Re: [Freesurfer] standardized community affiliation vector

[Chris Watson]

You would have to get a connectivity matrix (either from someone who has 
analyzed the data, or from analysis that you do yourself).

Even still, there won't be a "standard" because:
* there are different ways of measuring connectivity (probabilistic vs. 
deterministic tractography; resting-state fMRI seed-based correlations; 
structural (thickness) covariance; etc.)
* what kind of variables "should" be adjusted for? Age and sex might be 
universally agreed upon; what about head size/TIV? or SES? Should 
tractography streamline counts (or whatever you're using) be adjusted 
for seed/target ROI size? etc.
* there are different parcellations (Desikan-Killiany, Destrieux, AAL, 
voxel-based, random, etc.)

* there are different methods for community detection

However if you chose one method from the above bullet points and did the 
same for your data (e.g. if you have a patient group and you want to 
compare to a "standard" control group), I think it would be a reasonable 
comparison. Another issue would be different scanning sequences in the 
HCP vs. your study, and that HCP data hasn't been tested for 
validity/reliability (I'm thinking along the lines of IQ testing like 
the WISC).


Chris

On 01/20/2015 05:01 AM, Alexander Lebedev wrote:

*_Dear Colleagues,_*

I am sorry if my question is a bit out-of-topic...
I wonder if there is a an opportunity to find a community affiliation 
vector estimated using any of the large-scale datasets (like the Human 
Connectome Project, for example).. I was just thinking that having 
independently estimated community structure (assuming the same age 
group) for further extraction of modularity-based metrics makes more 
sense than using the exact same sets to estimate both community 
structure and related measures like participation and diversity 
coefficients.


Thanks in advance!
*===*
*Best Wishes,*
*Alex*

--
Alexander V. Lebedev MD PhD | Postdoctoral Researcher

Department of Neurobiology, Care Sciences and Society | Karolinska 
Institutet


Aging Research Center | 113 30 Stockholm, Sweden | Gävlegatan 16


Center for Age-Related Medicine | Researcher

Stavanger University Hospital

4011 Stavanger, Norway | Armauer Hansens vei 20


Mobile (Sweden): +46 7 659 04 649

Skype ID: alexander.vl.lebedev

alexander.vl.lebe...@gmail.com 
 | www.ki-su-arc.se 





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Re: [Freesurfer] Running analysis on a Linux Partition

[Chris Watson]

You should ask the sys admin to create a directory for you on the shared 
drive. If only root can write to it, that defeats the purpose of a 
shared drive...


On 02/10/2015 08:21 AM, Kate Riggall wrote:

Hello,

I am trying to run a paired analysis (a two time-point longitudinal 
analysis) on some subjects which have been longitudinally 
pre-processed for me on another computer. The computer I am now 
working on is originally a Windows computer, but is now running Linux 
on a partition (CentOS Release 6.6, Kernel Linux 2.6, GNOME 2.28.2). 
It has (apparently) 20.1 MiB of available disk space. My files are on 
a SAMBA shared drive, which I have mounted to /home/user/Shared.


Now, I have created the first FSGD file with no issues, but when I 
come to run mris_preproc I get one of three results, depending on 
where I run it:


1) If I run it in /home/user/folder it runs for a while, but then I am 
told


tee: lh.paired-diff.thickness.mris_preproc.log: No space left on device

and the output file is not created.

2) If I run it in the shared drive (in the same folder as the subject 
data) I am told


mkdir: cannot create directory `./tmp.mris_preproc.11318': Permission 
denied

ERROR: creating ./tmp.mris_preproc.11318

presumably because the shared folder belongs to the root user

3) If I run it in the shared drive using sudo mris_preproc etc. I am told

sudo: mris_preproc: command not found


I can't seem to find a way around this. I hope this makes sense, and 
thanks in advance for your assistance.


Kind Regards,

Kate Riggall


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Re: [Freesurfer] Power analysis for Qdec

[Chris Watson]

Here is a paper discussing post-experiment power analyses and why they 
are wrong:

http://amstat.tandfonline.com/doi/abs/10.1198/000313001300339897#.Um_aDtexGkc

On 10/29/2013 10:51 AM, MCLAREN, Donald wrote:
For anyone who wants G*Power, here is a link to the download page. It 
is free for all users.


http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General 
Hospital and

Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren 


Office: (773) 406-2464
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On Tue, Oct 29, 2013 at 10:40 AM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Good point Donald. Where can one get G*Power?
doug



On 10/29/2013 10:38 AM, MCLAREN, Donald wrote:

One comment on power calculations. You cannot do the power
calculations after you have completed the study. Any
reviewer/referee asking you to compute the power should be
politely informed that post-hoc power analyses are not valid
and are biased (because you would be computing the power of
the observed effect).

What you want to do is to compute the power of the experiment
before you conduct the experiment. You want to be able to say
that to compare an effect of X, we have have Y% power to
detect the effect with N subjects.

G*Power is an excellent program to compute power - although it
doesn't do it on the entire image.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts
General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren



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On Tue, Oct 29, 2013 at 10:25 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:


We don't have a way to do a power analysis directly from
QDEC. I have
some matlab code that does it for univariate analysis.

In the QDEC output folder, you will see a glm folder. In that
there will
be folders for each contrast. In the contrast folder, you
will see an
F.mgh file which will be the F-values. You can convert
this to a t =
sign(gamma.mgh)*sqrt(F)

doug


On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
> Hi
> Would you please let me know if it is possible to
calculate the
power for a group comparison in cortical thickness? Also, a
referee is requesting F-values and T map , are they
generated by
q-dec?
> That would be great if I can get an answer in more
detail since
I have
> seen the post in FAQ, just need more information in
detail regarding
> calculat

Re: [Freesurfer] LGI path problem

[Chris Watson]

Are you in the 'surf' directory? If not, then do "-overlay 
$subject/surf/lh.pial_lgi"


On 11/05/2013 11:26 AM, Linn Mittlestein wrote:

Hi,

Thank you very much, it works. I now however have another problem 
(sorry!). I have run the command on test subject and want to display 
using tksurfer. The file lh.pial_lgi has for sure been created, and i 
cd into correct subjects directory however when I try tksurfer  lh 
inflated -overlay lh.pial_lgi I get following error: ERROR: cannot 
find lh.pial_lgi


Any ideas?

Kind Regards,

Linn



On Mon, Oct 28, 2013 at 6:46 PM, Marie Schaer > wrote:



Hi Linn,

We have an issue using lGI with matlab 2013 in the current
version. It will be updated in the new version, but in the mean
time if you want to use it, it's a very small change that you have
to do. See the following post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html


Or there is a note on LGI and matlab 2013 in the "Release Notes"
page on the wiki.

Hope it works, let me know,

Marie


On Oct 28, 2013, at 3:38 AM, Linn Mittlestein
mailto:linnmit...@gmail.com>> wrote:


Dear Marie,

Thank you, I use bash and changed my .bashrc and this worked, I
previously had used wrong syntax. Thank you very much for your
help. However, I now recieve another error and do not know what
it means at all. I copy in the error ! Thank you.

Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A,
mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!



On Wed, Oct 23, 2013 at 4:04 PM, Marie Schaer
mailto:marie.sch...@unige.ch>> wrote:


Hi Linn,

If you are using tcsh, you have to edit the file $HOME/.cshrc
(.shrc should work as well) to add the following line:

setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY

Then close the terminal and open a new one. Use the env
command to be sure that your path has been modified, then the
getmatlab command from FreeSurfer should give you the correct
location.

Best,

Marie


On Oct 23, 2013, at 12:23 AM, Linn Mittlestein
mailto:linnmit...@gmail.com>>
 wrote:


Hi, thank you. I am using Linux. I not sure where to change
path, ie which file this should be done in and where this
file is located. This the error message I recieve, and as I
said It is launching the wrong matlab and I don't know how
change this.

Launching Matlab7p13

Warning: Unable to open display 'iconic'. You will not be
able to display graphics on the screen.


< M A T L A B (R) >

Copyright 1984-2011 The MathWorks, Inc.

R2011b (7.13.0.564) 32-bit (glnx86)

August 13, 2011



To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com
.


>> reading filled volume...

closing volume...

Undefined function 'fspecial' for input arguments of type
'char'.


Error in make_outer_surface (line 31)

Gaussian = fspecial('gaussian',[2 2],1);


>>

ERROR: make_outer_surface did not create output file
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09
CDT 2013 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58
BST 2013


Thank you very much for your time and help,


Kind Regards,Linn





On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer
mailto:marie.sch...@unige.ch>> wrote:


Hi Linn,

Sorry for the delay in answering. The path has to be set
directly in your environment variable (the variable
$PATH has to point to the correct version). I need a few
more details about what you tried and which OS you are
using to be able to help you.

If you are using mac, here is an example on how you can
set the path in the .shrc file:
setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"

You can also have a look at the following posts:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html

http://w

Re: [Freesurfer] Linux recon-all error

[Chris Watson]

You need to type "sudo yum update", not "command".

On 11/16/2013 01:29 PM, krista kelly wrote:
Thanks Alan for your response! I've tried typing sudo yum update into 
the terminal window, however it does not work. It says yum:command not 
found. I've tried googling how to do this, but I can't find anything. 
This is what I type into the terminal window:


sudo yum command

Am I doing it wrong?

Thanks!
Krista


On Thu, Nov 14, 2013 at 10:48 AM, Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:


Hi Krista:

You may want to update tcsh. You can do this by using SUDO and
'yum update'.

best,

Alan


On Thu, Nov 14, 2013 at 10:42 AM, krista kelly
mailto:krista.kell...@gmail.com>> wrote:

Hello,

I'm running freesurfer's recon-all using Linux and the past
few subjects I've run, recon-all has exited with errors. I've
ran a few subjects so far with no problems, and now all of a
sudden there's an issue and I can't figure out why. I have
been able to run these "problem'  subjects using Linux on
other computers with no issues, so it can't be a raw data
issue. I have pasted the terminal window text below. If anyone
has any idea why this is occurring, I'd love to know!

Thanks!

 freesurfer-Linux-centos4-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni

Freesurfer Virtual Machine
sudo password: freesurfer

fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache
-notal-check -cw256 -subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed
Oct 2 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux
-cw256 option is now persistent (remove with -clean-cw256)
/usr/local/freesurfer/subjects/BV33

 mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz

mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999683, 0.0209404, 0.0139622)
j_ras = (-0.0209424, 0.999781, 0)
k_ras = (-0.0139591, -0.000292399, 0.03)
writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz...
#
#@# MotionCor Thu Nov 14 10:28:28 EST 2013
Found 1 runs
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
/usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz

/usr/local/freesurfer/subjects/BV33

 mri_convert
/usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform
--cw256

mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform
--cw256
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999683, 0.0209404, 0.0139622)
j_ras = (-0.0209424, 0.999781, 0)
k_ras = (-0.0139591, -0.000292399, 0.03)
Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz...

 mri_add_xform_to_header -c
/usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz

INFO: extension is mgz
#-

Re: [Freesurfer] Problems dipslaying annotations in freeview

[Chris Watson]

I've seen this happen after making manual edits and then not finishing a 
re-run of recon-all.

Chris

On 12/10/2013 02:00 PM, Laura Taylor wrote:

Hi,

I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a 
subject.  When I use the freeview gui and select lh.aparc.a2009s.annot 
under the annotations menu a strange multicolored surface is loaded.  
It looks like something that has been tie-dyed and not like the 
examples of parcellation that are shown on some of the freesurfer pages.


I have attached a screenshot of the output that I get.

Any help would be appreciated.

Thank you,

Laura


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Re: [Freesurfer] bvals and bvecs for dt_recon

[Chris Watson]

dcm2nii should give you bvecs and bvals
If you just want to transpose the file, I wrote a script to do it 
(attached).


On 03/13/2014 04:50 PM, Gennan Chen wrote:

Anastasia,

The thing not clear from me is the format for those files. I did not see an 
example anywhere in the wiki or in the distribution.  And I am downing tutorial 
data now. Hope it is there. BTW, do you have an example? I know how to get 
those from private dicom tags.

Gen

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, March 13, 2014 1:37 PM
To: Gennan Chen
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] bvals and bvecs for dt_recon


How is the format different? Is it in 3 rows instead of 3 columns? If so, it 
should be straightforward to convert it yourself from 3 rows to 3 columns.

On Thu, 13 Mar 2014, Gennan Chen wrote:


Hi! All,

Is there an utility to extract bvals and bvecs from GE’s DTI dicom
files into the format dt_recon can use? I try to run dt_recon as it is
but it did not pick up those values. Those files are from ADNI.

Gen

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transpose.sh
Description: application/shellscript
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Re: [Freesurfer] mri_convert .tar.gz files of dicoms?

[Chris Watson]

FYI, you can also get the first file like this:

first_file=$(tar ztf ${in_file} | head -1)

It will be much faster than 'find'.

On 03/20/2014 05:18 PM, Nate Vack wrote:

Also, for what it's worth, here's a little script that wraps this up:

https://gist.github.com/njvack/9674025

Best,
-Nate

On Thu, Mar 20, 2014 at 12:29 PM, Nate Vack  wrote:

Thanks! If you're ever looking for a feature request, then, that's mine :)

Best,
-Nate

On Thu, Mar 20, 2014 at 12:10 PM, Douglas N Greve
 wrote:

no, sorry
doug
On 03/20/2014 11:28 AM, Nate Vack wrote:

Hi,

I'm testing mri_convert for our dicom conversion needs; one thing that
would be fantastic is to be able to feed it a .tar.gz (or .zip)
containing a dicom series we'd like to convert. Is there a way to do
that?

Alternately, if there were a way to make it use stdin, I could just
pipe the output of tar to it.

Thanks!
-Nate
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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
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Re: [Freesurfer] Anonymizing Siemens DICOM files

[Chris Watson]

You could also do it the following way: (you need to download dcmtk)
Assuming you have a bunch of files called MR.*

for dicom in MR.*
do
dcmodify -m "(0010,0010)=PatientsName" ${dicom}
dcmodify -m "(0010,0030)=MMDD" ${dicom}
done

This backs up all the dicoms (they become "MR.*.bak"), which you can 
delete when you verify the new header. Replace "PatientsName" with 
whatever you want.
However, as Michael Harms mentioned there may be identifying info 
elsewhere in the file.


On 03/21/2014 12:10 PM, Bruce Fischl wrote:

yup, that's it
thanks Caspar
Bruce
On Fri, 21 Mar 2014, Caspar M. Schwiedrzik wrote:


Thanks to all that have replied so far!
Bruce, are you referring to this: 
http://freesurfer.net/fswiki/BIRND-UP ?

