[Freesurfer] [Re] medial wall label in Freesurfer 6

2017-11-30 Thread M del Mar Velasco 
Hi,


We are not using the make_average_subject 6.0.0-patch. Do you think it would be 
a possible solution? Where can I find that patch?


On the other hand, we've noticed that recon-all, which is a final 
make_average_subject step, fails. I send you the recon-all.log. However, maybe 
it is not related with previous issue becuase label files are generated before.


All the best,


M del Mar


error.log
Description: error.log


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Estimated ICV much lower than mask volume?

2017-11-30 Thread Patrycja Naumczyk 
Shame to admit - we didn't think about it. After the visual inspection -
something obviously went wrong. We'll try to correct manually.
Thanks for the tip!

Best regards,
Patrycja

2017-11-28 16:00 GMT+01:00 Bruce Fischl :

> Hi Patrycja
>
> did you check to see if the talairach transform was reasonably accurate?
>
> cheers
> Bruce
> On Tue, 28 Nov 2017, Patrycja Naumczyk wrote:
>
> Hi experts!
>> We are doing some QA exams with one subject scanned on different 3T
>> scanners (with comparable/nearly
>> identical imaging parameters). Afterwards, we looked into aseg values to
>> compare them with the
>> standard recon-all procedure. And we came across a strange result.
>> Between two scanners the raw
>> volumes are roughly the same, but the eICV's differ a lot (almost 30%).
>> We looked into the data and
>> found that even the mask volumes are alike (they differ less than 5%
>> between the machines). the only
>> outlier value is the eICV of one of the scanners. As this value is
>> estimated, can this be a marker
>> of some difficulties in normalization to Talairach upon the data of the
>> scanner? Should it be
>> alarming when an eICV is 30% lower than the mask volume?
>>
>> Best regards,
>> Patrycja
>>
>> [icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
>> Wolny od wirusów. www.avast.com
>>
>>
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Re: [Freesurfer] Merging two groups

2017-11-30 Thread Ramesh Babu 
Dear Bruce,
Thank you very much for reply.

I have to link fsavarage also. Because recently I have formated my system,
the link between freesurfer and fsaverage is broken.
I hope following link will be the correct one. If not please correct me.

ln -s /usr/local/freesurfer/subjects/fsaverage
/mnt/backup_data/freesurfer_analysis/subjects/fsaverage

On Wed, Nov 29, 2017 at 8:38 PM, Bruce Fischl 
wrote:

> if you have two dirs, dir1 and dir2, with a set of subjects in each
> (subjects1 and subjects2), you would do:
>
> cd $dir2
> foreach s ($subjects1)
>   ln -s $dir1/$s
> end
>
> then all your subjects will be listed in dir2
>
> that should do the trick
>
> On Wed, 29 Nov 2017, Ramesh Babu wrote:
>
> Dear Bruce,
>>
>> Thank for your reply. I am getting confusion in creating symlink.
>> ln -s /usr/local/freesurfer/subjects/fsaverage
>> /mnt/backup_data/freesurfer_analysis/subjects/
>> ln -s /usr/local/freesurfer/subjects/fsaverage
>> /mnt/backup_data/freesurfer_analysis/subjects/fsaverage
>>
>>
>> Please let me know how to create symbolic link?
>>
>> Thank you
>> Ramesh
>>
>> On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl 
>> wrote:
>>   Hi Ramesh
>>
>>   probably easiest to symlink them
>>
>>   cheers
>>   Bruce
>>   On Tue, 28 Nov 2017, Ramesh Babu wrote:
>>
>> Hi, I have done recon-all -all processing for 2 groups in
>> separate subjects directories. I want to
>> put all subjects in one dkirectory. Should I copy paste all
>> subject’s folders in one directory or
>> is
>> there any others steps to merge?
>>
>> Thanks in advance
>> RB
>>
>>
>>
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[Freesurfer] Recon-all with masked face and ears

2017-11-30 Thread Buimer, E.E.L. 
Dear FreeSurfer experts,

We want to implement a deface method to ensure anonymity of participants before 
making the data available to researchers. Because the raw data is stored on the 
imaging platform XNAT, we preferred the mask_face method implemented on the 
XNAT server rather than FreeSurfer’s defacing. However, we will be using 
FreeSurfer for processing and segmentations afterwards. I am currently 
investigating the effect of face and earmasks on brain measures. I used 
FreeSurfer v5.3 (freesurfer-x86_64-unknown-linux-gnu-stable5-20130513) and the 
mask_face function developed for XNAT (Milchienko & Marcus, 2013) with the 
default normalized filter. The masks were not invasive and did not overlap with 
brain tissue.

