[Freesurfer] installing mris_decimate

2014-08-22 Thread Nicholas Heugel 
So I just redownloaded the recent version of Freesurfer for Mac, Lion
operating system, making sure to grab the most recent version.  I need to
use the tool mris_decimate but it is not in any of the files I downloaded,
nor was it in any of the files I had previously.  Where can I get
mris_decimate, and what are the steps for installing it?

Nicholas
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Re: [Freesurfer] labelled tissue segmentation mask back to native

2014-08-22 Thread Douglas Greve 


See if this helps:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


On 8/20/14 7:07 AM, Alejandra Machado wrote:

Hello,

I was wondering if FS has an output mask (labelled volume) for each 
tissue types (gm+wm+venctricular_csf) that I can then turn into each 
subject's native space. I understand I can use aseg.mgz or even 
aparc+aseg.mgz and then run mri_label2vol. But then how do I get 
correspondent labelling for each subject in it's own native space?


Thanks,
Alejandra


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Re: [Freesurfer] Fwd: Re: Custom aseg Color Lookup Table

2014-08-22 Thread Douglas Greve 

Hmmm, sounds like a job for Ruopeng ...



On 8/20/14 2:04 PM, C.P. Frost wrote:

Thanks for the reply, Doug.

The main problem is that areas not included in my custom table appear 
colored in freeview. These areas' numbers correctly correspond to 
their indices on the default FreeSurferColorLUT, although they don't 
appear labeled in the info panel, nor are they listed to the left of 
the main display. For instance, the left cerebral cortex (not on my 
list) is colored, and clicking on it yields an index of 3 in the info 
panel, but no label.


The good news is so far as I can tell, every area I specified does 
show up colored appropriately and has a label associated, but I have 
no idea where the ones I DIDN'T specify are coming from.


 Original Message 
Subject:Re: [Freesurfer] Custom aseg Color Lookup Table
Date:   Wed, 20 Aug 2014 11:12:56 -0400
From:   Douglas N Greve >

To: freesurfer@nmr.mgh.harvard.edu 



Try loading aseg.mgz as the aux volume so you can see the number at a
particular voxel. If the color is not correct, see what the number is
and what it corresponds to in the LUT
doug


On 08/19/2014 05:57 PM, C.P. Frost wrote:

Hi all,

I'm trying to use Freeview to display subcortical regions in aseg.mgz
with a custom color lookup table. RGB colors will indicate on a jet
scheme how well that region's volume correlates to performance on a
behavioral measure. In other words, an R^2 coefficient of -1 is dark
blue, 0 is green, and 1 is dark red. I adapted the approach for aseg
structures from this method:
http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/

When I try right now, by e.g. loading
subjects_dir/average/mri/aseg.mgz, and choosing Color map > Lookup
Table, Lookup Table > Load lookup table... and selecting my custom
table file, it *almost* works. The file is copied below (it has no
headers).

4 Left-Lateral-Ventricle 92 255 163 0
5 Left-Inf-Lat-Vent 224 255 31 0
7 Left-Cerebellum-White-Matter 112 255 143 0
8 Left-Cerebellum-Cortex 133 255 122 0
10 Left-Thalamus-Proper 153 255 102 0
11 Left-Caudate 102 255 153 0
12 Left-Putamen 61 255 194 0
13 Left-Pallidum 102 255 153 0
14 3rd-Ventricle 0 224 255 0
15 4th-Ventricle 61 255 194 0
16 Brain-Stem 71 255 184 0
17 Left-Hippocampus 102 255 153 0
18 Left-Amygdala 41 255 214 0
26 Left-Accumbens-area 92 255 163 0
28 Left-VentralDC 122 255 133 0
30 Left-vessel 102 255 153 0
31 Left-choroid-plexus 102 255 153 0
43 Right-Lateral-Ventricle 173 255 82 0
44 Right-Inf-Lat-Vent 122 255 133 0
41 Right-Cerebellum-White-Matter 82 255 173 0
42 Right-Cerebellum-Cortex 122 255 133 0
49 Right-Thalamus-Proper 173 255 82 0
50 Right-Caudate 143 255 112 0
51 Right-Putamen 92 255 163 0
52 Right-Pallidum 41 255 214 0
53 Right-Hippocampus 133 255 122 0
54 Right-Amygdala 20 255 235 0
58 Right-Accumbens-area 82 255 173 0
60 Right-VentralDC 122 255 133 0
62 Right-vessel 122 255 133 0
63 Right-choroid-plexus 143 255 112 0
72 5th-Ventricle 92 255 163 0
85 Optic-Chiasm 112 255 143 0
251 CC_Posterior 71 255 184 0
252 CC_Mid_Posterior 31 255 224 0
253 CC_Central 10 255 245 0