Thanks, Caspar



2014-03-20 17:40 GMT-04:00 Harms, Michael :

Hi Caspar,
I can't address your question regarding a specific tool, but wanted to
mention a note of caution.
You need to make sure that you scrub any identifying info from
Siemen's custom DICOM fields (not just the obvious public DICOM
fields).
The challenge of doing that is why the safest thing is to not enter
any identifying info at the scanner to begin with.

cheers,
-MH

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

From: "Caspar M. Schwiedrzik" 
Reply-To: Freesurfer support list 
Date: Thursday, March 20, 2014 4:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Cc: Julia Sliwa 
Subject: [Freesurfer] Anonymizing Siemens DICOM files

Hi Freesurfer Experts,
we are looking for a good way to remove subject names and dates of
birth from Siemens DICOM headers. Is there something implemented in
Freesurfer?

Matlab's Image Processing Toolbox has a function to anonymize DICOM
files (http://www.mathworks.com/help/images/ref/dicomanon.html), but
we later run into trouble with unpacksdcmdir when we use that.

Thanks, Caspar




 




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Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

[Chris Watson]

How have you configured NFS? e.g. a simple check is to type
# system-config-nfs

Then choose the filesystem and click "Properties". Make sure the bullet 
point labeled "Read/write" is chosen.



On 05/10/2013 01:45 PM, Garikoitz Lerma-Usabiaga wrote:

Hi,
Has anybody got problems using FS with NFS v4?
We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.

Many thanks,
Gari

-- Forwarded message --
From: *Garikoitz Lerma-Usabiaga* >

Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
To: Freesurfer >



Hi FS experts,
we have changed our file systems to NFS v4 and we found that FS cannot 
write to it (I mean, FS installed in an app server and subjects in the 
file system is not working).
Last new I have is that FS in CentOS could read but not write and in 
Red Hat could not write or read.


Is it a known problem? Is it something going on with FS or the problem 
is in our end? (the rest of the programs are working fine: FSL, Matlab...)



Many thanks,
Gari



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Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

[Chris Watson]

Can you check that the UID and GID both match on the client and server 
sides? Is it the same user that is able to use other programs, yet 
unable to write via Freesurfer? Is your user an NIS account?


Can you output
# ls -l $SUBJECTS_DIR

I assume that since you say other programs can write to the filesystem, 
it is mounted properly, but can you show what is in /etc/fstab? i.e. 
make sure you see "rw" instead of "ro".



On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote:

Thanks for the answers.
I am not the sys admin, but I think I can answer both questions:
> I assume the system is in read-write mode since the rest of the 
programs (i.e. Matlab) are working.

> The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have an account in 
that machine (and I can work normally if my SUBJECTS_DIR is in that 
machine)
--- I have a personal drive space in the NFS 4, and I used to have my 
SUBJECTS_DIR in that drive, but after they upgraded it to NFS 4, it 
didn't work again.
> We have a new cluster now, they are testing it, it has Red Hat 
installed, with FS 5.2, and I've been told that it cannot write (same 
problem).


The strange thing is that other programs work fine with this setup.

Do you think the problem is in the file system config (it seems so) or 
in FS config to be able to work with NFS 4?


I have asked the sys admin for the output of the system-config-nfs, I 
don't have admin privileges to run it.


thanks again!
Gari



On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky 
mailto:ni...@nmr.mgh.harvard.edu>> wrote:


Gari,

At the NMR Center we use NFS v4 without problems with freesurfer.
 Is the
SUBJECTS_DIR writable?  Note that in the default freesurfer
distribution,
the freesurfer/subjects directory is not writable (contains sample and
template subjects).

Nick


> Hi,
> Has anybody got problems using FS with NFS v4?
> We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
>
> Many thanks,
> Gari
>
> -- Forwarded message --
> From: Garikoitz Lerma-Usabiaga mailto:gariko...@gmail.com>>
> Date: Tue, May 7, 2013 at 5:25 PM
> Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
> To: Freesurfer mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hi FS experts,
> we have changed our file systems to NFS v4 and we found that FS
cannot
> write to it (I mean, FS installed in an app server and subjects
in the
> file
> system is not working).
>  Last new I have is that FS in CentOS could read but not write
and in Red
> Hat could not write or read.
>
> Is it a known problem? Is it something going on with FS or the
problem is
> in our end? (the rest of the programs are working fine: FSL,
Matlab...)
>
>
> Many thanks,
> Gari
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Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

[Chris Watson]

Can you paste the output of "ls -l $SUBJECTS_DIR", so we can see what 
the permissions are? You may also want to paste the output of the parent 
directory as well.


On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote:

Thanks Chris,
> ls -l $SUBJECTS_DIR: it works
> This is the output of the command (I cannot make sense out of it):

[glerma@cajal ~]$ cat /etc/fstab
/dev/VolGroup00/LogVol00 /   ext3defaults 
   1 1

LABEL=/boot   /boot   ext3defaults  1 2
tmpfs   /dev/shmtmpfs   defaults  0 0
devpts  /dev/ptsdevpts  gid=5,mode=620  0 0
sysfs   /syssysfs   defaults  0 0
proc  /proc   procdefaults0 0
/dev/VolGroup00/LogVol01 swapswapdefaults 
   0 0

/var/lib/swap/swap_cajal.imgswapswapdefaults0 0
#hippocampus-nfs:/data/datanfsdefaults0 2
#hippocampus-nfs:/home/BCBL/home/BCBLnfsdefaults0 2
ltm.bcbl.local:/root_vdm_1/home/bcbl/homenfs4defaults0 0
ltm.bcbl.local:/root_vdm_1/data/bcbl/data nfs4defaults0 0

#hippocampus-nfs:/home/BCBL  /home/BCBL nfs 
rw,bg,intr,hard,timeo=600,wsize=32768,rsize=32768,nfsvers=3,tcp,noacl 0 2



(this is in the old app server, which worked before the migration to 
the new file system)


thanks again!
Gari


On Sat, May 11, 2013 at 12:07 AM, Chris Watson 
<mailto:christopher.wat...@childrens.harvard.edu>> wrote:


Can you check that the UID and GID both match on the client and
server sides? Is it the same user that is able to use other
programs, yet unable to write via Freesurfer? Is your user an NIS
account?

Can you output
# ls -l $SUBJECTS_DIR

I assume that since you say other programs can write to the
filesystem, it is mounted properly, but can you show what is in
/etc/fstab? i.e. make sure you see "rw" instead of "ro".


On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote:

Thanks for the answers.
I am not the sys admin, but I think I can answer both questions:
> I assume the system is in read-write mode since the rest of the
programs (i.e. Matlab) are working.
> The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have an
account in that machine (and I can work normally if my
SUBJECTS_DIR is in that machine)
--- I have a personal drive space in the NFS 4, and I used to
have my SUBJECTS_DIR in that drive, but after they upgraded it to
NFS 4, it didn't work again.
> We have a new cluster now, they are testing it, it has Red Hat
installed, with FS 5.2, and I've been told that it cannot write
(same problem).

The strange thing is that other programs work fine with this setup.

Do you think the problem is in the file system config (it seems
so) or in FS config to be able to work with NFS 4?

I have asked the sys admin for the output of the
system-config-nfs, I don't have admin privileges to run it.

thanks again!
Gari



On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky
mailto:ni...@nmr.mgh.harvard.edu>> wrote:

Gari,

At the NMR Center we use NFS v4 without problems with
freesurfer.  Is the
SUBJECTS_DIR writable?  Note that in the default freesurfer
distribution,
the freesurfer/subjects directory is not writable (contains
sample and
template subjects).

Nick


> Hi,
> Has anybody got problems using FS with NFS v4?
> We cannot write subjects if the SUBJECTS_DIR is in a NFS v4
system.
>
> Many thanks,
> Gari
>
> -- Forwarded message --
> From: Garikoitz Lerma-Usabiaga mailto:gariko...@gmail.com>>
> Date: Tue, May 7, 2013 at 5:25 PM
> Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
> To: Freesurfer mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hi FS experts,
> we have changed our file systems to NFS v4 and we found
that FS cannot
> write to it (I mean, FS installed in an app server and
subjects in the
> file
> system is not working).
>  Last new I have is that FS in CentOS could read but not
write and in Red
> Hat could not write or read.
>
> Is it a known problem? Is it something going on with FS or
the problem is
> in our end? (the rest of the programs are working fine:
FSL, Matlab...)
>
>
> Many thanks,
> Gari
> ___
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Re: [Freesurfer] temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?

[Chris Watson]

You need to place the control points in the white matter, not around it.

On 05/22/2013 03:04 PM, Yizhou Ma wrote:

Dear FS experts,

I have a subject where large portions of temporal lobe is not included 
in the pial surface. A member in my lab has suggested edits on 
brain.finalsurfs.mgz. However, in the following page it is indicated 
that edits on brain.finalsurfs.mgz is only intended for cases 
regarding inclusion of cerebellum. Can anyone please let me know which 
volume I should be working on in this case?


http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits

Thanks,
Cherry


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Re: [Freesurfer] using two vs one scan(s) for optimal surface reconstruction

[Chris Watson]

I only have anecdotal evidence on this. (using version 5.1)
I found that if both scans had "a little" motion, then using both 
improved reconstruction.
If one scan was pretty bad, and the other was pretty good, then using 
the pretty good one on its own was better than using both.
If both were pretty bad, then using one or both didn't matter. (poor 
results either way)
If the scan was good in the first place, I didn't repeat acquisition. In 
one subject, the first scan only had a little motion, and the 2nd scan 
was very good; in this case using both was worse than using just the 
very good scan.


Unfortunately I can't define "pretty good" or "pretty bad". My 
impression is that the only times reconstruction failed were in the 
presence of very large lesions, or in a subject who would have moved too 
much no matter what, and averaging even a dozen scans wouldn't help.


On 07/15/2013 03:19 PM, Marie Schaer wrote:

Thanks a lot Doug for your super rapid response!

I was asking because I previously had the impression that using one run was giving better 
results, but lately with version 5.3 I've found that averaging 2 runs tends to reduce the 
amount of topological errors that have to be corrected. But as you said, it may largely 
be related to the acquisition's quality. Would you generally agree that if the contrast 
and resolution is good, then averaging two runs may add some "fuzziness" to the 
averaged scan, whereas it would increase the signal to noise in acquisitions that are not 
perfect in terms of contrast / resolution?

Marie



On Jul 15, 2013, at 12:04 PM, Douglas N Greve  wrote:


Hi Marie, I have not seen a publication on it. I've played around with
it a bit and could not convince myself that there was a huge win in
using 2, but it also depends a bit on your acquisition. If you have a
lot of acceleration or really small voxels, then maybe it makes a bigger
difference. Also, if you have a population that moves a lot, it might be
a good idea to get to scans even if you only use one
doug


On 07/15/2013 02:55 PM, Marie Schaer wrote:

Hi all,

Small question related to the number of structural runs required for optimal 
results: I was wondering whether someone tested the assumption that using two 
scans rather than one improves the segmentation process and the cortical 
surface reconstruction / thickness estimation? I've not been able to find any 
publication on it, but maybe my search was not extensive enough.

Thanks a lot for your answer,

Marie


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] [tracula] error running trac-all -prep

[Chris Watson]

You may have to transpose the bval and bvec files.

On 07/29/2013 11:17 AM, Borsodi Florian wrote:

Hello,

I have been trying to run tracula on my data and i keep getting the 
same kind of error repeatedly.
For my imput I am using dicoms from a Siemens scanner with a stadard 
diffusion protocol. However, tracula cannot read the bvec and bval 
data out of the dicom header. Therefore, I implemented bvec and bval 
files into the config file.
After doing so, I got the error which says that tracula cannot find 
the "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files.

I have tried many options, but still cannot find a solution.
I am hoping to get some troubleshooting help.

I have atteched my log- and config- files, as well as my bvec and bval 
files.
To uphold patient confidentiality, I have encode the name patient's 
data as "AA".


I believe the problems are the bvec and bval files or their 
structures. The log-file lete me assume this, especially the lines 202 
- 205, 264 - 268 and 1480 - 1484.


Thank you in advance for your help, and your speedy response.

With kind regards,

Florian Borsodi
Department of Neurology
Medical University of Graz


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[Freesurfer] Using gcut multiple times

[Chris Watson]

Hello,
Is there any value in running recon-all with "-gcut" multiple times? 
e.g. in a case where skull/dura continues to be left on brainmask.mgz?


Thanks,
Chris
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Re: [Freesurfer] Correction multiple comparisons for parcelated areas

[Chris Watson]

You can use FDR correction.

On 08/14/2013 08:16 AM, Anita van Loenhoud wrote:

Dear FreeSurfers,

I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons using
Bonferroni, only one area remains significant. Bonferroni is quite
conservative (alpha needs to be lower than 0.05/68= 0.000735). Could
you recommend any other, more lenient correction statistics for my
data?

In a search through the literature, I encountered adjusted Bonferroni
or Benjamini-Hochberg as alternatives. Do you think these would be
useful statistics, or have I missed other, more appropriate ones?

Thanks a lot,

Anna

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[Freesurfer] Group thickness analysis, 2x2x2

[Chris Watson]

Dear Doug et al.,

I have 2 groups, 2 genders, and 2 scanners (A and B). (I also have Age 
as a covariate). In my FSGD they are listed in this order:


ControlFemaleA
ControlFemaleB
ControlMaleA
ControlMaleB
CaseFemaleA
CaseFemaleB
CaseMaleA
CaseMaleB


I used the following contrast to test for a group X scanner interaction: 
[1 -1 1 -1 -1 1 -1 1 0]
And I also looked at a group X scanner X gender interaction: [1 -1 -1 1 
-1 1 1 -1 0]


For both, there are no significant results in either hemi. Would this 
mean that I can instead just have 4 groups (Control/Case Female/Male), 
or even just 2 groups (Control/Case)? Is that even appropriate?


Thanks,
Chris
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Re: [Freesurfer] gradient table question for Tracula

[Chris Watson]

I have GE data and never had to make any changes to the gradient table.

On 08/22/2013 01:05 PM, Anastasia Yendiki wrote:


Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE 
dicom headers is. If anyone else on the list uses dcm2nii on GE 
dicoms, they can chime in.