I compared output of the recon-all between T1 scans with and without masked 
face for a small sample. I found high correlations between the output of the 
two scans (extracted values: cortical thickness, surface area, (sub)cortical 
volume, global values). Slight differences seem to occur from the start of the 
recon-all (talairach transform). Adding ear masks to the face-masked scans, 
made the differences smaller (i.e. higher correlations with raw scans). Also, 
the recon-all run time appears to be reduced.

Could you explain how face and ear information is used in the recon-all and why 
adding ear masks to masked-face scans might reduce run-time and improve 
reliability? Could it be the case that skull stripping is easier without ears 
for example?
Thank you in advance.

Kind regards,
Elizabeth


Elizabeth Buimer, Research Assistant
Department of Psychiatry, UMC Utrecht
Room: A.01.161
e.e.l.bui...@umcutrecht.nl



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Re: [Freesurfer] GPU compile cuda8/centos7

2017-11-30 Thread Dr. M. Shahid 
On Wed, Nov 29, 2017 at 5:27 AM, R Edgar  wrote:

> On 28 November 2017 at 09:12, Dr. M. Shahid 
> wrote:
>
> > Has all of the GPU code also been updated in the new FS6.0 version or the
> > code is still from the old 5.x but can be compiled with new cuda
> toolkits?
>
> I made a small tweak for GCAMorph (primarily ca_register) which might
> have made it in to v6; I'm not aware of any other changes. However,
> being compiled with a new compiler for the new architectures should
> give a small speed boost.
>
>
Thanks for the info.

However if the cpu code in FS6 is changed a lot, but the cuda code not,
then the results would be different even if we get speed boost.
Then how would we take the different results?


Best regards,

--
Shahid.




> Richard
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Re: [Freesurfer] Recon-all with masked face and ears

2017-11-30 Thread Bruce Fischl 

Hi Elizabeth

I guess it could help by removing a feature that is variable across 
subjects so things like the talairach transform are more stable



cheers
Bruce
On Thu, 30 
Nov 2017, Buimer, E.E.L. wrote:




Dear FreeSurfer experts,

 

We want to implement a deface method to ensure anonymity of participants before 
making the data available to researchers.
Because the raw data is stored on the imaging platform XNAT, we preferred the 
mask_face method implemented on
the XNAT server rather than FreeSurfer’s defacing. However, we will be using 
FreeSurfer for processing and segmentations
afterwards. I am currently investigating the effect of face and earmasks on 
brain measures. I used FreeSurfer v5.3
(freesurfer-x86_64-unknown-linux-gnu-stable5-20130513) and the mask_face function 
developed for XNAT (Milchienko & Marcus,
2013) with the default normalized filter. The masks were not invasive and did 
not overlap with brain tissue.

 

I compared output of the recon-all between T1 scans with and without masked 
face for a small sample. I found high
correlations between the output of the two scans (extracted values: cortical 
thickness, surface area, (sub)cortical
volume, global values). Slight differences seem to occur from the start of the 
recon-all (talairach transform). Adding ear
masks to the face-masked scans, made the differences smaller (i.e. higher 
correlations with raw scans). Also, the
recon-all run time appears to be reduced. 

 

Could you explain how face and ear information is used in the recon-all and why 
adding ear masks to masked-face scans
might reduce run-time and improve reliability? Could it be the case that skull 
stripping is easier without ears for
example?   

Thank you in advance.

 

Kind regards,

Elizabeth

 



Elizabeth Buimer, Research Assistant

Department of Psychiatry, UMC Utrecht

Room: A.01.161

e.e.l.bui...@umcutrecht.nl 

 

 

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W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat 
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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

2017-11-30 Thread Hoopes, Andrew 
The make_average_subject patch can be downloaded here: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The readme file contains some instructions. This patch will definitely fix your 
recon-all error, but I don’t think it’s related to the labeling issue. Though, 
it’s worth a try.

best,
Andrew


On Nov 30, 2017, at 3:46 AM, M del Mar Velasco 
mailto:melly_2...@hotmail.com>> wrote:

Hi,

We are not using the make_average_subject 6.0.0-patch. Do you think it would be 
a possible solution? Where can I find that patch?

