Re: [Freesurfer] Any updates on recon-all GPU support?

[Dr. M. Shahid]

Hi,

I have one question here. If the code compiles using sdk 7.5 or latest,
will the resulting binary be FS v6? I wonder if the mri_ca_register_cuda
code is also changed in v6 tree...and if mixing of binaries from different
FS versions would not affect the results that much...

Best regards,

--
Shahid.



On Fri, Jul 1, 2016 at 2:46 AM, R Edgar  wrote:

> On 27 June 2016 at 01:27, Derek Pisner 
> wrote:
>
> > Was not able to resolve this quite yet. I figured out that I had to
> backtrack a bit because I was having trouble getting the complete set of
> data files from the Fs ftp server using "git annex ." And now it appears
> that freesurfer's entire ftp server is down and has been all day. I will
> try again tomorrow and let you know how it goes.
>
> Did it work out?
>
> Richard
>
> ___
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>
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[Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

[Halbertsma, HN (ohk)]

I’m having issues with the conversion of labels drawn in fsaverage to subject’s 
space (using mri_label2label).
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left 
and right hemisphere that I want to convert to a subjects brain. I’ve 
successfully managed to do this for the left hemisphere of all the subjects, 
where the V1-bins converted from the fsaverage fall perfectly within subject 
specific V1. However, for the right hemisphere, the bins seem slightly 
misaligned for all the subjects (they’re usually a bit bigger than they should 
be). Any idea what could have caused this?!

Many thanks.

Hinke




Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
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The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred message.
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Re: [Freesurfer] Any updates on recon-all GPU support?

[R Edgar]

On 1 July 2016 at 04:30, Dr. M. Shahid  wrote:

> I have one question here. If the code compiles using sdk 7.5 or latest, will
> the resulting binary be FS v6? I wonder if the mri_ca_register_cuda code is
> also changed in v6 tree...and if mixing of binaries from different FS
> versions would not affect the results that much...

The binary will be from whichever version of the source tree you
checked out. The GPU results are inevitably going to be slightly
different to the CPU ones, though. If, however, you find significant
differences, I'd like to know about them :-)

HTH,

Richard
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[Freesurfer] Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

[Kaiming Yin]

Dear guys,

Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum (including the subcortical structures while excluding the
ventricles and brain stem)? I'm not sure whether the
"SupraTentorialNotVent" can be the value for this measurement, and could it
be a bit bigger than the real value due to the partial volume effect?

Besides, could I also ask is there a value represent the volume of the
cerebellum? Currently I calculate the volume by adding the left/right
cerebellar GM/WM values in the detailed list in aseg.stats file.

Many thanks,
Kaiming
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Re: [Freesurfer] Intensity normalization issues leading to improper segmentation

[Bruce Fischl]

Hi Élodie

if you upload your subject we will take a look

cheers
Bruce
On Fri, 1 Jul 2016, Elodie 
Cauvet wrote:



Dear Freesurfer list,

Sorry to bother by posting again, but I am bit stuck by this issue and would
be really glad to get some help on that issue. Of course I can upload some
data if needed.

Thanks a lot!

Maybe I am hoping for a miracle with my question, but I am bit desperate
after unsuccessfully trying things around for over a year.
In a nutshell, I need advice on the intensity normalization options.

We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner
with a 32 channel coil (IR-FSPGR 3D volume). This coil has a huge problem in
a field inhomogeneity resulting in strong occipital hypersignal and frontal
hyposignal, from which I believe all my problems originate.

- The standard pipeline provide an incomplete temporal and frontal
segmentation (white and pial surfaces do not include enough) while over
including in occipital and parietal.
- We tried using the watershed 40 value from the skulltrip to get more of
the occipital (we had a few subjects having holes in occipital within the
brain segmentation). This option changed also the segmentation resulting in
better segmentation for temporal and frontal but worse in parietal and
occipital.
- We tried control points as well, without success (as you can imagine due
to the fronto-occipital inhomogeneity). We also tried manually removing
extra voxels from the white surface to correct it. But unfortunately, this
is not an option because we have about 200 scans to process.
- We tried using N4 intensity bias correction on the raw images before
feeding it to freesurfer, but the segmentation did not run through for all
participants (stuck in fixing topology for more than a week) and for those
working, the pial surface did not include enough grey matter.

I am now thinking about playing with the option of intensity normalization
(mri_ca_normalize) within freesurfer but would like to have your expert
opinion on that before roaming. Any advice on how to set up mri_ca_normalize
to retrieve a good white matter homogeneity? Or any other functions I should
be playing around with?