The index numbers were chosen to match those found in the default aseg
LUT, as listed on the FS wiki: FSTutorial > AnatomicalROI >
FreeSurferColorLUT. Some regions appear correctly, but others either
a) display with incorrect labels, particularly
Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical*
white matter and ribbon, or b) display with no label in the info
panel, which makes it unclear whether it's working.


Notes:
- Originally indices were simply 1 to n, but that caused a wider array
of problems, and I inferred (perhaps incorrectly) freeview was
matching regions with indices rather than label names.
-This particular map is mostly green since most correlations are
small, which is fine; others will have a broader range of values.
-I'm not sure what the effect is of pressing the "Show existing labels
only" toggle, which eliminates a couple areas from the label list, but
it's unclear how it chooses them.


Can anyone offer advice on how to ensure the correct colors are
displayed in the correct regions? (Or an easier way to do this?)

Cheers,
C.P. Frost
UW-Madison


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Re: [Freesurfer] Fwd: mpr2mni305 failed error

2014-08-22 Thread Bruce Fischl 

Hi Francesco

if you upload one of the dicom series that causes the problems we will 
take a look. If you can also send us the rawavg.mgz after your successful 
recon-all from the .nii that would also help


cheers
Bruce
On Wed, 20 Aug 2014, Francesco 
Deleo wrote:



Hi all!
Sorry for my late answer but I went on holiday and I didn't have access to
my mail.

The background is normal in original dicoms and it is not an avarage of more
than one run.

The problem I reported was solved in all cases converting dicoms to nifti
with dcm2nii and using the oriented volume. I don't know why but it
functioned

Is there a bug in freesurfer using directly dicoms?

Thank you all for attention and advice.

Francesco


2014-08-08 19:53 GMT+02:00 Bruce Fischl :
  can you tar and gzip the dicoms and send them to us? Is there a
  high background level in them as well? Is this the average of
  more than one run? You should check the mri/orig/00?.mgz
  volume(s) as well
  On Fri, 8 Aug 2014, Francesco Deleo wrote:


-- Forwarded message --
From: Francesco Deleo 
Date: 2014-08-08 18:06 GMT+02:00
Subject: Re: [Freesurfer] mpr2mni305 failed error
To: freesurfer 


It is not ok...

It seems to have a contrast problem... I can send a
snapshot, or if you want
I can send the rawavg.mgz

Francesco


2014-08-08 17:53 GMT+02:00 Bruce Fischl
:
      what does the rawavg.mgz look like? If it is
ok, can you email
      it to us?
      On Fri, 8 Aug 2014, Francesco Deleo wrote:

            Thank you all for attention and help!
            Maybe we're finding the problem: in
cases I received
            the mpr2mni305 error
            the orig.mgz is unintelligible (it is
white with
            some black point). But my
            dicoms are ok (I've checked!). I've
already tried
            converting dicom to tiff
            but I got the same error message and the
same
            unintelligible orig.mgz (and
            the tiff are ok too!).
            So I think the likely problem is in the
recon-all -i
            command!
            Any idea?

            It remains a mistery for me why I have
this problem
            only in some (and not in
            every one) MRI scans even if all the
parameters are
            the same.

            thanks again

            Francesco


            2014-08-07 17:16 GMT+02:00 Douglas N
Greve
            :
                  Have you looked in
            transforms/talairach_avi.log?