On the other hand, we've noticed that recon-all, which is a final 
make_average_subject step, fails. I send you the recon-all.log. However, maybe 
it is not related with previous issue becuase label files are generated before.

All the best,

M del Mar
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Re: [Freesurfer] license file error

2017-11-30 Thread Hoopes, Andrew 
Hi Ri,

It looks like there might be an issue with the license saved at 
/Applications/freesurfer6/.license. Try overwriting this file with your 
license.txt

best,
Andrew


On Nov 29, 2017, at 6:23 PM, Ritobrato Datta 
mailto:ridatpennc...@gmail.com>> wrote:

Hi All,

I am using Mac OS X Sierra and I downloaded free surfer 6 and when running 
recon I am getting the following error

reading from IM-0001-0001.dcm...
--
ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer6/.license
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--


The license.txt file is a valid license file and the permissions are set as 
follows

-rwxrwxrwx1 root  wheel136 Nov 29 12:48 license.txt

Can you please suggest what seems to be the problem ?

Thanks

Ri
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[Freesurfer] [Re] medial wall label in Freesurfer 6

2017-11-30 Thread M del Mar Velasco 
Hi,


I have installed the patch and it doesn't fix the label files problem. We have 
tried make_average_subject with the other 56 subjects and Medial_wall.label 
contains about 300 vertexs. It is very different from the other 60 subjects.

Nevertheless, we have also repeated the test with Freesurfer 5.3 and there is 
not any problem, all 116 subjects works fine.


Best,


M del Mar
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[Freesurfer] Concatenating .mgh surface space functional MRI runs

2017-11-30 Thread Abisan - 
Hi Freesurfer experts,

I want to concatenate multiple preprocessed fMRI runs in the form of .mgh
freesurfer surface space files (2-D matrices vertexes * time_frames). Is
there a tool that can do this easily, or do you have other recommendations
how to do this?

Thank you!
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Re: [Freesurfer] QDEC and comparing two conditions

2017-11-30 Thread Rizvi, Batool 
Hi - I'm still wondering what would be the best method to perform the mentioned 
steps. Additionally, would mri_compute_overlap provide output related to 
spatial overlap and difference, that we're looking for? Is it possible to do 
this with thickness, or maybe not - because it doesn't consider area? Just 
wondering, as we only performed QDEC using thickness so far.

Thanks so much,
Batool


From: Rizvi, Batool
Sent: Tuesday, November 28, 2017 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: QDEC and comparing two conditions

Hi FreeSurfer experts,

We calculated the correlation between thickness two different behavioral 
conditions using QDEC. We now want to compare the spatial overlap and 
difference in thickness-correlation between the two behavioral conditions. We 
would like to do this both visually as well as statistically. Is there an 
option to do this either in QDEC or in the command line?

Thanks for your time!
Batool
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[Freesurfer] TRACULA error "R: Subscript out of range"

2017-11-30 Thread Anna Mynick 
Hi all, 

I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is 
exiting with the output below. Most notably, I think, is the section of the 
output that says "R: Subscript out of range.” repeatedly and then the section 
afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame 
numbers are between 0 and 0”. Does anyone have thoughts on what might be going 
on here? 

I’ve attached my bvecs and bvals too, in case there is trouble there too. 

Thanks very much for any help. 

Best,
Anna 


0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.99649667739868 0.06475614756346 -0.05292384698987
0.60556709766388 0.42478442192078 0.67293894290924
0.86823248863220 0.03115228191018 -0.49517852067947
0.67013686895370 0.45375373959541 -0.58738726377487
-0.08319617807865 -0.97095906734467 0.22431358695030
0.19819127023220 -0.76370823383331 0.61438584327698
-0.38230711221695 0.40581783652306 0.83015239238739
0.21735191345215 -0.75227254629135 -0.62196791172028
0.02298471517861 0.97281080484390 -0.23045811057091
-0.07650605589151 0.04117560386658 0.99621850252151
-0.14655694365501 0.75338035821915 0.64104521274567
-0.57700997591019 -0.78357273340225 0.23037599027157
0.12379934638739 -0.96946108341217 -0.21170438826084
0.04432926326990 0.02168774046004 -0.99878138303757
0.26761892437935 -0.38499519228935 -0.88326603174210
-0.28756865859032 0.78847736120224 -0.54369783401489
0.38445866107941 0.07492686808109 0.92009633779526
-0.83095681667328 0.54706901311874 0.10112489014864
0.32437109947205 0.77897244691849 0.53664255142212
0.52829635143280 0.79588997364044 -0.29573988914490
-0.16789475083351 0.45606943964958 -0.87396329641342
-0.59607589244843 0.39722976088524 -0.69778358936310
-0.42442059516907 0.90444123744965 -0.04304528608918
0.37679037451744 -0.90613275766373 0.19222989678383
-0.62092286348343 -0.47927498817444 0.62028235197067
-0.07215544581413 0.96755516529083 0.24213692545891
-0.25669917464256 -0.76215481758118 0.59432780742645
-0.52350831031799 -0.05601207166910 0.85017740726471
0.18893271684647 0.76144242286682 -0.62008827924728
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0.71197289228439 0.66156578063965 0.23542550206184
-0.98868387937546 0.09445825219154 0.11654109507799
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0.65419042110443 -0.44598758220673 -0.610843658447270.00
0.00
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——