To make sure the gradient table is right, I'd always check the primary 
eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on 
dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need 
to do this on one of the data sets from your sequence just to make 
sure they're oriented correctly. Also, if the gradient vectors need 
flipping, the tracts from tracula will come out looking visibly wrong. 
So you'll know that something went wrong.


Hope this helps,
a.y

On Thu, 22 Aug 2013, Salil Soman wrote:


Hi Anastasia,
A question I had about the gradient tables for Tracula - I recently came
across this passage from Hui Zhang:

"To correct for any errors that you identify, you need to first 
modify the
gradient table, then repeat the tensor reconstruction. The 
modification of

the gradient table typically involves flipping the signs of the x or y
component of all gradient vectors. To determine the correct flipping 
of the
signs in a systematic way, it is necessary to understand why this 
happens.
The reason is that the gradient directions are always defined with 
respect
to some right-handed frame of reference, while the frame of reference 
of the

acquired image data is typically NOT right-handed. This mismatch is the
cause of the problem. The sign flipping intends to fix this mismatch 
and the

key is to identify the difference between the two frames of reference in
question. In our experience, if the data is acquired on SIEMENS 
scanners,
the signs of x gradient components need to be flipped; for GE 
scanners, it
is usually the y 
components."(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua

lizationTool).

Does this mean that the gradient tables i get from dcm2nii need to 
have the

Y component flipped for my GE acquisitions or is this adjusted in the
tracula processing?

Thank you.

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






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[Freesurfer] Tracula: pathway #7

[Chris Watson]

Hello,
When I go through trac-prep, pathway #7 always takes much much longer 
than any of the others. And for that pathway it always displays this:

INFO: Distances between consecutive points are 34 37 34 40
WARN: Could not find satisfactory control point fit - try 90


Has anyone else had this problem? Visually, they look right to me.

Thanks,
Chris
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Re: [Freesurfer] Fwd: Problems calling Free Surfer...

[Chris Watson]

Can you post the contents of your ~/.bash_profile


On 01/25/2013 01:41 PM, Rosalia Dacosta Aguayo wrote:


Dear Free Surfer experts,

Sorry for posting this again...but I have been trying this all the day 
and nothing seems to change the situation.


I am having problems with my FS installation. I am working with 
Linux/Ubuntu version 11.10...I have followed the indications of the FS 
wiki and it seems that it is installed but it does not work...it does 
not run in the terminal and I do not know why and how can I do:


osi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/FREE_SURFER/
freesurferrosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ 
export FREESURFER_HOME=/home/rosi/FREE_SURFER/freesurfer
rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ . 
$FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Linux-centos4-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/rosi/FREE_SURFER/freesurfer
FSFAST_HOME   /home/rosi/FREE_SURFER/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/rosi/FREE_SURFER/freesurfer/subjects
MNI_DIR   /home/rosi/FREE_SURFER/freesurfer/mni
FSL_DIR   /usr/share/fsl/4.1
rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ 
freesurfer


FreeSurfer is a set of tools for analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.

Users should consult the online documentation available at:

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

Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

freesurfer@nmr.mgh.harvard.edu 

*You are running this version of FreeSurfer:

  freesurfer-Linux-centos4-**stable-pub-v5.1.0

rosi@rosi-HP-Pavilion-dv9700-* *Notebook-PC:~/FREE_SURFER/**freesurfer$

How can I call FreeSurfer??

*Thanks in advance,

Rosalia.




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Re: [Freesurfer] dual installation question

[Chris Watson]

Usually what I do is create a sym link called "current" that I point to 
the newest version of Freesurfer. e.g.

cd /usr/local/freesurfer
ln -s $PWD/freesurfer-5.1.0 current

So then in my .bashrc file I set
FREESURFER_HOME='/usr/local/freesurfer/current'

Obviously you can change this if you wanted to use an older version.

Chris

On 02/21/2013 08:43 PM, Joshua Lee wrote:

Thanks.
Best,
-
Josh


On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh 
mailto:shant...@nmr.mgh.harvard.edu>> 
wrote:


Or you may have multiple freesurfer versions within the freesurfer
director, something like
/freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b,
/freesurfer/5.2 etc.
and then
export
FREESURFER_HOME=/freesurfer/5.1 etc
Hth, S.


On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote:
> Hi Josh,
> you can modify the SetUpFreeSurfer.sh to source the correct version.
> Hth, Shantanu
>
> On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
>> If I want to install the new Freesurfer version but retain the
older
>> Freesurfer install as well, what issues might I face?
>> Is it simply sourcing the usual setup scripts?
>>
>> export
FREESURFER_HOME=/freesurfer
>> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>
>> -
>> Josh
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu

>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Shantanu Ghosh, Ph.D.
> Harvard Medical School & Massachusetts General Hospital
> Martinos Center for Biomedical Imaging
>
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>
>
>


--
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging



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[Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

[Chris Watson]

Dear Freesurfer users, (apologies for cross-post)

I am pleased to announce the first major release of my R package
"brainGraph" (v1.0.0), a collection of functions for performing graph
theory analyses of brain MRI data. I chose R because it is free and is, in
my opinion, the best choice for just about any statistical analysis. It is
available on CRAN at
https://cran.r-project.org/web/packages/brainGraph/index.html and
development versions will be on my Github page (link below).

You can use it for gray matter covariance networks (cortical thickness,
volume, surface area, or LGI), DTI tractography data (FSL's "probtrackx2",
PANDA, TrackVis, etc.), and for resting-state fMRI (the Matlab toolbox
DPABI/DPARSF).
It is very heavily dependent on the fantastic R package "igraph" (see
igraph.org), which is based on C code and is quite a bit faster than many
other R applications.

My Github page for the package is https://github.com/cwatson/brainGraph
<https://email.tch.harvard.edu/owa/redir.aspx?REF=AuYw-ae9TnjtRShTO7f-UJbUR68DDbXJHlMywLq1BKdgp0I_NYDUCAFodHRwczovL2dpdGh1Yi5jb20vY3dhdHNvbi9icmFpbkdyYXBo>.
At the bottom is the "README.md" file which provides some basic
information. Most important is the link to the User Guide, which has
extensive installation and usage information (warning: it is a direct PDF
link). It is very long but should be helpful. You will find code for
getting your data into R, and I have documented many analysis steps and
include multiple figures. I hope this is intuitive for both veteran and
novice R users. Additionally, there are links for help learning R, and
links to other R packages relevant to neuroimaging applications.

Some features that should be of interest include:
* calculation of a large number of graph/vertex/edge measures (particularly
those most common in neuroimaging)
* between-group vertex-wise analysis using the GLM
* implementation of the network-based statistic (NBS)
* bootstrapping & permutation testing
* random graph generation, small-worldness, and global/local/nodal
efficiency
* rich-club calculations
* robustness ("targeted attack" or "random failure") & vulnerability
* a basic GUI to explore your networks (up to 2 groups/subject at a time)

Please see the NEWS.md file (
https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for the
changelog.

This remains a work-in-progress, so I am very happy to receive bug reports,
feature requests, general questions asking for help with code,
(constructive) criticism, etc.
Please join the Google Group that I set up for those purposes:
https://groups.google.com/forum/?hl=en#!forum/brainGraph-help

Chris Watson
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Re: [Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

[Chris Watson]

I apologize but the link to the Github page is:
https://github.com/cwatson/brainGraph

Chris

On Tue, Apr 11, 2017 at 7:37 PM, Chris Watson  wrote:

> Dear Freesurfer users, (apologies for cross-post)
>
> I am pleased to announce the first major release of my R package
> "brainGraph" (v1.0.0), a collection of functions for performing graph
> theory analyses of brain MRI data. I chose R because it is free and is, in
> my opinion, the best choice for just about any statistical analysis. It is
> available on CRAN at https://cran.r-project.org/
> web/packages/brainGraph/index.html and development versions will be on my
> Github page (link below).
>
> You can use it for gray matter covariance networks (cortical thickness,
> volume, surface area, or LGI), DTI tractography data (FSL's "probtrackx2",
> PANDA, TrackVis, etc.), and for resting-state fMRI (the Matlab toolbox
> DPABI/DPARSF).
> It is very heavily dependent on the fantastic R package "igraph" (see
> igraph.org), which is based on C code and is quite a bit faster than many
> other R applications.
>
> My Github page for the package is *MailScanner has detected a possible
> fraud attempt from "email.tch.harvard.edu" claiming to be*
> https://github.com/cwatson/brainGraph
> <https://email.tch.harvard.edu/owa/redir.aspx?REF=AuYw-ae9TnjtRShTO7f-UJbUR68DDbXJHlMywLq1BKdgp0I_NYDUCAFodHRwczovL2dpdGh1Yi5jb20vY3dhdHNvbi9icmFpbkdyYXBo>.
> At the bottom is the "README.md" file which provides some basic
> information. Most important is the link to the User Guide, which has
> extensive installation and usage information (warning: it is a direct PDF
> link). It is very long but should be helpful. You will find code for
> getting your data into R, and I have documented many analysis steps and
> include multiple figures. I hope this is intuitive for both veteran and
> novice R users. Additionally, there are links for help learning R, and
> links to other R packages relevant to neuroimaging applications.
>
> Some features that should be of interest include:
> * calculation of a large number of graph/vertex/edge measures
> (particularly those most common in neuroimaging)
> * between-group vertex-wise analysis using the GLM
> * implementation of the network-based statistic (NBS)
> * bootstrapping & permutation testing
> * random graph generation, small-worldness, and global/local/nodal
> efficiency
> * rich-club calculations
> * robustness ("targeted attack" or "random failure") & vulnerability
> * a basic GUI to explore your networks (up to 2 groups/subject at a time)
>
> Please see the NEWS.md file (https://github.com/cwatson/
> brainGraph/blob/master/NEWS.md) for the changelog.
>
> This remains a work-in-progress, so I am very happy to receive bug
> reports, feature requests, general questions asking for help with code,
> (constructive) criticism, etc.
> Please join the Google Group that I set up for those purposes:
> https://groups.google.com/forum/?hl=en#!forum/brainGraph-help
>
> Chris Watson
>
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] Longitudinal stats: target space

[Chris Watson]

Hi Doug, Martin, et al.,

I am going to use the LME tools for a study in kids 8-15 y.o. (some with
brain injury). RE the target space (mris_preproc and mri_surf2surf), the
LME wiki page

says "study_average". I am unclear if this should be

a) average of all subjects at TP 1 (or final, or mid)
b) average of all subjects and all TP's
c) average of all within-subject templates (created from recon-all -base)
d) *fsaverage*

I suspect (d) is wrong for this study and (c) is right, but want to
double-check. In that case, would I then follow the steps on the wiki page
for creating a template

?

Thanks,
Chris
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Re: [Freesurfer] Matlab 2016b and localGI

[Chris Watson]

Hi, I took a look at this and saw that the error comes from the "getmatlab"
script ($FREESURFER_HOME/fsfast/bin/getmatlab). It is a CSH script, which I
thought might be the issue.

Specifically, the script checks for the existence of matlab by
(unsurprisingly)

set MATLAB = `which matlab`;

On Dr. J's system, this was problematic due to "matlab" being aliased, so
calling "getmatlab" directly exited with the error. Hard-coding the path
for matlab in the "getmatlab" script is a (non-portable) solution.

However, I am not sure why it would throw an error, in any case. I tried it
on my system and it returned the correct location of matlab. I am running
CentOS 7.3 and using Freesurfer v5.3
(x86_64-unknown-linux-gnu-stable5-20130513). The version of "getmatlab" is
Revision 1.2

Chris

On Fri, Aug 11, 2017 at 12:27 PM, Alan Francis 
wrote:

> Hi Jennifer -
>
> Ostensibly your pathways and environment variables look correct. I ran
> into this problem once before, so I changed from BASH to the enhanced C
> shell and it worked. You may want to try that. All you need to do is to
> exit out of bash and set the environment in tcsh and it could work.
>
> best,
>
> Alan
>
> On Thu, Aug 10, 2017 at 4:56 PM, Juranek, Jenifer <
> jenifer.jura...@uth.tmc.edu> wrote:
>
>> Hi,
>>
>> Hope someone can identify my user error...I've listed below key bits of
>> info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat
>> startup.m).
>>
>> Really appreciate someone taking a look and walking me through a solution
>> to my error?
>>
>> Many Thanks!
>>
>> Jenifer
>>
>>
>> 1) Running Freesurfer_v6 on RHEL Centos7.3
>>
>> and matlab 2016b (with imaging processing toolbox)
>>
>> 2) recon-all -s  -localGI
>>
>> returns the following:
>>
>> #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017
>>
>>  mris_compute_lgi --i lh.pial
>>
>> ERROR: Matlab is required to run mris_compute_lgi!
>> Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19
>> 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>> 3) matlab is in my path
>>
>> [jjuranek@localhost subjects]$ echo $PATH
>> /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfa
>> st/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/
>> bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/
>> bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/
>> fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/
>> jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:
>> /usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/
>> home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab
>>
>>
>> 4) my .bashrc file is as follows
>>
>> # .bashrc
>>
>> # Source global definitions
>> if [ -f /etc/bashrc ]; then
>> . /etc/bashrc
>> fi
>>
>> # User specific aliases and functions
>>
>> export FREESURFER_HOME=/home/jjuranek/freesurfer
>> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>
>> matlab=/home/jjuranek/matlab/R2016b/bin/matlab
>> alias matlab=$matlab
>>
>> export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab
>>
>> #/home/jjuranek/matlab/R2016b/bin/matlab
>> #MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>>
>> 5) my startup.m file is as follows
>>
>> % FreeSurfer -%
>> fshome = getenv('FREESURFER_HOME');
>> fsmatlab = sprintf('%s/matlab',fshome);
>> if (exist(fsmatlab) == 7)
>> addpath(genpath(fsmatlab));
>> end
>> clear fshome fsmatlab;
>> %-%
>>
>> % FreeSurfer FAST %
>> fsfasthome = getenv('FSFAST_HOME');
>> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
>> if (exist(fsfasttoolbox) == 7)
>> path(path,fsfasttoolbox);
>> end
>> clear fsfasthome fsfasttoolbox;
>> %-%
>>
>> % FreeSurfer LGI %
>> FSH = getenv('FREESURFER_HOME');
>>
>> fshmatlab = sprintf('%s/matlab',FSH);
>> path(path,fshmatlab);
>> clear fshmatlab FSH;
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, 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.
>>
>>
>
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> *Alan N. Francis PhD*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~

[Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

[Chris Watson]

Dear Freesurfer users,

I am pleased to announce the 2nd major release of my R package for graph
theory analysis of brain MRI data, "brainGraph".
The main page on CRAN is at: https://cran.r-project.org/
web/packages/brainGraph/index.html
The GitHub repository is at: https://github.com/cwatson/brainGraph


*Installation*
The latest version is already on CRAN for Linux distributions, and should
be for Windows and Mac OS X soon (but there may be issues on non-Linux
systems; see Chapter 1 of the User Guide).