Thanks a lot in advance for your help,
Kind regards,

Élodie


Élodie CAUVET | PhD  

Karolinska Institutet Center of Neurodevelopmental Disorders
(KIND)  

Gävlegatan 22B, floor 8 | 113 30 Stockholm

+46 (0)8 514 527 10 | +46 (0)728 774 058
elodie.cau...@ki.se

http://ki.se/en/kind/startpage

http://elodiecauvet.wordpress.com/

Karolinska Institutet – a medical university

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Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

[Bruce Fischl]

Hi Hinke

we need more details if you want us to help you. Images, exact command 
lines and outputs, etc


cheers
Bruce
On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:


I’m having issues with the conversion of labels drawn in fsaverage to
subject’s space (using mri_label2label). 
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left
and right hemisphere that I want to convert to a subjects brain. I’ve
successfully managed to do this for the left hemisphere of all the subjects,
where the V1-bins converted from the fsaverage fall perfectly within subject
specific V1. However, for the right hemisphere, the bins seem slightly
misaligned for all the subjects (they’re usually a bit bigger than they
should be). Any idea what could have caused this?! 

Many thanks.

Hinke




Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl








De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes
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any way. The UMCG cannot be held responsible for incomplete reception or
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Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

[Halbertsma, HN (ohk)]

Hi Bruce,

Attached the image that show the fine conversion for the lh (on the left) and 
the misaligned conversion for the rh (on the right)

[cid:9B79D24B-8ECE-46FA-889C-B7919A94C7B2]

I used the following commands:

left hemisphere, first bin:
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface

right hemisphere
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface

The output is as follows:
left hemisphere, first bin:
srclabel = ./fsaverage/label/lh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = HHcon_8
trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 102 points in source label.
Starting surface-based mapping
Reading source registration
 /Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.white
Reading target registration
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  102 nlabel points
Performing mapping from target back to the source label 118606
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132
mri_label2label: Done

right hemisphere, first bin:
srclabel = ./fsaverage/label/rh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = con21_oxford
trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 209 points in source label.
Starting surface-based mapping
Reading source registration
 /Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.white
Reading target registration
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg
Rescaling ...  original radius = 99.
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  209 nlabel points
Performing mapping from target back to the source label 145838
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294
mri_label2label: Done

So for some reason the conversion for the right hemisphere works but is not 
perfect, which is also reflected in the fact that extracting the label 
statistics (using mris_anatomical_stats) will sometimes give different values 
after re-running the conversion.

Hope this helps.

Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl







On 01 Jul 2016, at 15:40, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Hinke

we need more details if you want us to help you. Images, exact command lines 
and outputs, etc

cheers
Bruce
On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:

I’m having issues with the conversion of labels drawn in fsaverage to
subject’s space (using mri_label2label).
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left
and right hemisphere that I want to convert to a subjects brain. I’ve
successfully managed to do this for the left hemisphere of all the subjects,
where the V1-bins converted from the fsaverage fall perfectly within subject
specific V1. However, for the right hemisphere, the bins seem slightly
misaligned for all the subjects (they’re usually a bit bigger than they
should be). Any idea what could have caused this?!
Many thanks.
Hinke
Hinke N. Halbertsma, MSc
PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl

De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
geadresseerde(n). Anderen dan de

[Freesurfer] dynamic monitor: freesurfer jobs on the Open Science Grid

[Krieger, Donald N.]

For those who are interested, we have deployed a crude dynamic monitor for 
freesurfer jobs running on the Open Science Grid.
It can be viewed at 
http://xd-login.opensciencegrid.org/scratch/donkri/fsurfPoll.html .
The display information is in addition to that which is currently accessible 
via "fsurf list" .

Each job runs in a sequence of three steps.
The second step runs in parallel as two separate OSG jobs.
These are your "recon-all -autorecon2" jobs.
At the lower right corner of the webpage, the number of jobs for each user at 
each step is listed.

Best - Don

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[Freesurfer] TRACULA problems

[Koubiyr, Ismail]

Hi everyone,

It’s been two weeks that I’ve been facing some issues with Tracula. I hope you 
could help me with that.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get this error 
but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space, but 
when the new bvecs  and bvals are created, they seem messed up. I will attach 
you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any 
additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.





bvals
Description: bvals


bvecs
Description: bvecs


bvecs.norot
Description: bvecs.norot


dwi_orig.mghdti.bvecs
Description: dwi_orig.mghdti.bvecs


dwi_orig.mghdti.bvals
Description: dwi_orig.mghdti.bvals
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
0
00 0 0
-0.203086 0.51882 -0.83041
0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
0.859934 0.178306 0.478247
0.979641 0.177715 0.0933861
0 0 0
-0.203086 0.51882 -0.83041
0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
0.859934 0.178306 0.478247
0.979641 0.177715 0.0933861
0 0 0
0 0 0___
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Re: [Freesurfer] longitudinal tracula

[Harms, Michael]

Hi Anastasia,
Looking through the
trac-preproc and
trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified
 within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis.  So, I've answered my previous question in that regard.




