[Freesurfer] Freeview to mark only one specific area

[Luis Fernado Silva Castro de Araújo]

 Hello Freesurfer experts,


I want either a 2D or 3D picture of one of my subjects image, but with only
one colored area. For example, I would like to mark
the lh_lateralorbitofrontal_area.

It seems that the tool to visualize images in Freesurfer is freeview,
however I can't find the label for the left hemisphere
lateralorbitofrontal_area in the GUI. It is not listed in the Volumes tab
with the aparc+aseg item ticked.

I did not find information in your website, maybe I missed.

Could you please provide a pointer towards the answer? Maybe I missed where
it is taught at the documentation, a simple link would do.

Thanks,

luis
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[Freesurfer] asegstats2table for all subjects in the directory

[Luis Fernado Silva Castro de Araújo]

Hi Freesurfer experts,

I wonder if there is a way of extracting the stats for all patients in my
last run at the same time. I have around 120 observations and the
asegstats2table syntax works in such a way that all the patients names
should be listed:

asegstats2table --subjects 004 021 040 067 080 092 \
  --segno 11 17 18 \
  --tablefile aseg.vol.table

I hope I am wrong, but it seems that the —subjects argument does not accept
substitution with wildcards, like * or *.*

Is there a way to make the command run the extraction of the statistics in
all subjects within the $SUBJECTS_DIR in order to avoid typing all the 120
folder names? A bash script would do too.

Thanks,

luis
​
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[Freesurfer] Virtual machine (in virtual box) generating error: Can't locate MNI/Startup.pm in @INC

[Luis Fernado Silva Castro de Araújo]

Hello freesurfers,

I installed freesurfer in a linux machine without problems, but when I am
trying to install it on a Windows computer within a virtualmachine I keep
getting the same error. I’ve tried the instructions in the tutorial and
also tried to set an entirely new virtual machine with the same steps I did
in my linux set up, to no avail.

When I run:

recon-all -s SUBJECT -all -i FILE.img

I get:

INFO: extension is mgz
#
#@# Talairach Tue Dec 22 18:00:14 EST 2015
/tmp/02_1_4/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
--no-rescale --i orig.mgz --o orig_nu.mgz

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

recon-all -s 02_1_4 exited with ERRORS at Tue Dec 22 18:00:18 EST 2015

For more details, see the log file /tmp/02_1_4/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The log file is too long to put in the body of the e-mail, so here is the
pastebin for recon-all.log .

Looking at it, it seems that the problem happens after

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz

So I cd’ed into the mri directory and run it, which gave me the error:

/media/sf_Desktop/Patients/A.o/03_1_4/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
Tue Dec 22 17:52:00 EST 2015
Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl
/usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14
/usr/local/lib/site_perl .) at
/usr/local/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at
/usr/local/freesurfer/mni/bin/nu_correct line 37.
tmpdir is ./tmp.mri_nu_correct.mni.2621
/media/sf_Desktop/Patients/A.o/03_1_4/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -3.72529e-09)
j_ras = (-1.86265e-09, -1.16415e-10, -1)
k_ras = (-7.45233e-09, 1, -5.82338e-11)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.2621/nu0.mnc...


Iteration 1 Tue Dec 22 17:52:03 EST 2015
nu_correct -clobber ./tmp.mri_nu_correct.mni.2621/nu0.mnc
./tmp.mri_nu_correct.mni.2621/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.2621/0/ -iterations 1000 -distance 50
Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl
/usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14
/usr/local/lib/site_perl .) at
/usr/local/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at
/usr/local/freesurfer/mni/bin/nu_correct line 37.



ERROR: file ./tmp.mri_nu_correct.mni.2621/nu1.mnc does not exist!

It seems that it fails finding some pearl scripts. I tried installing pearl
on the VM, also with any success.

Any pointers here would be really appreciated? What you think is happening
in this installation?

Best,

Luis
​
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Luis Fernado Silva Castro de Araújo]

Do I have to run recon-all entirely in order to extract volume for a few
Brodmann's areas? Or is there a way of optimizing the process by striping
it of any unneeded calculations?

It is taking 21h to analyze one subject.

Best,
luis

2015-12-22 9:44 GMT+11:00 Douglas N Greve :

> If you're doing anatomical analysis, then FSFAST is not needed (nor its
> directly structure). If you have an input anatomical volume  in any
> format, then just run
>
> recon-all -s yoursubjectname -all -i inputfile
>
> inputfile can include img but be warned that img does not have
> information about head orientation. This may cause a catastrophic
> failure (eg, the head is upside down). If the head is left-right
> reversed, then it probably won't fail but everything will be left-right
> reversed. don't say I did not warn you:)
>
>
> On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
> >
> > Dear Douglas,
> >
> > It's an anatomical analysis. Perhaps I misunderstood the requirement
> > for setting up the directories in the FSFAST for the recon-all command.
> >
> > If that is the case, it is then a matter of converting my img files
> > into mgz and run recon-all on them, am I right?
> >
> > Does the command recon-all also gives me volumes for specific
> > Brodmann's areas? Or do I have to run a labeling to that?
> >
> >
> > Thank you,
> >
> > luis
> >
> >
> >
> >
> > ___
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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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> is
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Luis Fernado Silva Castro de Araújo]

Dear Douglas,

It's an anatomical analysis. Perhaps I misunderstood the requirement for
setting up the directories in the FSFAST for the recon-all command.

If that is the case, it is then a matter of converting my img files into
mgz and run recon-all on them, am I right?

Does the command recon-all also gives me volumes for specific Brodmann's
areas? Or do I have to run a labeling to that?


Thank you,

luis
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[Freesurfer] Help importing files from a previous SPM analysis

[Luis Fernado Silva Castro de Araújo]

Hi all,

I am just starting to learn to analyse neuroimaging data. So these are my
first steps with FreeSurfer. I apologize if the question is too basic to
the mail list.

I set myself the goal of finding volumes for several areas in a dataset
from the lab I am working on, but I got stuck very early on the exercise.
As far as I understood by reading the Tutorials, all the magic happens with
the recon-all command, right? But it seems that it requires a specific
directory structure to run properly (the FSFAST structure
).

The problem is that the dataset for my exercise is organized in a different
structure. It was previously analysed in SPM. The structure is as follows.

For patients:

/experiment/patients/A.o/

and for controls:

/experiment/controls/A.o/

Within each directory there are .hdr, .img, .mat and .mask files for each
observation, which was obtained in two different times. So the naming of
the files have the following order:

experiment_subjectnumber_time1.img

and for the second acquisition reads:

experiment_subjectnumber_time2.img

The same with all the before mentioned extensions (hdr, mat, mask).

It seems that in the FreeSurfer workflow the command unpacksdcmdir
 is used to
extract data from the nii and dicon types and organize them in the FSFAST
structure. Can it be used on directory structures like the one I have? Or
is there anyway of automating the conversion from this structure into the
FSFAST’s?

Thank you,

luis
​
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