                  On 08/07/2014 07:57 AM, Francesco
Deleo wrote:
                  > Thank you Doug!
                  > but i tried it in many cases but
I've always
            received the same
                  error
                  > message...
                  > Is there something else I can
try?
                  >
                  > Francesco
                  >
                  >
                  > 2014-08-07 0:46 GMT+02:00
Douglas N Greve
                   >:
            >
            >     Try it with -notal-check
            >     doug
            >
            >     On 08/06/2014 04:39 PM, Francesco
Deleo wrote:
            >     > I all!
            >     >
            >     > I am a new freesurfer user.
            >     > I have a problem when I perform
the
            recon-all -all, in about
            15% of
            >     > MRI scans, all made with the
same scanning
            protocol (T1 MPRAGE
            in a
            >     > SIEMENS Avanto 1,5 T).
            >     >
            >     > I can't recognize any difference
between
            those scans which
            work
            >     > correctly and those not.
            >     > I have never found the same
error on 3T MRI
            scans.
            >     >
            >     > I've already tried to add these
flags to the

[Freesurfer] 3dvolreg.afni error during mc-sess

2014-08-22 Thread Milde, Christopher 
Dear Freesurfer Experts,

I'm struggling with running only motion correction.
After running mktemplate-sess which ran well, the mc-sess terminates with the 
following error.

The terminal otput is attached:

"3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
ERROR: 3dvolreg.afni"

Some important comments:
1.) 3dvolreg.afni is within the bin-folder of Freesurfer
2.) I use partial-field-of-view EPI
3.) I run mc-sess und dcm2nii formated DICOM-files (is it a prerequisite to use 
unpacksdcmdir)?

Thank you, for your support!!!

Greets Christopher

TERMINAL OUTPUT:

mc-sess -s PM_00031 -d $FSF_DIR -per-run  -fstem -outfmt nii.gz

[christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 
-outfmt nii.gz
fmt: Undefinierte Variable.
[christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20
Logfile is 
/home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold.log
---
/home/christopher/Desktop/freesurfer/subjects/S1/PM_00923
RunList: 001 002 004
  --- ** ---
  --- Motion Correcting Run 001 ---
  --- ** ---
sess = PM_00923
Fr 22. Aug 09:35:07 CEST 2014
mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o 001/fmcpr.nii.gz --mcdat 
001/fmcpr.mcdat
/home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz
log file is 001/fmcpr.nii.gz.mclog
mcdat file is 001/fmcpr.mcdat
tmp dir is 001/tmp.mc-afni2.19767
#@# 
/home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 
--ndrop 0 -odt float
mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 
--ndrop 0 -odt float
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 001/template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.218143, 0.975917)
k_ras = (0, -0.975917, -0.218143)
writing to 001/tmp.mc-afni2.19767/tempvol.nii.gz...
#@# 
/home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float
mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 001/20.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.218143, 0.975917)
k_ras = (0, -0.975917, -0.218143)
writing to 001/tmp.mc-afni2.19767/invol.nii.gz...
#@# 
/home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat 
-base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix 
001/tmp.mc-afni2.19767/outvol.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
ERROR: 3dvolreg.afni
Ungültiger leerer Befehl.



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[Freesurfer] anatorig vs anat in dlabel

2014-08-22 Thread Kirstie Whitaker 
Hi

I have a very minor question about the naming scheme for tracula output.

I have the folders anat and anatorig in the dlabel folder. Am I right that:
anatorig is the T1 image in "freesurfer space" (256 x 256 x 256; LIA)
anat is a rotated version of the T1 image in freesurfer space that lines up 
with the standard orientation used by FSL (256 x 256 x 256; LAS)
So neither is actually in the same space as the *original* file that was passed 
to recon-all (176 x 240 x 256; LAS)?
I ran mri_label2vol with dlabel/anat/anat_brain_mask.nii.gz as the --temp 
argument and the labels didn't line up nicely. They did line up with anatorig 
though. Is this what you'd expect?

Kx

--
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
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Re: [Freesurfer] Left and Right Vessels

2014-08-22 Thread Mohammed Goryawala 
Thank you.