The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool).
  Thus, the bvecs/bvals are not identical for all the time points of a given subject.  We can specify the bvec file for each subject/time point using the
bveclist configuration parameter.  But there is no analog available for bvals, since only a single
bvalfile can be specified.  




I see that this issue has been raised in a couple other posts relatively recently (2015):

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html

but no working solution was provided at that time.



I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist”
 capability?  If not, it doesn’t look like it would be too difficult to modify 
trac-all  to include that capability (modeling after what is already
 in trac-all for the
bveclist/bvecfile
stuff).  But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries
 that would need modifications as well.  [I don’t see anything in the sections related to the BASE-specific processing in
trac-preproc involving bvals/bvecs, so think we are fine there.  But it is harder for me to tell what is going on in
trac-paths].




thanks,

-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:  on behalf of "Harms, Michael" 
Reply-To: Freesurfer support list 
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list 
Subject: [Freesurfer] longitudinal tracula







Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-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




 



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Re: [Freesurfer] Any updates on recon-all GPU support?

[Derek Pisner]

Hi Richard,

Sorry for the delay again. I had to get in touch with Zeke at Fs to get the 
repo working (it was broken for a week)

Despite a fresh source download and following your instructions carefully, I am 
still experiencing the same set of libcuda util errors upon running make.

See attached pastebin text file for the complete output. I cannot figure out 
what the issue is. Also, since our GPU is a Tesla K80 and we are using cuda 
toolkit 6.5, would the --enable-fermi-gpu option with ./configure still make 
sense? 

Many thanks,
Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of R Edgar 
[freesurfer@gmail.com]
Sent: Thursday, June 30, 2016 5:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Any updates on recon-all GPU support?

On 27 June 2016 at 01:27, Derek Pisner  wrote:

> Was not able to resolve this quite yet. I figured out that I had to backtrack 
> a bit because I was having trouble getting the complete set of data files 
> from the Fs ftp server using "git annex ." And now it appears that 
> freesurfer's entire ftp server is down and has been all day. I will try again 
> tomorrow and let you know how it goes.

Did it work out?

Richard

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Re: [Freesurfer] Any updates on recon-all GPU support?

[R Edgar]

On 1 July 2016 at 17:48, Derek Pisner  wrote:
> Here is the output attachment.

Hmmm this is the actual error:
==
gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I../include/dicom
-I../xml2 -I../include/NrrdIO -DTEEM_DIO=0 -DTEEM_32BIT=0
-DTEEM_QNANHIBIT=1 -DTEEM_ENDIAN=1234 -I../jpeg -I../tiff -I../expat
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/BasicFilters
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Common
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/IO
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics/Statistics
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/itk/current/include/InsightToolkit/Utilities
-DHAVE_ITK_LIBS  -I../glut -DHAVE_GLUT_LIBS
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/vxl/current/include/vxl/core
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/vxl/current/include/vxl/vcl
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt
-I/usr/local/cuda/include -DHAVE_ZLIB -g -O3 -msse2 -mfpmath=sse -Wall
 -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinux -DANSI
-fdata-sections -ffunction-sections -Wl,--gc-sections
-I/home/scanlab/Desktop/Derek/centos6-x86_64-packages/mni/current/include
-DFS_CUDA -I/usr/local/cuda/include -DGCAMORPH_ON_GPU  -MT
libutils_cuda_a-mrisurf.o -MD -MP -MF
.deps/libutils_cuda_a-mrisurf.Tpo -c -o libutils_cuda_a-mrisurf.o
`test -f 'mrisurf.c' || echo './'`mrisurf.c
In file included from /usr/local/cuda/include/cuda_runtime.h:59:0,
 from ../include/mrisurf_cuda.h:28,
 from mrisurf.c:664:
/usr/local/cuda/include/host_config.h:159:2: error: #endif without #if
 #endif /* !__HOST_CONFIG_H__ */
==

I've just tried doing a git pull, and restarting from
./setup_configure, and I can't reproduce this, I'm afraid.

You do absolutely want to have --enable-fermi-gpu set, though. Fermi
is five years old, and that flag enables most of the acceleration of
mri_ca_register.

Richard
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