To install directly from CRAN:
> install.packages('brainGraph')

In the meantime (and for development versions), you may install from GitHub
using the R package "devtools":
> devtools::install_github('cwatson/brainGraph')


*Getting help*
The new User Guide has been completely overhauled, and now has a permanent
link at: my GitHub Pages site (PDF warning)
<https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Please start at
the "Preface".

You may also get help by opening an Issue
<https://github.com/cwatson/brainGraph/issues> on the GitHub
repository, or join
the Google Group
<https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>.


*New features*
You can find the release notes/changelog in NEWS.md, at:
https://github.com/cwatson/brainGraph/blob/master/NEWS.md

Major additions (since v1.0.0) that should be of interest include:

   - Vertex- and graph-level *mediation analysis* (chapter 11 of the Guide)
   - Multi-threshold permutation correction (MTPC) for GLM analyses
   (chapter 9)
   - Extension of GLM-based functions (including the *network-based
   statistic [NBS]* and MTPC) to allow for multiple contrasts in a single
   function call, and to allow for both T- and F-contrasts
   - Permutation/randomization is now done using the *Freedman-Lane
   algorithm* (as in *randomise* and *PALM*), although models are limited
   to simple GLM's
   - Introduction of R's *S3 classes* to simplify plotting and summarizing
   results
   - Calculation of a network's *s-core* membership
   - Calculation of network *communicability* and vertex *communicability
   betweenness centrality*

Please let me know if you have any issues, bug reports, feature requests,
etc.
Chris Watson
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Re: [Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

[Chris Watson]

Dear Dr. Robert,
It hadn't occurred to me, as I am the sole developer of the package. The
User Guide should have enough information to get started (so please check
it out), but I might add some content to GitHub Pages with specific,
tutorial-like information (as opposed to the documentation-style of the
User Guide).

Chris

On Wed, Feb 7, 2018 at 6:00 AM, gabriel robert <
gabriel.hadrien.rob...@gmail.com> wrote:

> Dear Dr Watson,
>
> Many thanks for developping your toolbox,
>
> Is there any project to propose any "courses" or anything related to
> courses to get started with your toolbox,
>
> Best wishes,
>
> Gabriel Robert, MD, PhD
> Rennes, France
>
> 2018-02-07 2:14 GMT+01:00 Chris Watson :
>
>> Dear Freesurfer users,
>>
>> I am pleased to announce the 2nd major release of my R package for graph
>> theory analysis of brain MRI data, "brainGraph".
>> The main page on CRAN is at: https://cran.r-project.org/web
>> /packages/brainGraph/index.html
>> The GitHub repository is at: https://github.com/cwatson/brainGraph
>>
>>
>> *Installation*
>> The latest version is already on CRAN for Linux distributions, and should
>> be for Windows and Mac OS X soon (but there may be issues on non-Linux
>> systems; see Chapter 1 of the User Guide).
>>
>> To install directly from CRAN:
>> > install.packages('brainGraph')
>>
>> In the meantime (and for development versions), you may install from
>> GitHub using the R package "devtools":
>> > devtools::install_github('cwatson/brainGraph')
>>
>>
>> *Getting help*
>> The new User Guide has been completely overhauled, and now has a
>> permanent link at: my GitHub Pages site (PDF warning)
>> <https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Please start
>> at the "Preface".
>>
>> You may also get help by opening an Issue
>> <https://github.com/cwatson/brainGraph/issues> on the GitHub repository,
>> or join the Google Group
>> <https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>.
>>
>>
>> *New features*
>> You can find the release notes/changelog in NEWS.md, at:
>> https://github.com/cwatson/brainGraph/blob/master/NEWS.md
>>
>> Major additions (since v1.0.0) that should be of interest include:
>>
>>- Vertex- and graph-level *mediation analysis* (chapter 11 of the
>>Guide)
>>- Multi-threshold permutation correction (MTPC) for GLM analyses
>>(chapter 9)
>>- Extension of GLM-based functions (including the *network-based
>>statistic [NBS]* and MTPC) to allow for multiple contrasts in a
>>single function call, and to allow for both T- and F-contrasts
>>- Permutation/randomization is now done using the *Freedman-Lane
>>algorithm* (as in *randomise* and *PALM*), although models are
>>limited to simple GLM's
>>- Introduction of R's *S3 classes* to simplify plotting and
>>summarizing results
>>- Calculation of a network's *s-core* membership
>>- Calculation of network *communicability* and vertex *communicability
>>betweenness centrality*
>>
>> Please let me know if you have any issues, bug reports, feature requests,
>> etc.
>> Chris Watson
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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>
>
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> 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
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> but does not contain patient information, please contact the sender and
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[Freesurfer] Tracula with multi-shell data

[Chris Watson]

Dear Anastasia et al.

I have data DTI that has multiple b-values. I worked around this by 
skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to 
'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an 
error thrown. Specifically when 'dmri_pathstats' is called, because it 
is looking for dtifit_{L1, L2, L3, V1, ...}. Do you have a workaround 
for this? Should I just run dtifit on the data?


Also, merged_avg33_mni_bbr.nii.gz wasn't created, but I was able to 
create it (I copied the code from around line 400 of 'trac-paths'). When 
I view it with freeview, though, there is a light blue/greenish 
background. I assume those voxels are supposed to be 0's, but for some 
reason aren't here?



Thanks,
Chris
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Re: [Freesurfer] Tracula trac-all -stat flag -stat unrecognized

[Chris Watson]

Do you have the latest version of Tracula? There was an update posted 
after FS 5.3 came out.


On 07/18/2014 04:48 PM, Cat Chong wrote:

Hello Anastasia,

I have just converted pathstas.overall.txt files to a table for group 
analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a 
table for group analyses using the command:

trac-all -stat -c
I am receiving the error message: ERROR: flag -stat unrecognized

I am working on a mac using bash script using Freesurfer version 5.3

Do you have any ideas?
Cheers,
Cat


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Re: [Freesurfer] Cortical Thickness Correction Factor

[Chris Watson]

In your FSGD you'll have to add a covariate for "scanner"

On 08/08/2014 12:34 PM, David Tate wrote:

FreeSurfer Gurus,
I would like to pose this question again to the group if possible.  We 
are working with data that comes from two different scanners.  Our 
experimental group was collected on one scanner and then control data 
was acquired on another scanner.  Not the optimal situation I realize 
but unavoidable.  We were fortunate to be able to acquire imaging for 
a subsample of patients on both scanners in the same day.  Preliminary 
results suggest that one site measures cortical thickness and 
subcortical volumes in a non-significant (statistically) but 
consistent direction with one scanner producing larger volume and 
thickness measures.


My question is whether or not it is possible to mathematically account 
for these differences in any analysis that we are doing using 
FreeSurfer and if so where can I find those procedures for practically 
implementing the correction?


Thanks in advance for any help with this.

David


On Apr 17, 2014, at 11:07 AM, David Tate > wrote:


We are working on a study that includes data from multiple scanners 
and initial indication suggest that there may be small differences in 
cortical thickness measures that are scanner related (human and other 
phantom data were acquired at both sites).


Is it possible to include a correction factor adjusting for the 
scanner differences when using glmfit or qdec?


Thanks,

David

David F. Tate, Ph.D.
Research Neuropsychologist
Defense and Veterans Brain Injury Center
Contractor, General Dynamics Information Technology
Brooke Army Medical Center MCHE MDU (DVBIC)
3551 Roger Brooke Drive
JSBA Ft. Sam Houston, TX 78234-4504

Office (210) 916-8090







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Re: [Freesurfer] From bedpostX and recon-all to tracula

[Chris Watson]

If you sym link the already finished bedpostx directory to 
$SUBJECT/dmri.bedpostX, you should be able to run trac-all -prep and 
trac-all -path without any issues (adjusting the config that comes with 
tracula)


On 09/03/2014 05:04 PM, Katherine Damme wrote:

Hello Freesurfer Community!

I have sucessfully completed diffusion preprocessing in FSL and the 
recon-all of the structural image and would like to use tracula for 
the tract reconstruction. I keep having trouble with my configuration 
file.


Does anyone have a bedpostX tracula config file they could share as an 
example?


Thank you!

Kate


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Re: [Freesurfer] problems with tracula pre-processing (bvecs)

[Chris Watson]

You can try just re-running "trac-prep -prior" and "trac-paths" for the 
L uncinate and no other tracts


On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I re-ran the case with the set reinit option. It "half" 
worked!...in the sense that the new results show the left uncinate 
right, but the right-side one is still a dot (see screenshot of the 
brain view from the bottom).

Any further suggestion?
Thanks.

Inline image 2





On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari 
mailto:cavallari.mich...@gmail.com>> wrote:


Thanks! it's running...

On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp
mailto:bakk@googlemail.com>> wrote:

Hi Michele,

Don't think there is anything wrong with the attached
dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path
to your configuration file.
Right now it reads the path to your file as a flag, which is
of course not what you want.

Best,
Barbara




On 11/09/2014 17:49, Michele Cavallari wrote:

Hi Anastasia,
I am probably doing something wrong with the syntax of the
dmrirc file.
I get this error message

trac-all -prior

/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial

ERROR: flag

/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
unrecognized

-prior

/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial


Could you please check the attached file?


On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:


Thanks, Michele. Hard to tell what's causing this,
perhaps a bit of distortion orbitofrontally. You may be
able to fix this type of thing by reinitializing the
tract reconstruction: Add "set reinit = 1" to your
configuration file, set the pathlist to include only the
left and right uncinate, and then rerun the -prior and
-path steps of trac-all on this subject.

On Wed, 10 Sep 2014, Michele Cavallari wrote:

uploaded (and activated).Thanks!



On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

  Hi Michele - The anatomical segmentation does
look good, but from the
  screenshot the DWI data seems to be noisy in
the orbitofrontal area, which
  may be affecting the uncinate. It's hard to
tell just from one slice.

  If you upload all the tracula output
directories of this subject (dmri,
  dmri.bedpostX, dlabel, dpath) for me here, I'll
take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/

  Thanks!
  a.y

  On Wed, 10 Sep 2014, Michele Cavallari wrote:

Hi Anastasia,I completed the tracula
processing.
By looking at the tractography results in
the viewer I noticed
that the uncinate
fasciculus is pretty small (see attached
screenshot). It
actually appears as a small
blue dot. And the problem is both on the
left and right side.
The other tracts look
fine. I played with threshold, but the
size didn't increase. So,
I guess that something
wrong happened with the tractography of
that particular bundle.
I checked the aparc+aseg
output (attached): it seems right to me,
but could you please
double-check?
Let me also know if you have any
suggestions, and if you need
more information or output
files.
Best,
Michele

Inline image 1



On Thu, Sep 4, 2014 at 11:55 PM,
Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

  Hi Ludy - If your gradient table is
formatted in 3 rows
you need to
  either:

  1. Convert it to 3 columns so you
can use it with the 5.3
 

Re: [Freesurfer] quick quality assessment for MPRAGE images

[Chris Watson]

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


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


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


cheers,
-MH

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

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

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

Subject: [Freesurfer] quick quality assessment for MPRAGE images

Dear Freesurfer Users,

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


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



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Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

[Chris Watson]

Have you tried installing 'xauth' on the server and connecting via 'ssh 
-X'? That should show all graphical output on the local machine.



On 11/05/2014 05:03 PM, Bruce Fischl wrote:

Hi PPJ

I'm not sure it is. Tksurfer has an offscreen rendering option :
setenv renderoffscreen 1

used to work, and maybe still does, but I don't think we ever 
implemented it in tkmedit, and I'm not sure about freeview. Ruopeng 
can answer that part


On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote:

I'm sorry if this has been answered before, I have browsed the 
mailing and

found nothing answering this.
I need to generate three views of the T1 data superimposed with Aseg 
data

automatically for Quality Control without using FreeView or Tkmedit (the
server generating this has no X11)

Is it possible to do it with the command line tools?

Thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441






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Re: [Freesurfer] [Fwd: Re: Modeling cortical thickness question]

[Chris Watson]

No, just include "age^3", if the mean function is

E(thickness | X) = B_0 + B_1 * age^3

It's similar to taking the logarithm of one of your predictors. Just 
remember that the units for the parameter estimate will be different 
than if you were just including age.


On 12/10/2014 12:12 PM, Alexandra Tanner wrote:

Hi Doug,
Thanks for your response! Please see Josh's follow-up question below.
Thanks again for your help!

Best,
Alex

 Original Message 
Subject: Re: [Fwd: Re: [Freesurfer] Modeling cortical thickness question]
From:"Roffman, Joshua L.,M.D." 
Date:Wed, December 10, 2014 11:52 am
To:  "Alexandra Tanner" 
--

Maybe...if we take this approach I guess we would want the cube root of
age, not age cubed? The relationship we are testing is whether y=x^3
(where x is age and y is cortical thickness). So if we took the cube root
of both sides, that might be closer to what we want?

(Alex: could you forward this to the list)

Thx
Josh

Sent from my iPhone


On Dec 10, 2014, at 9:32 AM, "Alexandra Tanner"

 wrote:

Hi Josh,
Below is Doug's response...does this answer your question?

Thanks,
Alex

 Original Message 
Subject: Re: [Freesurfer] Modeling cortical thickness question
From:"Douglas N Greve" 
Date:Tue, December 9, 2014 4:48 pm
To:  freesurfer@nmr.mgh.harvard.edu
--


Do you mean a polynomial of age? If so, just add age age^2 and age^3 as
variables in the FSGD file
doug


On 12/09/2014 02:04 PM, Alexandra Tanner wrote:
Hello Freesurfers,

Our group is wondering if any of you know whether it is possible to model
cortical thickness as a third order polynomial? The specific question is:
we are looking at whether there is a hyperbolic relationship between
cortical thickness and date of birth among a cohort of individuals born
over a 6 year period. Any insights would be greatly appreciated!

Thanks,
Alex
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] Command '-qa' in TRACULA

[Chris Watson]

No, she is saying that you should open a terminal, and type only 
"trac-all". This should display the help for that program, including the 
program's flags. If you don't see "-qa" listed, then the trac-all you're 
using is an older version.
You need to verify that you have downloaded the latest version and 
overwritten the older one (or change your $PATH to look for the newer one).