INFO: SUBJECTS_DIR is 
/mindhive

Re: [Freesurfer] QDEC and comparing two conditions

2017-11-30 Thread Bruce Fischl 

hmmm, it might be easiest to do at least some of this in matlab

cheers
Bruce
On Thu, 30 
Nov 2017, Rizvi, Batool wrote:




Hi – I’m still wondering what would be the best method to perform the mentioned 
steps. Additionally, would
mri_compute_overlap provide output related to spatial overlap and difference, 
that we’re looking for? Is it possible to do
this with thickness, or maybe not – because it doesn’t consider area? Just 
wondering, as we only performed QDEC using
thickness so far.

 

Thanks so much,

Batool

 

 

From: Rizvi, Batool
Sent: Tuesday, November 28, 2017 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: QDEC and comparing two conditions

 

Hi FreeSurfer experts,

 

We calculated the correlation between thickness two different behavioral 
conditions using QDEC. We now want to compare the
spatial overlap and difference in thickness-correlation between the two 
behavioral conditions. We would like to do this
both visually as well as statistically. Is there an option to do this either in 
QDEC or in the command line?

 

Thanks for your time!

Batool


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Re: [Freesurfer] Trouble building 6.0.0 on centos7

2017-11-30 Thread Hoopes, Andrew 
Hi Sol, 6.0 is built with qt 4.7, and the freesurfer development branch 
currently uses qt 4.8.5