Mohammed


On Thu, Aug 21, 2014 at 10:23 AM, Bruce Fischl 
wrote:

> Hi Mohammed
>
> these are dark regions, usually in inferior pallidum/putamen. There
> intensity is different enough from gray matter that having it be a separate
> class helps us label them more accurately. They could also be lacunae and
> not vessels.
>
> cheers
> Bruce
>
>
>
> On Tue, 19 Aug 2014, Mohammed Goryawala wrote:
>
>  Hello Freesurfer experts,
>>
>> In a study I found significant differences in the volume of the left and
>> right vessels of the freesurfer atlas.
>>
>> I wanted to know what regions are included in that ROI and if there are
>> any
>> known functions of these regions.
>>
>> Thank you
>>
>> Mohammed Goryawala, PhD
>> Miller School of Medicine,
>> University of Miami
>>
>>
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Re: [Freesurfer] Left and Right Vessels

2014-08-22 Thread Matt Glasser 
Virchow­Robin spaces is another name for those (they are normal in small
amounts, not old strokes, and filled with CSF-like fluid).

Peace,

Matt.

On 8/21/14, 9:23 AM, "Bruce Fischl"  wrote:

>Hi Mohammed
>
>these are dark regions, usually in inferior pallidum/putamen. There
>intensity is different enough from gray matter that having it be a
>separate 
>class helps us label them more accurately. They could also be lacunae and
>not vessels.
>
>cheers
>Bruce
>
>
>On Tue, 19 Aug 2014, Mohammed Goryawala
>wrote:
>
>> Hello Freesurfer experts,
>> 
>> In a study I found significant differences in the volume of the left and
>> right vessels of the freesurfer atlas.
>> 
>> I wanted to know what regions are included in that ROI and if there are
>>any
>> known functions of these regions.
>> 
>> Thank you
>> 
>> Mohammed Goryawala, PhD
>> Miller School of Medicine,
>> University of Miami
>> 
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>properly
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[Freesurfer] Fwd: Best Way To Edit?

2014-08-22 Thread Lindsay Gubernick 
Hello,

I was just looking for some suggestions for the best way to manually edit
an image such as the one attached. As you can see, there is both white and
gray matter excluded from the pial surface on the medial aspect of the
right hemisphere. Is this best corrected by adding voxels to the
brainmask.mgz, adding a new control set, both, or something else entirely?
Thank you very much for the help.

Lindsay Gubernick

[image: Inline image 1].
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[Freesurfer] head surface

2014-08-22 Thread Meryem Ayse Yucel 
Hi Doug,

I used mkheadsurf function.

Meryem


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Re: [Freesurfer] installing mris_decimate

2014-08-22 Thread Z K 
Hello Nicholas

I can verify that mris_decimate was not included in the Lion Freesurfer 
v5.3 release. I am not exactly sure why, but I suspect it has to do with 
compatibility issues with some of the 3rd party libs required to 
successfully build on the OSX platform.

I am working on building mris_decimate and will email you and the 
freesurfer list once this is complete. If all goes smoothly, it should 
be ready by end of the day.

-Zeke




On 08/21/2014 04:45 PM, Nicholas Heugel wrote:
> So I just redownloaded the recent version of Freesurfer for Mac, Lion
> operating system, making sure to grab the most recent version.  I need
> to use the tool mris_decimate but it is not in any of the files I
> downloaded, nor was it in any of the files I had previously.  Where can
> I get mris_decimate, and what are the steps for installing it?
>
> Nicholas
>
>
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[Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Borzello, Mia 
Hi Freesurfers,

I'm in the process of creating the ct.mgz file, but it is erroring and saying 
there is a "segmentation fault (core dumped)."

What can I do to remedy this?