On 12/11/2014 09:38 PM, Anri WATANABE wrote:

Thanks, Anastasia.
I'm worried about that a quality assessment step is not run because 
there are no presentation about "-qa" when I type "trac-all" in 
terminal (other steps are presented.)

Do you mean QA step will be run even if no mention about it?

Thanks in advance,
Anri



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

2014-12-12 4:48 GMT+09:00 Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>>:



Hi Anri - This is not a command itself, it's an option of the
trac-all command. So you need to run:
trac-all -qa -c the_name_of_your_configuration_file

Or, if you just run the entire preprocessing:
trac-all -prep -c the_name_of_your_configuration_file
then the motion QA measures will be computed by default as one of
the many steps of the preprocessing.

You can run "trac-all" without any arguments to see usage
information on all the the different options.

Hope this helps,
a.y


On Tue, 9 Dec 2014, Anri WATANABE wrote:

Thank you, Anastasia.
I had downloaded the updated software and unzipped it, but I
couldn't find
the command "-qa."
I found "-qa" in the trac-all text file in the updated software.
However there are no "-qa" in terminal when I run "trac-all."
Do I have to move the file somewhere?

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

2014-11-22 7:22 GMT+09:00 Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>>:

  Hi Anri - See here, and follow the link "software update":

http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments

  The -qa option was added after 5.3 was released.

  a.y

  On Mon, 10 Nov 2014, Anri WATANABE wrote:

Dear FreeSurfer experts,

I'm running pre-processing steps in TRACULA
separatelly and could neither find the context about
quality
assessment step nor run the command 'trac-all -qa -c
.
I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion
(64-bit).
Could anyone solve this problem?
Thank you.

Anri


   
**

京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
   
**

WATANABE ANRI
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine
   
**



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HelpLine at
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Re: [Freesurfer] From bedpostX and recon-all to tracula

[Chris Watson]

You may have to transpose the bvecs and bvals files. I think that's how 
Tracula expects them. You can use the attached script to do it.


On 12/17/2014 09:18 PM, Katherine Damme wrote:
Thanks! That was exactly it! It was a FAT server and so that resolved 
that issue.


Tracula is claiming that the bvecs and bvals don't have the same 
number of entries. These were the bvecs and bval files created during 
the trac-all prep process, but when I preprocesed the data previously 
with FSL the bvecs and bvals that were created did have equal numbers. 
I tried to specify to use these fsl made bvecs and bvals in the 
configuration file and it continues to default to the ones that it made.


 Any ideas?

Thank you!

Kate

On Mon, Dec 15, 2014 at 7:42 PM, Watson, Christopher 
> wrote:


I think certain filesystems don't support sym linking (e.g.
FAT32). So that might be it.


From: freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu
] on behalf of
Katherine Damme [katherine.da...@gmail.com
]
Sent: Monday, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula

After removing this I have a new (possibly unrelated error):
mv -f /media/Sokol/Subj/041/dmri/bvecs
/media/Sokol/Subj/041/dmri/bvecs.norot
xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog
/media/Sokol/Subj/041/dmri/bvecs.norot
/media/Sokol/Subj/041/dmri/bvecs
ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz
/media/Sokol/Subj/041/dmri/data.nii.gz
ln: creating symbolic link
`/media/Sokol/Subj/041/dmri/data.nii.gz': Operation not permitted

This persists even when I run the command as the root user and
regardless of the permissions settings of the folder and the
fdwi.nii.gz file.

Any ideas?

On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>>> wrote:

It's hard to tell what's causing the error without seeing the
entire trac-all.log. However, by glancing at your config file you
seem to still have B0 inhomogeneity correction turned on (dob0 =
1) but without specifying any field map dicoms. I'd turn it off
and see if that fixes it.


On Mon, 15 Dec 2014, Katherine Damme wrote:

Where would I be specifying a directory as an input/output?

I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep
-c dmri.fy

On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>> wrote:
  Hi Katerine

  the COR-* format is an old one that we don't use anymore. If
you specify a directory as an
  input/output we will assume that it contains COR files,
which is probably what you are seeing.

  cheers
  Bruce


  On Sun, 14 Dec 2014, Katherine Damme wrote:

At what point is the COR-*.info file made?
I got the following error:

corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter Exp $
reading from /media/Sokol/Subj/...
Linux kate.ad.wcas.northwestern.edu

2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec
13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 12 12:54:40
CST 2014

[ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>>> wrote:

  No, those are field maps used to correct for
inhomogeneities in
  the main magnetic field (which in MRI lingo is
referred to as
  the B0 field, not to be confused with the b=0
images). You can
  skip that correction (you have to skip it if you
don't have
  field maps).

  On Thu, 11 Dec 2014, Katherine Damme wrote:

I am sorry, I am a bit confused. What am I
supposed
to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from
diffusion.

Thank you!

   

Re: [Freesurfer] Freeview update error

[Chris Watson]

External Email - Use Caution

Hi Kelly, you can try

yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel

And if it still doesn't work, you can try

yum install harfbuzz

On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn 
wrote:

> External Email - Use Caution
>
> Hello FreeSurfer community,
>
> I believe I have installed both freetype and freetype-devel now.
> I now get a new error, that is similar, but may have a slightly different
> solution:
>
> Freeview:symbol lookup error:
> /usr/local/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5: undefined symbol:
> hb_font_funcs_set_font_h_extents_func
>
> Does anyone have any advice regarding this error?
>
> 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20190416-14809f1
> 2) Platform: Red Hat Enterprise Linux 7
>
> On Wed, Apr 17, 2019 at 3:06 PM Kelly Vaughn 
> wrote:
>
>> Thank you for your help!
>>
>> When I look within /usr/lib64 (using ls *libfreetype*) , I see:
>> lib64/libfreetype.so.6  lib64/libfreetype.so.6.10.0
>>
>> When I type:
>> strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format
>> I do not get any output.
>>
>> When I type:
>> sudo yum install freetype.x86_64 freetype-devel.x86_64
>> the first package installs, but I get the following error message for the
>> second package:
>> No package freetype-devel.x86_64 available.
>> Error: Nothing to do
>>
>> I have seen these types of errors on this computer many times when I try
>> to install or use different programs, so I understand if it is not actually
>> a FreeSurfer problem. If anyone has any advice, I would love to hear it.
>> I'll continue to try to solve it on my own as well.
>>
>> On Wed, Apr 17, 2019 at 2:03 PM fsbuild  wrote:
>>
>>> ​Hello Kelly,
>>>
>>> Do you have libfreetype installed on your system (which defines that
>>> symbol)?
>>>
>>> $ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format
>>> FT_Get_Font_Format
>>>
>>> If not, you can install it with,
>>>
>>> $ sudo yum install freetype.x86_64 freetype-devel.x86_64
>>>
>>> - R.
>>>
>>> On Apr 17, 2019, at 10:09, Kelly Vaughn 
>>> wrote:
>>>
>>> libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format
>>>
>>>
>>>
>>
>> --
>> Kelly Vaughn, Ph.D.
>> Postdoctoral Research Fellow
>> Children's Learning Institute
>>
>
>
> --
> Kelly Vaughn, Ph.D.
> Postdoctoral Research Fellow
> Children's Learning Institute
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[Freesurfer] trac-all -prep error

[Chris Watson]

Hello, in running trac-all -prep, I get an error saying that it can't 
open "lowb.nii.gz.hdr":

fslroi 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 
0 1
fslmaths 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 
-Tmean 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
bet 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
 
-m -f 0.3
Can't open 
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 
17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012

The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this 
problem with other subjects that I am processing. Any thoughts?

Thanks,
Chris

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Re: [Freesurfer] trac-all -prep error

[Chris Watson]

Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for lowb.nii.gz
  type: nii
dimensions: 96 x 96 x 56
   voxel sizes: 2.5000, 2.5000, 2.5000
  type: FLOAT (3)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -70.0, zend: 70.0
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r 
= 0.9450
  : x_a =   0., y_a =   1., z_a =   0., c_a =
31.8560
  : x_s =   0., y_s =   0., z_s =   1., c_s =
25.3936
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.5000   0.   0.   120.9450
0.   2.5000   0.   -88.1440
0.   0.   2.5000   -44.6064
0.   0.   0. 1.

voxel-to-ras determinant -15.625

ras to voxel transform:
   -0.4000   0.   0.48.3780
   -0.   0.4000  -0.35.2576
   -0.  -0.   0.400017.8426
0.   0.   0. 1.

It looks normal in fslview/freeview.
Chris

Anastasia Yendiki wrote:
> Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first 
> guess, too. Does this lowb.nii.gz actually exist? Anything looks strange 
> when you run mri_info/freeview/fslview on it?
>
> a.y
>
> On Wed, 15 Feb 2012, Chris Watson wrote:
>
>   
>> Hello, in running trac-all -prep, I get an error saying that it can't
>> open "lowb.nii.gz.hdr":
>>
>> fslroi
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>> 0 1
>> fslmaths
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>> -Tmean
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>> bet
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
>> -m -f 0.3
>> Can't open
>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
>> Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10
>> 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012
>>
>> The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this
>> problem with other subjects that I am processing. Any thoughts?
>>
>> Thanks,
>> Chris
>>
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>>
>>
>>
>> 
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> 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] trac-all -prep error

[Chris Watson]

Yes, the same error.
Chris

Anastasia Yendiki wrote:
>
> When you run that bet command line outside of trac-all, does it give 
> you the same error?
>
> On Wed, 15 Feb 2012, Chris Watson wrote:
>
>> Here's output from mri_info:
>> [freesurfer@occipital dmri]$ mri_info lowb.nii.gz
>> Volume information for lowb.nii.gz
>>  type: nii
>>   dimensions: 96 x 96 x 56
>>  voxel sizes: 2.5000, 2.5000, 2.5000
>> type: FLOAT (3)
>>   fov: 240.000
>>   dof: 0
>>xstart: -120.0, xend: 120.0
>>ystart: -120.0, yend: 120.0
>>zstart: -70.0, zend: 70.0
>>   TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
>> 0.00 degrees
>>   nframes: 1
>>   PhEncDir: UNKNOWN
>> ras xform present
>>   xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
>> 0.9450
>> :  x_a =   0., y_a =   1., z_a =   0., c_a = 
>> 31.8560
>> :  x_s =   0., y_s =   0., z_s =   1., c_s = 
>> 25.3936
>> Orientation   : LAS
>> Primary Slice Direction: axial
>>
>> voxel to ras transform:
>>   -2.5000   0.   0.   120.9450
>>0.   2.5000   0.   -88.1440
>>0.   0.   2.5000   -44.6064
>>0.   0.   0. 1.
>>
>> voxel-to-ras determinant -15.625
>>
>> ras to voxel transform:
>>   -0.4000   0.   0.48.3780
>>   -0.   0.4000  -0.35.2576
>>   -0.  -0.   0.400017.8426
>>0.   0.   0. 1.
>>
>> It looks normal in fslview/freeview.
>> Chris
>>
>> Anastasia Yendiki wrote:
>>>  Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
>>>  guess, too. Does this lowb.nii.gz actually exist? Anything looks 
>>> strange
>>>  when you run mri_info/freeview/fslview on it?
>>>
>>>  a.y
>>>
>>>  On Wed, 15 Feb 2012, Chris Watson wrote:
>>>
>>>
>>> >  Hello, in running trac-all -prep, I get an error saying that it 
>>> can't
>>> >  open "lowb.nii.gz.hdr":
>>> > >  fslroi
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
>>>  
>>>
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>  
>>>
>>> >  0 1
>>> >  fslmaths
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>  
>>>
>>> >  -Tmean
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>  
>>>
>>> >  bet
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>  
>>>
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
>>>  
>>>
>>> >  -m -f 0.3
>>> >  Can't open
>>> >  
>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
>>>  
>>>
>>> >  Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue 
>>> Jan 10
>>> >  17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>>> > >  trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012
>>> > >  The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't 
>>> encounter this
>>> >  problem with other subjects that I am processing. Any thoughts?
>>> > >  Thanks,
>>> >  Chris
>>> > >  ___
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>>> >  Freesurfer@nmr.mgh.harvard.edu
>>> >  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > > > >
>>>  ___
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>>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>  The information in this e-mail is intended only for the person to 
>>> whom it
>>>  is
>>>  addressed. If you believe this e-mail was sent to you in error and the
>>>  e-mail
>>>  contains patient information, please contact the Partners Compliance
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>>>  http://www.partners.org/complianceline . If the e-mail was sent to 
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Re: [Freesurfer] trac-all -prep error

[Chris Watson]

Actually, it now works when I re-source my .bash_profile and .bashrc 
files. Not sure why that would be.
Chris

Chris Watson wrote:
> Yes, the same error.
> Chris
>
> Anastasia Yendiki wrote:
>   
>> When you run that bet command line outside of trac-all, does it give 
>> you the same error?
>>
>> On Wed, 15 Feb 2012, Chris Watson wrote:
>>
>> 
>>> Here's output from mri_info:
>>> [freesurfer@occipital dmri]$ mri_info lowb.nii.gz
>>> Volume information for lowb.nii.gz
>>>  type: nii
>>>   dimensions: 96 x 96 x 56
>>>  voxel sizes: 2.5000, 2.5000, 2.5000
>>> type: FLOAT (3)
>>>   fov: 240.000
>>>   dof: 0
>>>xstart: -120.0, xend: 120.0
>>>ystart: -120.0, yend: 120.0
>>>zstart: -70.0, zend: 70.0
>>>   TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
>>> 0.00 degrees
>>>   nframes: 1
>>>   PhEncDir: UNKNOWN
>>> ras xform present
>>>   xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
>>> 0.9450
>>> :  x_a =   0., y_a =   1., z_a =   0., c_a = 
>>> 31.8560
>>> :  x_s =   0., y_s =   0., z_s =   1., c_s = 
>>> 25.3936
>>> Orientation   : LAS
>>> Primary Slice Direction: axial
>>>
>>> voxel to ras transform:
>>>   -2.5000   0.   0.   120.9450
>>>0.   2.5000   0.   -88.1440
>>>0.   0.   2.5000   -44.6064
>>>0.   0.   0. 1.
>>>
>>> voxel-to-ras determinant -15.625
>>>
>>> ras to voxel transform:
>>>   -0.4000   0.   0.48.3780
>>>   -0.   0.4000  -0.35.2576
>>>   -0.  -0.   0.400017.8426
>>>    0.   0.   0. 1.
>>>
>>> It looks normal in fslview/freeview.
>>> Chris
>>>
>>> Anastasia Yendiki wrote:
>>>   
>>>>  Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
>>>>  guess, too. Does this lowb.nii.gz actually exist? Anything looks 
>>>> strange
>>>>  when you run mri_info/freeview/fslview on it?
>>>>
>>>>  a.y
>>>>
>>>>  On Wed, 15 Feb 2012, Chris Watson wrote:
>>>>
>>>>
>>>> 
>>>>>  Hello, in running trac-all -prep, I get an error saying that it 
>>>>>   
>>>> can't
>>>> 
>>>>>  open "lowb.nii.gz.hdr":
>>>>>   
>>>>>>  fslroi
>>>>>> 
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  0 1
>>>>>  fslmaths
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  -Tmean
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  bet
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz
>>>>  
>>>>
>>>> 
>>>>>  -m -f 0.3
>>>>>  Can't open
>>>>>  
>>>>>   
>>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr
>>>>  
>>>>
>>>> 
>>>>>  Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue 
>>>>>   
>>>> Jan 10
>>>> 
>>>>>  17:25:58 

[Freesurfer] trac-all -path error

[Chris Watson]

Hello, I successfully ran trac-all -bedp, and when I run the next step I 
get the following error:

Loading BEDPOST parameter samples from 
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
niiRead(): error opening file 
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read 
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 
04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012

Word too long.


Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 
and FSL 4.1.9.
Here's what's in the dmri.bedpostX directory:

[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
bvals  bvecs  commands.txt  diff_slices  logs  monitor  
nodif_brain_mask.nii.gz  xfms

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Re: [Freesurfer] trac-all -path error

[Chris Watson]

[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz  
mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz  
th1samples.nii.gz


Come to think of it, when I ran bedpostx, it only output "1 slice 
processed", but repeated 70 times, or however many slices there are. The 
data is from a Siemens 3T, by the way.

On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:
>
> What's in the diff_slices directory? That's a temporary directory that 
> bedpostx creates and that gets deleted after the results get "merged". 
> So my guess would be that bedpostx didn't finish processing.
>
> On Fri, 23 Mar 2012, Chris Watson wrote:
>
>> Hello, I successfully ran trac-all -bedp, and when I run the next step I
>> get the following error:
>>
>> Loading BEDPOST parameter samples from
>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
>> niiRead(): error opening file
>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
>>  
>>
>> ERROR: Could not read
>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
>>  
>>
>> Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7
>> 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
>>
>> Word too long.
>> 
>>
>> Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0
>> and FSL 4.1.9.
>> Here's what's in the dmri.bedpostX directory:
>>
>> [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
>> bvals  bvecs  commands.txt  diff_slices  logs  monitor
>> nodif_brain_mask.nii.gz  xfms
>>
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>>
>>
>
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> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
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Re: [Freesurfer] trac-all -path error

[Chris Watson]

Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:
>
> Oh, ok. That's a known issue, it has to do with changes in the command 
> line of the latest version of bedpostx. We've updated trac-all and 
> it'll be working in our next release but for now you'll have to run 
> bedpostx by itself and not through trac-all. Sorry for the inconvenience!
>
> On Fri, 23 Mar 2012, Chris Watson wrote:
>
>> [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
>> dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz 
>> mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz 
>> th1samples.nii.gz
>>
>>
>> Come to think of it, when I ran bedpostx, it only output "1 slice 
>> processed", but repeated 70 times, or however many slices there are. 
>> The data is from a Siemens 3T, by the way.
>>
>> On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:
>>>
>>>  What's in the diff_slices directory? That's a temporary directory that
>>>  bedpostx creates and that gets deleted after the results get 
>>> "merged". So
>>>  my guess would be that bedpostx didn't finish processing.
>>>
>>>  On Fri, 23 Mar 2012, Chris Watson wrote:
>>>
>>> >  Hello, I successfully ran trac-all -bedp, and when I run the next 
>>> step I
>>> >  get the following error:
>>> > >  Loading BEDPOST parameter samples from
>>> >  
>>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
>>> >  niiRead(): error opening file
>>> >  
>>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
>>>  
>>> > >  ERROR: Could not read
>>> >  
>>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
>>>  
>>> > >  Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed 
>>> Mar 7
>>> >  04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>>> > >  trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
>>> > >  Word too long.
>>> >  
>>>  
>>>
>>> > >  Indeed, the "merged" file doesn't exist. I am running 
>>> Freesurfer 5.1.0
>>> >  and FSL 4.1.9.
>>> >  Here's what's in the dmri.bedpostX directory:
>>> > >  [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
>>> >  bvals  bvecs  commands.txt  diff_slices  logs  monitor
>>> >  nodif_brain_mask.nii.gz  xfms
>>> > >  ___
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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
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Re: [Freesurfer] Clarification on centos version/updates/patches

[Chris Watson]

H i Nick,
Will the centos5 build of v5.1 work with centos6? I'm getting a new 
workstation and want to know which version of centos is better to install.

On 04/10/2012 10:08 AM, Nick Schmansky wrote:
> Wil,
>
> Hi, the contents of that 'misc' directory is just a filedrop of sorts to
> supply fixes to individuals who need particular updates.  We dont supply
> formal patches, as it gets too unwieldy to track versions.  Rather bug
> fixes are documented (mostly!) on the ReleaseNotes page with links to
> fixes.
>
> We have a centos6 build, but dont release it.  We will for the next
> release, v5.2, hopefully by the end of May, as the centos6 build runs a
> little faster than the centos4/5 build because it uses a newer gcc, but
> this will mean it wont be possible to mix versions, and a centos6 platform
> (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed.
>
> mri_info versioning wont affect the stream.  i dont think it has any bug
> fixes outstanding.
>
> i think the trac-all script is the same, the versioning is different
> because our 'dev' tree version was committed to our 'stable' branch, and
> the two have different versions (but the file is the same).
>
> n.
>
>
>
>> Hi-
>>
>> It would appear the stable release for centos6 is ready for primetime
>> 'stable5.1-bin.tgz'; Is this correct?  There is an updated version of
>> 'mri_info' based on file size
>> (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
>>
>>
>> mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45
>> mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32
>>
>> Which version is the most current?
>>
>> Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin
>> to overwrite the extant files?
>>
>> Additionally, there is a versioning discrepancy between 'trac-all' located
>> in
>> (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/)
>>
>> '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a
>>
>> and the version packaged with the cenos6_x86_65  'stable5.1-bin.tgz'
>>
>> '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $'
>>
>> I did not comprehensively look for any other discrepancies-these just
>> happened to stand out based on the work I was doing today.
>>
>> Thanks much,
>> Wil
>>
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Re: [Freesurfer] trac-all -path error

[Chris Watson]

Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" 
isn't getting created, I think. This is after I ran bedpostx on its own, 
per your instructions from this thread.


Here are the last few lines of output from trac-all -path:
Loading BEDPOST parameter samples from 
/raid2/fmri8/control/H008B/dmri.bedpostX
niiRead(): error opening file 
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read 
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
/parietal/freesurfer/current/bin/dmri_mergepaths --indir 
/raid2/fmri8/control/H008B/dpath --in --out 
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab 
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15

ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX":
bvals diff_slices   logs   
mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz   
mean_S0samples.nii.gz   merged_ph2samples.nii.gz  
nodif_brain_mask.nii.gz
commands.txt  dyads2.nii.gz mean_f2samples.nii.gz  
mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms


Thanks,
Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:


Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

  Oh, ok. That's a known issue, it has to do with changes in the command
  line of the latest version of bedpostx. We've updated trac-all and it'll
  be working in our next release but for now you'll have to run bedpostx by
  itself and not through trac-all. Sorry for the inconvenience!

  On Fri, 23 Mar 2012, Chris Watson wrote:


  [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
  dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
  mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
  th1samples.nii.gz


  Come to think of it, when I ran bedpostx, it only output "1 slice
  processed", but repeated 70 times, or however many slices there are. The
  data is from a Siemens 3T, by the way.

  On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

   What's in the diff_slices directory? That's a temporary directory
   that
   bedpostx creates and that gets deleted after the results get
  "merged". So
   my guess would be that bedpostx didn't finish processing.

   On Fri, 23 Mar 2012, Chris Watson wrote:


   Hello, I successfully ran trac-all -bedp, and when I run the next

  step I

   get the following error:

   Loading BEDPOST parameter samples from

  /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX

   niiRead(): error opening file


  
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

   ERROR: Could not read

  
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

   Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed

  Mar 7

   04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

   trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
   Word too long.

  


   Indeed, the "merged" file doesn't exist. I am running

  Freesurfer 5.1.0

   and FSL 4.1.9.
   Here's what's in the dmri.bedpostX directory:

   [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/

   bvals  bvecs  commands.txt  diff_slices  logs  monitor
   nodif_brain_mask.nii.gz  xfms

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Re: [Freesurfer] trac-all -path error

[Chris Watson]

Yes, I figured out that I had previously run "trac-all -bedp" and it 
created "data_slice_0002". I deleted this directory, and bedpostx 
finished, but now I get this error from "trac-all-path":

Segmentation fault (core dumped)
/parietal/freesurfer/current/bin/dmri_mergepaths --indir 
/raid2/fmri8/control/H008B/dpath --in --out 
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab 
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15

ERROR: must specify input volume(s)

What should be specified here?

Thanks,
Chris

PS When running bedpostx I was simply using the defaults, so "bedpostx 
H008B/dmri.bedpostX" was the command line.


On 05/07/2012 02:28 PM, Priti Srinivasan wrote:

Hi Chris,

The diff_slices folder is still there, which means that bedpostX probably
did not finish processing. That folder usually gets deleted after bedpostX
processing completes. It's strange that you have merged_ph2samples.nii.gz
and not merged_ph1samples.nii.gz.

Did you accidentally run bedpostX twice and exit out of it in the middle?
It is quite possible that you'd already finished processing bedpostX(and
all files were properly created) and started running it again, which would
explain the diff_slices and the absence of merged_ph1samples (but not
merged_ph2samples).

You could potentially back up your current bedpostx folder and re-run
bedpostX to see if that solves your issue.

Could you also send the commandline you're using for bedpostX?

Thanks,
Priti


Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz"
isn't getting created, I think. This is after I ran bedpostx on its own,
per your instructions from this thread.

Here are the last few lines of output from trac-all -path:
Loading BEDPOST parameter samples from
/raid2/fmri8/control/H008B/dmri.bedpostX
niiRead(): error opening file
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
/parietal/freesurfer/current/bin/dmri_mergepaths --indir
/raid2/fmri8/control/H008B/dpath --in --out
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15
ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX":
bvals diff_slices   logs
mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz
mean_S0samples.nii.gz   merged_ph2samples.nii.gz
nodif_brain_mask.nii.gz
commands.txt  dyads2.nii.gz mean_f2samples.nii.gz
mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms

Thanks,
Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:


Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

   Oh, ok. That's a known issue, it has to do with changes in the
command
   line of the latest version of bedpostx. We've updated trac-all and
it'll
   be working in our next release but for now you'll have to run
bedpostx by
   itself and not through trac-all. Sorry for the inconvenience!

   On Fri, 23 Mar 2012, Chris Watson wrote:


   [freesurfer@occipital dmri.bedpostX]$ ls
diff_slices/data_slice_0002/
   dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
   mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
   th1samples.nii.gz


   Come to think of it, when I ran bedpostx, it only output "1 slice
   processed", but repeated 70 times, or however many slices there
are. The
   data is from a Siemens 3T, by the way.

   On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

What's in the diff_slices directory? That's a temporary directory
that
bedpostx creates and that gets deleted after the results get
   "merged". So
my guess would be that bedpostx didn't finish processing.

On Fri, 23 Mar 2012, Chris Watson wrote:


Hello, I successfully ran trac-all -bedp, and when I run the
next

   step I

get the following error:

Loading BEDPOST parameter samples from

   /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX

niiRead(): error opening file


   
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

ERROR: Could not read

   
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed

   Mar 7

04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
Word too long.

   


  

Re: [Freesurfer] wm edits

[Chris Watson]

If you use mris_wm_volume, it will compute the volume enclosed by the 
$h.white surfaces. It's more accurate than using mris_anatomical_stats 
for white matter. I believe you don't need to edit wm.mgz, assuming the 
$h.white surfaces accurately follow the white matter in your images.


Nasim Maleki wrote:

Hi Sita,

Thanks for your reply.

A follow up question I have and that is so how about measurements in  
mris_anatomical_stats? Wouldn't total WM volume be affected by an  
inaccurate wm.mgz or does freesurfer use surfaces to compute the  
volumes?


Thank you,
Nasim


On Mar 3, 2009, at 6:26 PM, Sita Kakunoori wrote:

  

Hi Nasim,


1-Will I  get accurate results if I do the edits (erasing  
misclassified
  

white

matter in wm.mgz) to my white matter mask only in those 10% areas  
that
  

the wm

surface is not accurate or should I correct the wm.mgz 'every  
where' no

matter what?
  

You can just make edits in the problem areas and run recon-all. That
should fix the errors and give you accurate results.



2- Will you necessarily get more accurate results by editing your  
wm.mgz

where pixels are classified  as white by mistake BUT your final white
  

matter


surface is accurate?
  

No. You don't have to edit wm.mgz if the white surface is accurate.



3-How much on average takes you to do the manual white matter edits  
for
  

each


of your subjects?!
  
It really varies from scan to scan and mostly will depend on the  
quality

of the scan acquired. For a good scan, it'll probably take an hour or
less.


Sita.





On Tue, 3 Mar 2009, Nasim Maleki wrote:



Dear Freesurfers,

I have a question on manual white matter edits:

I have cases where a considerable amount of gray matter is  
classified as white in my wm.mgz and therefore the original surface  
(green) is not accurate but then that is fixed in the next steps  
and the wm surface (yellow) is accurate in 90% of the areas but not  
accurate in other 10% .


Now my questions are:

1-Will I  get accurate results if I do the edits (erasing  
misclassified white matter in wm.mgz) to my white matter mask only  
in those 10% areas that the wm surface is not accurate or should I  
correct the wm.mgz 'every where' no matter what?


2- Will you necessarily get more accurate results by editing your  
wm.mgz where pixels are classified  as white by mistake BUT your  
final white matter surface is accurate?


3-How much on average takes you to do the manual white matter edits  
for each of your subjects?!