best,
Andrew

> On Nov 27, 2017, at 5:32 PM, Sol Jerome  wrote:
> 
> Andrew,
> 
> Thanks, this helped me get past the error I was receiving. I am now
> trying to determine exactly which QT libraries are required to
> successfully complete compilation. I've tried both qt5-qtbase-devel as
> well as qt-devel. Here are the resulting errors from each:
> 
> 
> qt5-qtbase-devel:
> 
> main.cpp:1:30: fatal error: QtGui/QApplication: No such file or directory
> #include 
>  ^
> compilation terminated.
> make[3]: *** [nmovie_qt-main.o] Error 1
> make[3]: *** Waiting for unfinished jobs
> make[3]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/nmovie_qt'
> make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/nmovie_qt'
> make[2]: *** [all] Error 2
> make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0'
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
> 
> 
> 
> qt-devel:
> 
> make[3]: *** [freeview-moc_Cursor2D.o] Error 1
> make[3]: *** Waiting for unfinished jobs
> make[3]: *** [freeview-moc_Cursor3D.o] Error 1
> In file included from GenericRenderView.h:27:0,
> from moc_GenericRenderView.cpp:9:
> QVTKWidget.h:92:42: error: 'Qt::WFlags' has not been declared
>   QVTKWidget(QWidget* parent = NULL, Qt::WFlags f = 0);
>  ^
> In file included from moc_GenericRenderView.cpp:9:0:
> GenericRenderView.h:55:49: error: 'Qt::WFlags' has not been declared
>   GenericRenderView(QWidget* parent = NULL, Qt::WFlags f = 0);
> ^
> make[3]: *** [freeview-moc_GenericRenderView.o] Error 1
> make[3]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/freeview'
> make[2]: *** [all] Error 2
> make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/freeview'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0'
> make: *** [all] Error 2
> 
> 
> 
> Thanks,
> Sol
> 
> * Oct 05, 2017, at 19:54:55 PM, Hoopes, Andrew  
> wrote:
>> It looks like you’re missing the hexdump program xxd, which converts the 
>> help text to a header file. I believe it’s found in the vim-common package:
>> yum install vim-common
>> 
>> Andrew
>> 
>> 
>> On Oct 5, 2017, at 1:42 PM, Sol Jerome 
>> mailto:s...@utdallas.edu>> wrote:
>> 
>> The header file does not exist.
>> 
>> Here is the output from `make`:
>> 
>> # make
>> make: *** No rule to make target `lta_convert.help.xml.h', needed by `all'.  
>> Stop.
>> 
>> Here is the content of the Makefile:
>> 
>> # Makefile.in generated by automake 1.13.4 from Makefile.am.
>> # lta_convert/Makefile.  Generated from Makefile.in by configure.
>> 
>> # Copyright (C) 1994-2013 Free Software Foundation, Inc.
>> 
>> # This Makefile.in is free software; the Free Software Foundation
>> # gives unlimited permission to copy and/or distribute it,
>> # with or without modifications, as long as this notice is preserved.
>> 
>> # This program is distributed in the hope that it will be useful,
>> # but WITHOUT ANY WARRANTY, to the extent permitted by law; without
>> # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
>> # PARTICULAR PURPOSE.
>> 
>> 
>> 
>> 
>> 
>> am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
>> am__make_running_with_option = \
>> case $${target_option-} in \
>> ?) ;; \
>> *) echo "am__make_running_with_option: internal error: invalid" \
>> "target option '$${target_option-}' specified" >&2; \
>>exit 1;; \
>> esac; \
>> has_opt=no; \
>> sane_makeflags=$$MAKEFLAGS; \
>> if $(am__is_gnu_make); then \
>>   sane_makeflags=$$MFLAGS; \
>> else \
>>   case $$MAKEFLAGS in \
>> *\\[\ \   ]*) \
>>   bs=\\; \
>>   sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
>> | sed "s/$$bs$$bs[$$bs $$bs   ]*//g"`;; \
>>   esac; \
>> fi; \
>> skip_next=no; \
>> strip_trailopt () \
>> { \
>>   flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
>> }; \
>> for flg in $$sane_makeflags; do \
>>   test $$skip_next = yes && { skip_next=no; continue; }; \
>>   case $$flg in \
>> *=*|--*) continue;; \
>>   -*I) strip_trailopt 'I'; skip_next=yes;; \
>> -*I?*) strip_trailopt 'I';; \
>>   -*O) strip_trailopt 'O'; skip_next=yes;; \
>> -*O?*) strip_trailopt 'O';; \
>>   -*l) strip_trailopt 'l'; skip_next=yes;; \
>> -*l?*) strip_trailopt 'l';; \
>> -[dEDm]) skip_next=yes;; \
>> -[JT]) skip_next=yes;; \
>>   esac; \
>>   case $$flg in \
>> *$$target_option*) has_opt=yes; break;; \
>>   esac; \
>> done; \
>> test $$has_opt = yes
>> am__make_dryrun = (target_option=n; $(am__make_running_with_option))
>> am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
>> pkgdatadir = $(datadir)/freesurfer
>> pkgincludedir = $(includedir)/freesurfer
>> pkglibdir = $(libdir)/frees

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

2017-11-30 Thread Hoopes, Andrew 
Okay, can you upload the compressed average subject to our ftp server 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) and I will take a 
look?

thanks,
Andrew

On Nov 30, 2017, at 12:30 PM, M del Mar Velasco 
mailto:melly_2...@hotmail.com>> wrote:

Hi,

I have installed the patch and it doesn't fix the label files problem. We have 
tried make_average_subject with the other 56 subjects and Medial_wall.label 
contains about 300 vertexs. It is very different from the other 60 subjects.
Nevertheless, we have also repeated the test with Freesurfer 5.3 and there is 
not any problem, all 116 subjects works fine.