Thanks,
m
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Re: [Freesurfer] head surface

2014-08-22 Thread Douglas N Greve 

Can you include the previous correspondence? I've already forgotten the 
details of the previous email
doug

On 08/22/2014 12:05 PM, Meryem Ayse Yucel wrote:
> Hi Doug,
>
> I used mkheadsurf function.
>
> Meryem
>
>
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Re: [Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Douglas N Greve 


Hi Mia, do you realize that your description of the problem is too vague 
for us to help you? If you want help in a timely fashion, please include 
more detail like the problem you ran, the command-line arguments, the 
terminal output, etc. Please see the following web page for the types 
information we are looking for:

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The easier you make it for us, the more likely you are to get help.

thanks
doug


On 08/22/2014 12:17 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm in the process of creating the ct.mgz file, but it is erroring and 
> saying there is a "segmentation fault (core dumped)."
>
> What can I do to remedy this?
>
> Thanks,
> m
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled

2014-08-22 Thread Douglas N Greve 

Looks like your fsgd file was created under a windows machine or old 
macos, try converting the fsgd like this

cat old.fsgd | sed 's/\\r/\\n/g' > new.fsgd




On 08/22/2014 02:51 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> We run mri_glmfit and encountered the following error:
>
> INFO: gd2mtx_method is doss
> Saving design matrix to 
> LTHV_Thickness_LH_correlation_memory2.glmdir/Xg.dat
> Normalized matrix condition is 1e+08
> Design matrix --
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>
> The command line is as follow:
>
> mri_glmfit --y LTHV_lh_thickness.15.mgh --fsgd 
> LTHV_fsgd_correlation_memory2.txt doss --glmdir 
> LTHV_Thickness_LH_correlation_memory2.glmdir --surf average_LTHV_TP1 
> lh --C LTHV_Design_corr.mat —cortex
>
> The FSGD and Design files are attached
>
> We did not find the problem.
>
> Thanks in advance for your help.
>
> Regards
> Jürgen Hänggi
>
> 
> Jürgen Hänggi, Ph.D.
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
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>
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Fax: 617-726-7422

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Re: [Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Borzello, Mia 
Right, sorry. I was running a command with mri_convert in order to convert the 
ct dicoms to mgz format. The error I ran into was:
UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 22, 2014 12:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] problem with format of CT dicoms

Hi Mia, do you realize that your description of the problem is too vague
for us to help you? If you want help in a timely fashion, please include
more detail like the problem you ran, the command-line arguments, the
terminal output, etc. Please see the following web page for the types
information we are looking for:

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The easier you make it for us, the more likely you are to get help.

thanks
doug


On 08/22/2014 12:17 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm in the process of creating the ct.mgz file, but it is erroring and
> saying there is a "segmentation fault (core dumped)."
>
> What can I do to remedy this?
>
> Thanks,
> m
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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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
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Re: [Freesurfer] 3dvolreg.afni error during mc-sess

2014-08-22 Thread Douglas N Greve 

Hmm, that means that 3dvolreg.afni that comes with FS does not run 
properly on your system. Do you already have a full version of AFNI 
installed on your system?
doug


On 08/22/2014 05:00 AM, Milde, Christopher wrote:
> Dear Freesurfer Experts,
>
> I'm struggling with running only motion correction.
> After running mktemplate-sess which ran well, the mc-sess terminates 
> with the following error.
>
> The terminal otput is attached:
>
> "3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: 
> afni_ncerr
> ERROR: 3dvolreg.afni"
>
> Some important comments:
> 1.) 3dvolreg.afni is within the bin-folder of Freesurfer
> 2.) I use partial-field-of-view EPI
> 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a 
> prerequisite to use unpacksdcmdir)?
>
> Thank you, for your support!!!
>
> Greets Christopher
>
> *TERMINAL OUTPUT:*
>
> mc-sess -s PM_00031 -d $FSF_DIR -per-run  -fstem -outfmt nii.gz
>
> [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run 
> -fstem 20 -outfmt nii.gz
> fmt: Undefinierte Variable.
> [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run 
> -fstem 20
> Logfile is 
> /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold.log
> ---
> /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923
> RunList: 001 002 004
>   --- ** ---
>   --- Motion Correcting Run 001 ---
>   --- ** ---
> sess = PM_00923
> Fr 22. Aug 09:35:07 CEST 2014
> mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o 
> 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat
> /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
> mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz
> log file is 001/fmcpr.nii.gz.mclog
> mcdat file is 001/fmcpr.mcdat
> tmp dir is 001/tmp.mc-afni2.19767
> #@# 
> /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
> mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz 
> --nskip 0 --ndrop 0 -odt float
> mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz 
> --nskip 0 --ndrop 0 -odt float
> nskip = 0
> ndrop = 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 001/template.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, -0.218143, 0.975917)
> k_ras = (0, -0.975917, -0.218143)
> writing to 001/tmp.mc-afni2.19767/tempvol.nii.gz...
> #@# 
> /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
> mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float
> mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 001/20.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, -0.218143, 0.975917)
> k_ras = (0, -0.975917, -0.218143)
> writing to 001/tmp.mc-afni2.19767/invol.nii.gz...
> #@# 
> /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold
> 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 
> 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix 
> 001/tmp.mc-afni2.19767/outvol.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz
> 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: 
> afni_ncerr
> ERROR: 3dvolreg.afni
> Ungültiger leerer Befehl.
>
>
>
>
>
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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
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Re: [Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Douglas N Greve 