Thank you,
Nasim



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[Freesurfer] mri_convert with old GE-LX data

[Chris Watson]

Hello,
I'm trying to use mri_convert to convert old (~1999) functional data 
that was acquired on a GE LX scanner. However, nothing seems to work. 
I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: 
(results are similar if I omit the -in_type flag)

[matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm "image"
mri_convert I.001.s01 -it lx -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001.s01...
genesisRead(): can't determine file name format for 
/raid2/fmri5/LDProj/BOSEN/functional/I.001.s01

[matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm "image"
mri_convert I.001.s01 -it ge -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001.s01...
fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d
genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001

[matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm 
"image"
mri_convert I.001.s01 -it dicom -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001.s01...
Starting DICOMRead2()
dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01
dcmdir = /raid2/fmri5/LDProj/BOSEN/functional
ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file

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Re: [Freesurfer] mri_convert with old GE-LX data

[Chris Watson]

I renamed them all to "I.1, I.2, ..., I.8000" (there are 8000 images 
total), and I got the same error messages. (With the "-it ge" option, it 
is still looking for the old filename, it seems)

[matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm "image"
mri_convert I.1 -it lx -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.1...
genesisRead(): can't determine file name format for 
/raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1

[matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm "image"
mri_convert I.1 -it ge -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.1...
fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
genesisRead(): error opening file 
/raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001

[matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm "image"
mri_convert I.1 -it dicom -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.1...
Starting DICOMRead2()
dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func
ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file



Douglas N Greve wrote:
> can you rename your files to remove the .s01?
>
> Chris Watson wrote:
>   
>> Hello,
>> I'm trying to use mri_convert to convert old (~1999) functional data 
>> that was acquired on a GE LX scanner. However, nothing seems to work. 
>> I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: 
>> (results are similar if I omit the -in_type flag)
>>
>> [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm "image"
>> mri_convert I.001.s01 -it lx -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.001.s01...
>> genesisRead(): can't determine file name format for 
>> /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01
>>
>> [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm "image"
>> mri_convert I.001.s01 -it ge -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.001.s01...
>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d
>> genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001
>>
>> [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm 
>> "image"
>> mri_convert I.001.s01 -it dicom -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.001.s01...
>> Starting DICOMRead2()
>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01
>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional
>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file
>>
>> ___
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>>
>>
>>   
>> 
>
>   
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Re: [Freesurfer] mri_convert with old GE-LX data

[Chris Watson]

It got a little further (with "-it ge" and without any --in_type flag), 
but I get this error:

[matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm "image"
mri_convert I.001 -it ge -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001...
fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
zero frames specified in file - setting to 1
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (nan, nan, nan)
j_ras = (nan, nan, nan)
k_ras = (nan, nan, nan)
Reslicing using trilinear interpolation
MRIresample(): error inverting matrix; determinant is nan, matrix is:
 nan   nan   nan   nan;
 nan   nan   nan   nan;
 nan   nan   nan   nan;
 0.000   0.000   0.000   1.000;

Douglas N Greve wrote:
> sorry, it's a little finicky, I think it is looking for a %03d format, 
> meaning I.001 for slices numbers less than 1000, and I.1001 for greater
>
> Chris Watson wrote:
>   
>> I renamed them all to "I.1, I.2, ..., I.8000" (there are 8000 images 
>> total), and I got the same error messages. (With the "-it ge" option, 
>> it is still looking for the old filename, it seems)
>>
>> [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm "image"
>> mri_convert I.1 -it lx -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.1...
>> genesisRead(): can't determine file name format for 
>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
>>
>> [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm "image"
>> mri_convert I.1 -it ge -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.1...
>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>> genesisRead(): error opening file 
>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001
>>
>> [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm "image"
>> mri_convert I.1 -it dicom -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.1...
>> Starting DICOMRead2()
>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func
>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a 
>> dicom file
>>
>>
>>
>> Douglas N Greve wrote:
>> 
>>> can you rename your files to remove the .s01?
>>>
>>> Chris Watson wrote:
>>>  
>>>   
>>>> Hello,
>>>> I'm trying to use mri_convert to convert old (~1999) functional data 
>>>> that was acquired on a GE LX scanner. However, nothing seems to 
>>>> work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command 
>>>> line: (results are similar if I omit the -in_type flag)
>>>>
>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm 
>>>> "image"
>>>> mri_convert I.001.s01 -it lx -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.001.s01...
>>>> genesisRead(): can't determine file name format for 
>>>> /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01
>>>>
>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm 
>>>> "image"
>>>> mri_convert I.001.s01 -it ge -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.001.s01...
>>>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d
>>>> genesisRead(): error opening file 
>>>> /raid2/fmri5/LDProj/BOSEN/functional/I.001
>>>>
>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot 
>>>> spm "image"
>>>> mri_convert I.001.s01 -it dicom -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.001.s01...
>>>> Starting DICOMRead2()
>>>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01
>>>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional
>>>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom 
>>>> file
>>>>
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>   
>>>> 
>>>   
>>>   
>> 
>
>   
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Re: [Freesurfer] mri_convert with old GE-LX data

[Chris Watson]

Still get an error:

[matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 
-ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 "image"
 
mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 
1 0 -ikd 0 0 1 image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001...
fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
zero frames specified in file - setting to 1
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
Reslicing using trilinear interpolation
MRIresample(): error inverting matrix; determinant is nan, matrix is:
 1.000   0.000   0.000   nan;
 0.000   1.000   0.000   nan;
 0.000   0.000   1.000   nan;
 0.000   0.000   0.000   1.000;


Douglas N Greve wrote:
> You can try specifying the input geometry with something like -iis 1 
> -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1
>
> this is undoubtedly wrong, but should allow the command to finish
>
> Chris Watson wrote:
>   
>> It got a little further (with "-it ge" and without any --in_type 
>> flag), but I get this error:
>>
>> [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm "image"
>> mri_convert I.001 -it ge -ot spm image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.001...
>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>> zero frames specified in file - setting to 1
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (nan, nan, nan)
>> j_ras = (nan, nan, nan)
>> k_ras = (nan, nan, nan)
>> Reslicing using trilinear interpolation
>> MRIresample(): error inverting matrix; determinant is nan, matrix is:
>> nan   nan   nan   nan;
>> nan   nan   nan   nan;
>> nan   nan   nan   nan;
>> 0.000   0.000   0.000   1.000;
>>
>> Douglas N Greve wrote:
>> 
>>> sorry, it's a little finicky, I think it is looking for a %03d 
>>> format, meaning I.001 for slices numbers less than 1000, and I.1001 
>>> for greater
>>>
>>> Chris Watson wrote:
>>>  
>>>   
>>>> I renamed them all to "I.1, I.2, ..., I.8000" (there are 8000 images 
>>>> total), and I got the same error messages. (With the "-it ge" 
>>>> option, it is still looking for the old filename, it seems)
>>>>
>>>> [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm "image"
>>>> mri_convert I.1 -it lx -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.1...
>>>> genesisRead(): can't determine file name format for 
>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
>>>>
>>>> [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm "image"
>>>> mri_convert I.1 -it ge -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.1...
>>>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>>>> genesisRead(): error opening file 
>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001
>>>>
>>>> [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm "image"
>>>> mri_convert I.1 -it dicom -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.1...
>>>> Starting DICOMRead2()
>>>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
>>>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func
>>>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a 
>>>> dicom file
>>>>
>>>>
>>>>
>>>> Douglas N Greve wrote:
>>>>
>>>> 
>>>>> can you rename your files to remove the .s01?
>>>>>
>>>>> Chris Watson wrote:
>>>>>  
>>>>>  
>>>>>   
>>>>>> Hello,
>>>>>> I'm trying to use mri_convert to convert old (~1999) functional 
>>>>>> data that was acquired on a GE LX scanner. However, nothing seems 
>>>>>> to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my 
>>>>>> command line: (results are similar if I omit the -in_type flag)
>>>>>>
>>>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot 
>>>>>> spm "image"
>>>>

Re: [Freesurfer] mri_convert with old GE-LX data

[Chris Watson]

It completed but it's only giving me 1 .img file, and when I loaded it 
into mricro, it thinks the z dimension is 8000 (the number of slices 
total). It should give me 400 volumes (20 slices each). So I want 
image001.img, 002.img, and so on. How can I do this? Do I have to rename 
the files differently?

Douglas N Greve wrote:
> sorry, also add -ic 0 0 0
>
> Chris Watson wrote:
>   
>> Still get an error:
>>
>> [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 
>> -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 "image"
>>
>> mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 
>> 0 1 0 -ikd 0 0 1 image
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from I.001...
>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>> zero frames specified in file - setting to 1
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (1, 0, 0)
>> j_ras = (0, 1, 0)
>> k_ras = (0, 0, 1)
>> Reslicing using trilinear interpolation
>> MRIresample(): error inverting matrix; determinant is nan, matrix is:
>> 1.000   0.000   0.000   nan;
>> 0.000   1.000   0.000   nan;
>> 0.000   0.000   1.000   nan;
>> 0.000   0.000   0.000   1.000;
>>
>>
>> Douglas N Greve wrote:
>> 
>>> You can try specifying the input geometry with something like -iis 1 
>>> -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1
>>>
>>> this is undoubtedly wrong, but should allow the command to finish
>>>
>>> Chris Watson wrote:
>>>  
>>>   
>>>> It got a little further (with "-it ge" and without any --in_type 
>>>> flag), but I get this error:
>>>>
>>>> [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm "image"
>>>> mri_convert I.001 -it ge -ot spm image
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from I.001...
>>>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>>>> zero frames specified in file - setting to 1
>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>>> i_ras = (nan, nan, nan)
>>>> j_ras = (nan, nan, nan)
>>>> k_ras = (nan, nan, nan)
>>>> Reslicing using trilinear interpolation
>>>> MRIresample(): error inverting matrix; determinant is nan, matrix is:
>>>> nan   nan   nan   nan;
>>>> nan   nan   nan   nan;
>>>> nan   nan   nan   nan;
>>>> 0.000   0.000   0.000   1.000;
>>>>
>>>> Douglas N Greve wrote:
>>>>
>>>> 
>>>>> sorry, it's a little finicky, I think it is looking for a %03d 
>>>>> format, meaning I.001 for slices numbers less than 1000, and I.1001 
>>>>> for greater
>>>>>
>>>>> Chris Watson wrote:
>>>>>  
>>>>>  
>>>>>   
>>>>>> I renamed them all to "I.1, I.2, ..., I.8000" (there are 8000 
>>>>>> images total), and I got the same error messages. (With the "-it 
>>>>>> ge" option, it is still looking for the old filename, it seems)
>>>>>>
>>>>>> [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm "image"
>>>>>> mri_convert I.1 -it lx -ot spm image
>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>>>> reading from I.1...
>>>>>> genesisRead(): can't determine file name format for 
>>>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1
>>>>>>
>>>>>> [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm "image"
>>>>>> mri_convert I.1 -it ge -ot spm image
>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>>>> reading from I.1...
>>>>>> fname_format  : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d
>>>>>> genesisRead(): error opening file 
>>>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001
>>>>>>
>>>>>> [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm 
>>>>>> "image"
>>>>>> mri_convert I.1 -it dicom -ot spm image
>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>>>> reading from I.1...
>>>>>

Re: [Freesurfer] modifying dicom headers

[Chris Watson]

dcmtk works pretty well and is easy to use:
http://dicom.offis.de/dcmtk.php.en

Jared Price wrote:
> Hi all,
> I am looking for a powerful, robust tool for modifying dicom headers 
> that can be called from the command-line and scripted.  For example, I 
> may need to alter the subject ID with which a dicom study was uploaded.  
> We are managing a multi-site study and the various sites do not always 
> uplaoded the images with the correct study-wide ID.   Anyone know of a 
> good one?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>   
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[Freesurfer] COR-files

[Chris Watson]

Hello, this is my first time using Freesurfer.

I was making some edits to the brainmask.mgz and T1.mgz volumes, and 
saved them and left Friday evening. I would like to continue making 
edits today. How do I open these volumes so that they include the edits 
I made? When I saved, 256 COR-files were created in the 
SUBJECTS_DIR//mri directory. Do I use mri_convert? If so, what 
is the syntax?


mri_convert --in_type cor COR-001 --out_type spm  ???

Thanks,
Chris
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Re: [Freesurfer] COR-files

[Chris Watson]

So in place of  I should place brainmask.mgz? I 
believe that is the volume I saved over. It's unfortunate that I'll have 
to re-do the edits to the T1.mgz volume...


thanks,
Chris

Bruce Fischl wrote:

Hi Chris,

in the future you should just save over the .mgz files. So they were 
saved directly in mri and not in a subdir? That means that there is 
only one volume, not two (brainmask.mgz and T1.mgz), do you know which 
one it is? To convert from cor to .mgz do:


mri_convert  

cheers,
Bruce


On Mon, 5 Nov 2007, Chris Watson wrote:


Hello, this is my first time using Freesurfer.

I was making some edits to the brainmask.mgz and T1.mgz volumes, and 
saved them and left Friday evening. I would like to continue making 
edits today. How do I open these volumes so that they include the 
edits I made? When I saved, 256 COR-files were created in the 
SUBJECTS_DIR//mri directory. Do I use mri_convert? If so, 
what is the syntax?


mri_convert --in_type cor COR-001 --out_type spm  ???

Thanks,
Chris
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[Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

[Chris Watson]

Hello all,
I was wondering if there is a quick way to make edits to multiple slices 
of the aseg.mgz (or the brainmask.mgz) volume.


Specifically, I am working on my first subject, and it seems that on 
almost every slice, pieces of the dura/skull/arachnoid/what-have-you get 
segmented as cortex (less often, pieces of dura are included within the 
boundary of the pial surface). I've worked on some slices by manually 
removing/de-segmenting the pixels that need to go, but this is proving 
to be extraordinarily time-consuming (some of the slices I've worked on 
can take 10 minutes easily; perhaps I am obsessing too much, but am 
trying to get it as close to perfect as it should look). For over 100 
slices, even 5 minutes/slice of editing will take several hours. I tried 
changing the mri_watershed parameter on another subject, but that didn't 
seem to fix anything.


Any tips to save me hours will be greatly appreciated.

-Chris
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Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

[Chris Watson]

The output says that the voxel size is .7031, .7031, 1.5 (slice 
thickness is 1.5). Could this be causing the dura to be segmented as 
cortex in some areas?


Bruce Fischl wrote:
you can use mri_info on your dicoms to find out the resolution. 
Hopefully it's not too far from 1mm isotropic. If it's 1.5 or bigger 
in any dimension that might explain the trouble.