Best,

M del Mar
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Re: [Freesurfer] error hipp subfields

2017-11-30 Thread Hoopes, Andrew 
Hi John, I’ve tried to replicate this issue with no success. I’m still a bit 
confused as to when this errors occurs - are some subjects able to run 
successfully? Is it subject-dependent or is there no clear pattern? It’s 
possible that the matlab libraries have been corrupted, so one option would be 
to try to reinstall freesurfer (or neurodebian). Do you mind sending the output 
of “ldd /usr/local/freesurfer/stable/MCRv80/bin/glnxa64/libmwmclmcr.so”?

thanks,
Andrew

On Nov 13, 2017, at 4:09 PM, John Papatriantafyllou 
mailto:epikti...@gmail.com>> wrote:

Hi
yes, i can run some subjects and suddenly i get an error.
Actually today i got another kind of error (attach)
And all this only for Hip subfields.
I run fs 6 under neurodebian 8.00 (64b) through virtual box on an i7, 32gb ram 
machine and windows 10.
I have an identical machine with same verification and there is not any problem.
John


On Mon, Nov 13, 2017 at 9:07 PM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi John,

So you've been able to run some subjects successfully through the subfield 
stream? Can you provide some more information like freesurfer 
version/buildstamp (run the command ‘bugr') as well as your operating system 
and version?

thanks,
Andrew

On Nov 13, 2017, at 7:36 AM, John Papatriantafyllou 
mailto:epikti...@gmail.com>> wrote:

dear Eugenio,
i get the massage randomly after processing 10-15 patients' mri.
And this is only for the subfields.
I run them under the same platform.
John

On Mon, Nov 13, 2017 at 10:45 AM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Dear John,
This looks like a library error. You’re saying that you only get it with some 
subjects? Are you running them all on the same platform?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of John Papatriantafyllou 
mailto:epikti...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, 12 November 2017 at 19:41
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] error hipp subfields

dear Fs experts
i have the whole process to get the hipp subfields.
But after some mr's  that are processed well i get an error (attachment)
I have to do the whole process from the beggining
And so on
Is there an answer?
John

[mage removed by 
sender.]

Virus-free. 
www.avast.com



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[Freesurfer] FA to MNI

2017-11-30 Thread John Anderson 
Dear Freesurfer experts,
I want to register FA map in subject space to MNI. How can I do it using 
freesurfer tools?

Any advice is highly appreciated!
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Re: [Freesurfer] FA to MNI

2017-11-30 Thread Bruce Fischl 
Hi John

if your FA map is registered to the structurals (e.g. using bbregister) 
then you would just compose that transform with the talairach.xfm in the 
subject's mri/transforms dir.

cheers
Bruce
On Thu, 30 Nov 2017, John Anderson wrote:

> Dear Freesurfer experts,
> I want to register FA map in subject space to MNI. How can I do it using 
> freesurfer tools?
> 
> Any advice is highly appreciated!
> J
> 
>
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Re: [Freesurfer] FA to MNI

2017-11-30 Thread John Anderson 
Dear Dr Bruce,
Thank you so much for the quick response. Yes I used bbregister, but I don't 
know how to transform correctly.
I appreciate your guidance!

peace
J

>  Original Message 
> Subject: Re: [Freesurfer] FA to MNI
> Local Time: November 30, 2017 3:54 PM
> UTC Time: November 30, 2017 8:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson , Freesurfer support list 
> 
>
> Hi John
>
> if your FA map is registered to the structurals (e.g. using bbregister)
> then you would just compose that transform with the talairach.xfm in the
> subject's mri/transforms dir.
>
> cheers
> Bruce
> On Thu, 30 Nov 2017, John Anderson wrote:
>
>> Dear Freesurfer experts,
>> I want to register FA map in subject space to MNI. How can I do it using 
>> freesurfer tools?
>> Any advice is highly appreciated!
>> J
>
> 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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Re: [Freesurfer] GPU compile cuda8/centos7

2017-11-30 Thread R Edgar 
On 30 November 2017 at 09:42, Dr. M. Shahid  wrote:

>> > Has all of the GPU code also been updated in the new FS6.0 version or
>> > the
>> > code is still from the old 5.x but can be compiled with new cuda
>> > toolkits?
>>
>> I made a small tweak for GCAMorph (primarily ca_register) which might
>> have made it in to v6; I'm not aware of any other changes. However,
>> being compiled with a new compiler for the new architectures should
>> give a small speed boost.
>
> Thanks for the info.
>
> However if the cpu code in FS6 is changed a lot, but the cuda code not, then
> the results would be different even if we get speed boost.
> Then how would we take the different results?

I don't know if there have been changes in the relevant portions of
the CPU code. And unfortunately, there aren't any automated
comparisons. If there have, then there will obviously be larger
deviations between the CPU and GPU streams (they will never be
identical anyway).

Richard
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