Hi Mia, please follow the instructions on the web site below for 
submitting bug reports.
thanks
doug

On 08/22/2014 12:37 PM, Borzello, Mia wrote:
> Right, sorry. I was running a command with mri_convert in order to convert 
> the ct dicoms to mgz format. The error I ran into was:
> UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, August 22, 2014 12:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] problem with format of CT dicoms
>
> Hi Mia, do you realize that your description of the problem is too vague
> for us to help you? If you want help in a timely fashion, please include
> more detail like the problem you ran, the command-line arguments, the
> terminal output, etc. Please see the following web page for the types
> information we are looking for:
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> The easier you make it for us, the more likely you are to get help.
>
> thanks
> doug
>
>
> On 08/22/2014 12:17 PM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I'm in the process of creating the ct.mgz file, but it is erroring and
>> saying there is a "segmentation fault (core dumped)."
>>
>> What can I do to remedy this?
>>
>> Thanks,
>> m
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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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
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[Freesurfer] LGI Topological Defect

2014-08-22 Thread Tara Miskovich 
Hi all,

I am getting an error that seems common for people running LGI where it
crashes due to a topological defect.

I have run mris_euler_number and everything looks fine. Plus, I went
through each slice and made sure the surfaces looked good.

Any advice on any other steps I can take? I have already tried rerunning
recon-all.

Thank you!
Tara
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Re: [Freesurfer] installing mris_decimate

2014-08-22 Thread Z K 
Hello,

The latest version of mris_decimate for MacOS platform can be downloaded 
using this the following link:

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Darwin_lion_x86_64/mris_decimate

-Zeke

On 08/21/2014 04:45 PM, Nicholas Heugel wrote:
> So I just redownloaded the recent version of Freesurfer for Mac, Lion
> operating system, making sure to grab the most recent version.  I need
> to use the tool mris_decimate but it is not in any of the files I
> downloaded, nor was it in any of the files I had previously.  Where can
> I get mris_decimate, and what are the steps for installing it?
>
> Nicholas
>
>
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Re: [Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Borzello, Mia 
Hi Freesurfers, 

Apologies, I've never used this format before.
Here's the error:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

For additional information: 
1. Neuropace2JB
2. mri_convert -i 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
 -o ct.mgz
3. UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks so much, 
m

From: Borzello, Mia
Sent: Friday, August 22, 2014 1:14 PM
To: Freesurfer support list
Subject: RE: [Freesurfer] problem with format of CT dicoms

Hi Freesurfers,

Apologies, I've never used this format before.
Here's the error:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

For additional information:
1. Neuropace2JB
2. mri_convert -i 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
 -o ct.mgz
3. UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks so much,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 22, 2014 12:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with format of CT dicoms

Hi Mia, please follow the instructions on the web site below for
submitting bug reports.
thanks
doug

