e.g., offspring of parents with MDD;
individuals with past MDD). These studies employ a variety of approaches,
including high-density EEG, fMRI, PET, MRS, molecular genetics, and assays
of hormonal/inflammatory markers, and often a treatment component (e.g.,
CBT). Opportunities will be available to pursue independent research and
interdisciplinary collaborations across Harvard Medical School. Depending
on research focus, candidates will have access to three research-dedicated
human MRI scanners (3 T, 4 T) and one animal MRI scanner (9.4 T), as well
as 128-channel EEG systems. A strong background in EEG/ERP or fMRI
techniques is required, and clinical training is a plus. To apply, send a
CV and a cover letter describing your research interests, and arrange for
three letters of recommendation to be sent to David Crowley (
djcrow...@mclean.harvard.edu). Review of applications will begin
immediately (expected start date: Summer 2016).



McLean Hospital, which is an affiliate of Harvard Medical School, is an
Equal Opportunity Employer.  As an equal opportunity employer, McLean seeks
qualified candidates for all posted employment opportunities without regard
to race, color, age, religion, gender, national origin, disability or
veteran status. McLean particularly welcomes applications from minorities,
women, and persons with disabilities.
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Re: [Freesurfer] FreeSurfer Ubuntu Server

[Rudolph Pienaar]

Yes, FreeSurfer can be installed on Ubuntu without any issues. There is 
also no functional difference between Ubuntu server and Ubuntu Desktop.

Do you have a compelling reason for wanting to use Ubuntu 12.04? It was 
released in 2012 and is rather ancient in Ubuntu terms. The current 
version of Ubuntu is 15.04 and in fact 15.10 is about to released in 
three weeks.

I'd strongly recommend you update to a modern Ubuntu.

Having said that, certainly on Ubuntu 14.04 and above, once installed 
you need to simply symlink some libraries since the versions FreeSurfer 
has been compiled against are depreciated on Ubuntu 14.04 and later.

In a terminal, simply type (make sure that each command is on a single 
line -- the email formatting might have split it in two):

For Trackvis and dtk

sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.5 
/usr/lib/x86_64-linux-gnu/libtiff.so.3

sudo ln -s /usr/lib/x86_64-linux-gnu/libmng.so.2.0.2 
/usr/lib/x86_64-linux-gnu/libmng.so.1

For FreeSurfer:

sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl_algo.so 
/usr/lib/x86_64-linux-gnu/libvnl_algo.so.1.14

sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl.so 
/usr/lib/x86_64-linux-gnu/libvnl.so.1.14

sudo ln -s /usr/lib/x86_64-linux-gnu/libv3p_netlib.so 
/usr/lib/x86_64-linux-gnu/libv3p_netlib.so.1.14

HTH
-=R

On 10/1/15 15:58 , Bruno LAD wrote:
> Hi, could you help me please, because a couldn't find the answer for my
> question in the wiki.
>
> Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if
> it's possible?
>
>
> Thank you.
>
> --
> Best Regards
> Bruno Bragança Mendes
> Laboratório de Alto Desempenho LAD/PUCRS
> Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120
> +55 51 33538001 
>
>
>
> ___
> 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.
>


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

[Thục Trinh]

​
 NCP140539_2_recon.rar

​Hi Freesurfer Experts,

We are on the process of troubleshooting our subjects's recon and we came
across with this error that we can not determine what kind of problem this
is:
It seems there is no white matter and pial errors on all slices as we check
on three different views (sagital,coronal and axial);however, when we load
rh.inflated.nofix surface on both freeview and tksurfer, there is a big
difference that at the frontal cortex (area near the medial wall), it
appears a handle error and also some hole errors on freeview while it does
not on tksurfer.
Would you explain how it is visualized that makes us so confused to
troubleshoot since we can not find anything wrong on white matter volume to
be fixed?
Here is our data,

Have a nice day,

Trinh
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