On Tue, 6 Nov 2007, Watson, Christopher wrote:

The acquisitions are SPGRs, taken on either a GE 3T or 1.5T (I'm not 
exactly sure, I'm new to the job). Yea, in a lot of areas the dura is 
adjacent to the grey matter. Those are certainly the problem areas - 
in most other areas the segmentation is excellent. I'm not sure of 
the resolution.



-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

Hi Chris,

what type of acquisition are you using? Dura can be really hard to deal
with, as it can look just like gm, depending on your MR parameters, and
it is can also be physically adjacent to gm. That said, it's only 
usually a

problem in localized areas. What resolution is your data? We have some
newer sequences and code that avoid the dura, but they are by no means
standard (and we only have them for Siemens).

cheers,
Bruce


On Tue, 6 Nov 2007, Chris Watson wrote:


Hello all,
I was wondering if there is a quick way to make edits to multiple 
slices of

the aseg.mgz (or the brainmask.mgz) volume.

Specifically, I am working on my first subject, and it seems that on 
almost
every slice, pieces of the dura/skull/arachnoid/what-have-you get 
segmented
as cortex (less often, pieces of dura are included within the 
boundary of the
pial surface). I've worked on some slices by manually 
removing/de-segmenting

the pixels that need to go, but this is proving to be extraordinarily
time-consuming (some of the slices I've worked on can take 10 
minutes easily;
perhaps I am obsessing too much, but am trying to get it as close to 
perfect
as it should look). For over 100 slices, even 5 minutes/slice of 
editing will
take several hours. I tried changing the mri_watershed parameter on 
another

subject, but that didn't seem to fix anything.

Any tips to save me hours will be greatly appreciated.

-Chris
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[Freesurfer] White matter hypointensities?

[Chris Watson]

What are white matter hypointensities supposed to represent? I'm seeing 
this segmentation group a lot around the lateral ventricles, caudate, etc.


thanks,
Chris
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Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

[Chris Watson]

Hi,
So if the volumes are estimated from the surfaces and not aseg.mgz, does 
this mean it is unnecessary to edit aseg.mgz? Or is it still necessary, 
but only for the subcortical structures? Is it best to make pial 
surface/wm.mgz edits and control points for grey and white matter, and 
aseg.mgz for the subcortical volumes?

I hope I am being clear enough.

Thanks,
Chris

Bruce Fischl wrote:

Hi Jim,

yes, I think that should be fine

Bruce
On Mon, 10 Dec 2007, James N. Porter wrote:


Hello Bruce-

From the wiki, I gather that I would rerun recon-all from -finalsurfs 
onward, as that is the step that calls make_final_surfaces. In order 
to insert the fix_mtl flag I'll have to run that section via a 
separate command line outside of recon-all. Are there any other 
subsequent steps that require manual intervention or nonstandard 
parameters, or would something like the code below do the work?


for S in $SUBJ; do
  for H in $HEMI; do
  mris_make_surfaces --noaparc --mgz -T1 --fix_mtl brain.finalsurfs 
$S $H

  done
recon-all -s $S -cortribbon -autorecon3
done

Thanks,

Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota





Bruce Fischl wrote:

Hi Jim,

you can actually run mris_make_surfaces with -fix_mtl and it will 
inhibit all deformations in these regions. I didn't enable that by 
default as I was afraid it would mean missing a bit of entorhinal. 
In general it doesn't really matter as the gray and white volumes 
computed from the surfaces will exclude amygdala and hippocampal 
voxels that are interior to the surface.


For your second question: we use the gray matter volume estimated 
from the surfaces instead of the aseg, as we find it to be more 
accurate than the voxel-based techniques.


cheers,
Bruce


 On Tue, 27 Nov 2007, James N. Porter wrote:


Hello FreeSurfer Folks-

I've seen several threads in the archives discussing the expected 
inaccuracies in the pial, white, and orig surfaces running through 
subcortical structures. However, I've been unable to ascertain 
exactly how much and what kind of inaccuracy is acceptable. It 
makes sense to me that if the entirety of a structure, say the 
amygdala, were included or excluded in the pial surface, then it 
would be easy to adjust later measurements. However, what we see in 
all of our subjects is a random pattern of half in/half out, with 
weird shapes, when it comes to the surfaces running in and around 
subcortical structures. For example, take a look the image at this 
link.


  http://www.tc.umn.edu/~norb0062/Amygdala.tiff

There you will see the how the hippocampus and amygdala are both 
half included in the pial surface. Item 1 has a strange 
guitar-shaped chunk taken out of the amygdala, and item 2 has a 
triangle and a peanut-shaped area removed. Are these the types of 
expected and accepted inaccuracies, or is there something afoul 
here that needs to be corrected?


I have one other question regarding the interactions of aseg and 
surface information. Item 3 in the image points out a section of 
apparent subdural matter that has been classified as grey matter in 
the aseg but has been excluded from the pial surface. When the 
final statistics are spit out of recon-all, is there a section of 
processing that says something like, "Based on the aseg values my 
grey matter volume is X, but since Y of that is outside of the pial 
surface I'll call my total volume X-Y"? Or, is this another item to 
that requires correction and re-running of recon-all?


Many thanks in advance,







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[Freesurfer] General editing questions

[Chris Watson]

Hello,
I've been looking through the archives and still have some questions 
about getting the best data for GM volume, WM volume, and the volumes of 
each sub-cortical structure. This is lengthy, but I'm trying to save a 
lot of future man-hours that I wasted on the first dataset I was doing.


*1)* I ran recon-all -autorecon-all overnight, not knowing that I could 
make edits in the middle of the process. Does this mean that, e.g if I 
need to add control points, I have to do /
recon-all -autorecon2-cp -autorecon3, /and then make edits to the new 
wm.mgz and do /recon-all -autorecon2-wm -autorecon3/, *then* make edits 
to the pial surface and run everything to the end? Or, if I add control 
points, then only run recon-all -autorecon2-cp, this will be acceptable? 
And then edit wm.mgz, and run /recon-all -autorecon2-wm/? And so on?

*
2)* This brings me to another head-scratcher for me: wm.mgz. Should all 
subcortical structures fall within the main surface (including ventral 
DC)? Sometimes the main surface cuts into the hippocampus/amygdala, so 
do I have to add/delete voxels so it goes around it? I would think the 
pial and main surfaces should exclude these two structures. The pial and 
main surfaces are ~identical  around the midline and subcortical 
structures; is this the desired result?
   If i want to change the main surface in general, what is the 
significance of the white voxels vs. grey voxels? I think I understand 
that the white voxels are there just so the surface will go around it. 
So, in theory, if I wanted the main surface to include all of the 
hippocampus, I could fill in white voxels for the hippocampus, and then 
run recon-all? If I delete grey voxels, will this change the main 
surface (I suppose this would be like the opposite of control points)? I 
read in some places that the WM volume produced by mris_anatomical_stats 
is taken from all the voxels that are "on" in wm.mgz. If this is the 
case, then the ventricles are included? Some parts of the dura are "on" 
in wm.mgz (although do not fall within ?h.white); would I have to go 
slice-by-slice deleting these annoying voxels?

*
3)* Is the data from mri_segstats and mri_anatomical_stats reliable? 
I've seen threads saying mris_wm_volume and mris_volume are better, 
since the GM and WM data are calculated using the surfaces. I don't have 
the former (I'm using FS v3.0.4). I noticed the WM volume given by 
/mris_volume rh.white - /{sum of volumes of subcortical structures} is 
very close to that given by mri_segstats, which is similar to using 
mris_wm_volume. Is this correct?


So, in the future, when I do recon-all for a subject, is it best to do 
it step-by-step, and make the edits as I go along?


Thanks for the help,
Chris
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[Freesurfer] brainGraph (graph theory analysis in R) major release v3.0.0

[Chris Watson]

External Email - Use Caution

Dear Freesurfer users, (apologies for cross-posting)

I am pleased to announce the 3nd major release of my R package for graph
theory analysis of brain MRI data, "brainGraph".
The main page on CRAN is at:
https://cran.r-project.org/web/packages/brainGraph/index.html
The GitHub repository is at: https://github.com/cwatson/brainGraph

*Installation*
The latest version is already on CRAN for Linux distributions, and should
be for Windows and Mac OS X soon.

To install directly from CRAN:
> install.packages('brainGraph')

In the meantime (and for development versions), you may install from GitHub
using the R package "devtools":
> devtools::install_github('cwatson/brainGraph')

*Getting help*
The User Guide can be found at: my GitHub Pages site (PDF warning)
<https://cwatson.github.io/files/brainGraph_UserGuide.pdf>.
Chapter 4 gives a general Overview, and Chapter 5 has some basic details
for getting started.
Chapters 6 and 7 provide code and details for structural covariance and
single-subject networks, respectively.

You may also get help by opening an Issue
<https://github.com/cwatson/brainGraph/issues> on the GitHub repository, or
you may join the Google Group
<https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>.

*New features*
You can find the release notes/changelog in NEWS.md, at:
https://github.com/cwatson/brainGraph/blob/master/NEWS.md

There are too many differences to list here, but the most significant new
feature is related to GLM-based analyses (including for Multi-threshold
Permutation Correction, Network Based Statistic, and mediation analysis).
They are now significantly faster, and (in certain situations) is faster
than other solutions in R.

Please let me know if you have any issues, bug reports, feature requests,
etc.

Chris Watson
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[Freesurfer] Script to get recon processing time

[Chris Watson]

Hello,
Do you guys have a script that parses recon-all.log and spits out the 
processing time for each step? Something that would be similar to this 
in recon-all --help:
  -motioncor< 5 min
  -nuintensitycor 3 min
  -talairach  4 min
  -normalization  3 min
  -skullstrip 1 min
  -gcareg 8 min
  -canorm 1 min
  -careg 10 hours

and so on.

Thanks,
Chris
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Re: [Freesurfer] recon-all error

[Chris Watson]

Thanks, that did the trick.
Chris

Nick Schmansky wrote:
> you will need to get a fixed version of mri_ca_label from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
>
> n.
>
> On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote:
>   
>> I was running a subject, and got this error:
>> recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010
>>
>> make: *** 
>> [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 
>> 1
>>
>> The disk is not full, and permissions are in order. I've run several other 
>> subjects with no problems. Initially my command line was "recon-all 
>> -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", 
>> and saw the same error.
>>
>> It exits at SubCort Seg 
>> (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z 
>> /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca 
>> aseg.auto_noCCseg.mgz)
>>
>> The last several lines of output are:
>> mri_ca_label GCA sequential renormalization: label 28 not consistently 
>> computed.
>>
>> not using caudate to estimate GM means
>> setting label Right_VentralDC based on Left_VentralDC = 1.15 x +  0
>> estimating mean gm scale to be 1.01 x + 0.0
>> estimating mean wm scale to be 1.00 x + 0.0
>> estimating mean csf scale to be 1.01 x + 0.0
>> saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
>> Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 
>> 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
>>
>> Any ideas?
>> Chris
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>>
>>
>> 
>
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[Freesurfer] tksurfer display problem

[Chris Watson]

Hi, when trying to look at surfaces in tksurfer, all I see is a small 
part of the data in the posterior of the brain (see attached for 
example). There are no errors on the command line when I run tksurfer.
This only started happening very recently. Here's some system info: 
(CentOS 5.5, 64-bit; FreeSurfer v5.0)


[freesurfer@occipital TGA]$ uname -a
Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 
12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux


[freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv
40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 
560] (rev a1)


I wouldn't think I need to update my graphics card driver. But, does 
anyone know how to fix this?


Thanks,
Chris
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Re: [Freesurfer] tksurfer display problem

[Chris Watson]

I d/l'ed the new driver, and it now works. Thanks.
Chris

Nick Schmansky wrote:
> what is the version of your driver?  ie
>
> cat /proc/driver/nvidia/version
>
> the latest is around 260.19.12
>
> the problem you see is something we've seen with old nvidia drivers,
> whereby updating the driver has fixed the problem.  not sure why this
> would just happen now for you.
>
> to update (must be root or use sudo):
>
> /sbin/init 3
> /usr/bin/nvidia-installer --update
>
>
> n.
>
>
> On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote:
>   
>> Hi, when trying to look at surfaces in tksurfer, all I see is a small 
>> part of the data in the posterior of the brain (see attached for 
>> example). There are no errors on the command line when I run tksurfer.
>> This only started happening very recently. Here's some system info: 
>> (CentOS 5.5, 64-bit; FreeSurfer v5.0)
>>
>> [freesurfer@occipital TGA]$ uname -a
>> Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 
>> 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux
>>
>> [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv
>> 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 
>> 560] (rev a1)
>>
>> I wouldn't think I need to update my graphics card driver. But, does 
>> anyone know how to fix this?
>>
>> Thanks,
>> Chris
>> ___
>> 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
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>
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Re: [Freesurfer] tksurfer display problem

[Chris Watson]

Hello again,
After a system reboot, I am seeing these messages when trying to open 
tkmedit or tksurfer:

Xlib:  extension "GLX" missing on display ":0.0".
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
display: :0.0

I've searched around, and seen that changing "nv" to "nvidia" and adding 
"Load glx" in xorg.conf should work; however, the X server doesn't start 
when I do either or both.
Has anyone had trouble with this?

Thanks,
Chris

Nick Schmansky wrote:
> what is the version of your driver?  ie
>
> cat /proc/driver/nvidia/version
>
> the latest is around 260.19.12
>
> the problem you see is something we've seen with old nvidia drivers,
> whereby updating the driver has fixed the problem.  not sure why this
> would just happen now for you.
>
> to update (must be root or use sudo):
>
> /sbin/init 3
> /usr/bin/nvidia-installer --update
>
>
> n.
>
>
> On Fri, 2011-01-14 at 13:19 -0500, Chris Watson wrote:
>   
>> Hi, when trying to look at surfaces in tksurfer, all I see is a small 
>> part of the data in the posterior of the brain (see attached for 
>> example). There are no errors on the command line when I run tksurfer.
>> This only started happening very recently. Here's some system info: 
>> (CentOS 5.5, 64-bit; FreeSurfer v5.0)
>>
>> [freesurfer@occipital TGA]$ uname -a
>> Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 
>> 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux
>>
>> [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv
>> 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 
>> 560] (rev a1)
>>
>> I wouldn't think I need to update my graphics card driver. But, does 
>> anyone know how to fix this?
>>
>> Thanks,
>> Chris
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
>   
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