On 08/22/2014 12:37 PM, Borzello, Mia wrote:
> Right, sorry. I was running a command with mri_convert in order to convert 
> the ct dicoms to mgz format. The error I ran into was:
> UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, August 22, 2014 12:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] problem with format of CT dicoms
>
> Hi Mia, do you realize that your description of the problem is too vague
> for us to help you? If you want help in a timely fashion, please include
> more detail like the problem you ran, the command-line arguments, the
> terminal output, etc. Please see the following web page for the types
> information we are looking for:
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> The easier you make it for us, the more likely you are to get help.
>
> thanks
> doug
>
>
> On 08/22/2014 12:17 PM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I'm in the process of creating the ct.mgz file, but it is erroring and
>> saying there is a "segmentation fault (core dumped)."
>>
>> What can I do to remedy this?
>>
>> Thanks,
>> m
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone

Re: [Freesurfer] problem with format of CT dicoms

2014-08-22 Thread Douglas N Greve 

These dicoms are run-length encoded, which FS does not read. What you 
can do is the following

cd /place/where/dicoms/are

foreach dcm (*.dcm)
dcmdrle $dcm $dcm
end

then run mri_convert, like

mri_convert -it dicom IMG10.dcm ct.mgz

I did this and it converts, but the slice thickness looks wrong. I don't 
know how to fix it because we always trust the slice thickness in the dicom

doug



On 08/22/2014 01:51 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> Apologies, I've never used this format before.
> Here's the error:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
> For additional information:
> 1. Neuropace2JB
> 2. mri_convert -i 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
>  -o ct.mgz
> 3. UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks so much,
> m
> 
> From: Borzello, Mia
> Sent: Friday, August 22, 2014 1:14 PM
> To: Freesurfer support list
> Subject: RE: [Freesurfer] problem with format of CT dicoms
>
> Hi Freesurfers,
>
> Apologies, I've never used this format before.
> Here's the error:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
> For additional information:
> 1. Neuropace2JB
> 2. mri_convert -i 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT//1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
>  -o ct.mgz
> 3. UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks so much,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, August 22, 2014 12:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] problem with format of CT dicoms
>
> Hi Mia, please follow the instructions on the web site below for
> submitting bug reports.
> thanks
> doug
>
> On 08/22/2014 12:37 PM, Borzello, Mia wrote:
>> Right, sorry. I was running a command with mri_convert in order to convert 
>> the ct dicoms to mgz format. The error I ran into was:
>> UseSliceScaleFactor 0 (slice 0: 1)
>> Segmentation fault (core dumped)
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, August 22, 2014 12:31 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] problem with format of CT dicoms
>>
>> Hi Mia, do you realize that your description of the problem is too vague
>> for us to help you? If you want help in a timely fashion, please include
>> more detail like the problem you ran, the command-line arguments, the
>> terminal output, etc. Please see the following web page for the types
>> information we are looking for:
>>
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>> The easier you make it for us, the more likely you are to get help.
>>
>> thanks
>> doug
>>
>>
>> On 08/22/2014 12:17 PM, Borzello, Mia wrote:
>>> Hi Freesurfers,
>>>
>>> I'm in the process of creating the ct.mgz file, but it is erroring and
>>> saying there is a "segmentation fault (core dumped)."
>>>
>>> What can I do to remedy this?
>>>
>>> Thanks,
>>> m
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422

[Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

2014-08-22 Thread raij 

Hi,

Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use
the "noveau" drivers that come with CentOS 6.5 or would it be better to go
with the proprietary drivers from NVIDIA?

I would imagine that since FS 5.3 does not use GPU for analysis, this is
mainly relevant for visualization (freeview etc) requiring 3D rendering of
volumes, surfaces, and tractography results simultaneously.

In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here.

Thanks!

Tommi

---
Tommi Raij, MD, PhD


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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Transforming functional image while retaining voxel size

2014-08-22 Thread Jackie Lam 
Hello all,

I’m trying to register and transform a functional image to my high resolution 
anatomical image. As I understand, it can be done with mri_vol2vol, but the 
resulting functional image is resampled into 1x1x1 voxels (the resolution of my 
high res anatomical). Is there a way to transform the functional image so that 
it is in the same space as the anatomical image while retaining its original 
voxel size?

Many thanks,

Jack


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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.

Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

2014-08-22 Thread Z K 
Tommi,

Here at the Martinos Center we use the proprietary drivers from NVIDIA. 
We have no reasons to believe the Nouveau drivers would work better, but 
that isnt to say one doesnt exist.

-Zeke

On 08/22/2014 03:23 PM, r...@nmr.mgh.harvard.edu wrote:
>
> Hi,
>
> Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use
> the "noveau" drivers that come with CentOS 6.5 or would it be better to go
> with the proprietary drivers from NVIDIA?
>
> I would imagine that since FS 5.3 does not use GPU for analysis, this is
> mainly relevant for visualization (freeview etc) requiring 3D rendering of
> volumes, surfaces, and tractography results simultaneously.
>
> In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here.
>
> Thanks!
>
> Tommi
>
> ---
> Tommi Raij, MD, PhD
>
>
> ___
> Freesurfer mailing list
> 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 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.

Re: [Freesurfer] Transforming functional image while retaining voxel size

2014-08-22 Thread Douglas N Greve 
I'm not entirely sure what you mean by that, but if you add 
--no-resample to mri_vol2vol it will not change the pixels at all and 
just update the geometry info in the header so that it shares an RAS 
space with the anatomical

On 08/22/2014 04:04 PM, Jackie Lam wrote:
> Hello all,
>
> I’m trying to register and transform a functional image to my high resolution 
> anatomical image. As I understand, it can be done with mri_vol2vol, but the 
> resulting functional image is resampled into 1x1x1 voxels (the resolution of 
> my high res anatomical). Is there a way to transform the functional image so 
> that it is in the same space as the anatomical image while retaining its 
> original voxel size?
>
> Many thanks,
>
> Jack
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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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.

Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

2014-08-22 Thread dgw 
Just to add. If you are not using the CUDA options (which in my
understanding aren't being updated anyway), I find that the gpu
included in modern Intel cpus is more than sufficient for my
FreeSurfer and MNE uses.


HTH
D

On Fri, Aug 22, 2014 at 4:15 PM, Z K  wrote:
> Tommi,
>
> Here at the Martinos Center we use the proprietary drivers from NVIDIA.
> We have no reasons to believe the Nouveau drivers would work better, but
> that isnt to say one doesnt exist.
>
> -Zeke
>
> On 08/22/2014 03:23 PM, r...@nmr.mgh.harvard.edu wrote:
>>
>> Hi,
>>
>> Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use
>> the "noveau" drivers that come with CentOS 6.5 or would it be better to go
>> with the proprietary drivers from NVIDIA?
>>
>> I would imagine that since FS 5.3 does not use GPU for analysis, this is
>> mainly relevant for visualization (freeview etc) requiring 3D rendering of
>> volumes, surfaces, and tractography results simultaneously.
>>
>> In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here.
>>
>> Thanks!
>>
>> Tommi
>>
>> ---
>> Tommi Raij, MD, PhD
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

2014-08-22 Thread Z K 
Great. Thanks for the information.

-Zeke

On 08/22/2014 04:18 PM, dgw wrote:
> Just to add. If you are not using the CUDA options (which in my
> understanding aren't being updated anyway), I find that the gpu
> included in modern Intel cpus is more than sufficient for my
> FreeSurfer and MNE uses.
>
>
> HTH
> D
>
> On Fri, Aug 22, 2014 at 4:15 PM, Z K  wrote:
>> Tommi,
>>
>> Here at the Martinos Center we use the proprietary drivers from NVIDIA.
>> We have no reasons to believe the Nouveau drivers would work better, but
>> that isnt to say one doesnt exist.
>>
>> -Zeke
>>
>> On 08/22/2014 03:23 PM, r...@nmr.mgh.harvard.edu wrote:
>>>
>>> Hi,
>>>
>>> Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use
>>> the "noveau" drivers that come with CentOS 6.5 or would it be better to go
>>> with the proprietary drivers from NVIDIA?
>>>
>>> I would imagine that since FS 5.3 does not use GPU for analysis, this is
>>> mainly relevant for visualization (freeview etc) requiring 3D rendering of
>>> volumes, surfaces, and tractography results simultaneously.
>>>
>>> In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here.
>>>
>>> Thanks!
>>>
>>> Tommi
>>>
>>> ---
>>> Tommi Raij, MD, PhD
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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