Re: [Freesurfer] eTIV as a covariate

2017-11-18 Thread Bruce Fischl 

usually we use eTIV for volume and surface area but not for thickness

cheers
Bruce
On 
Sun, 19 Nov 2017, 郑凤莲 wrote:



Hi Professor,

I ran three steps of "recon-all" and get the cortical thickness, surfarea, 
GrayVol in lh.aparc.stats
and subcotical volume in aseg.stats. If I want to use SPSS software for 
statistics， should I use
eTIV as a covariate for everyone?
Thank you very much.

Sincerely,
Zheng








 


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[Freesurfer] eTIV as a covariate

2017-11-18 Thread 郑凤莲 
Hi Professor,

I ran three steps of "recon-all" and get the cortical thickness, surfarea, 
GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use 
SPSS software for statistics， should I use eTIV as a covariate for everyone?
Thank you very much.


Sincerely,
Zheng







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[Freesurfer] (无主题)

2017-11-18 Thread 郑凤莲 
Hi Professor,
I ran three steps of "recon-all" and get the cortical thickness, surfarea, 
GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use 
SPSS software for statistics.


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Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

2017-11-18 Thread Bruce Fischl 

Hi Michelle

probably best to tar and gzip the entire subject directory and ftp it to 
us:


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

cheers
Bruce

On 
Sat, 18 Nov 2017, Michelle VanTieghem wrote:



Hi, 
Yes I can send you the data - should I just attach the mprage file in the 
email, or is there another
way to share the data with freesurfer? Also, should I send one scan or multiple 
scans? 

Thanks,
Michelle

On Sat, Nov 18, 2017 at 10:37 AM, Bruce Fischl  
wrote:
  Hi Michelle

  are you doing anything out of the ordinary? Do you want to send us a 
dataset and we will
  take a look? I don't think 6.0 is very different from 5.3 in regard to 
skull stripping,
  although it is probably a bit better

  Bruce

  On Fri, 17 Nov 2017, Michelle VanTieghem wrote:

Hello, 
I have posted several times about problems with skull-stripping 
with our
dataset. We have tried gcut
and multiple other options in other packages (AFNI, FSL, ANTS) to 
remove
skull from structural
images in our dataset with little success.

Recently, a colleague suggested this may be due to versions: that 
6.0 deals
with skull stripping
much better than 5.3. 

 I wanted to ask if indeed this could be the case before I go 
install 6.0
and re-run everything in
my study.

Thank you, 
Michelle 

--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu




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--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu

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Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

2017-11-18 Thread Michelle VanTieghem 
Hi,

Yes I can send you the data - should I just attach the mprage file in the
email, or is there another way to share the data with freesurfer? Also,
should I send one scan or multiple scans?

Thanks,
Michelle

On Sat, Nov 18, 2017 at 10:37 AM, Bruce Fischl 
wrote:

> Hi Michelle
>
> are you doing anything out of the ordinary? Do you want to send us a
> dataset and we will take a look? I don't think 6.0 is very different from
> 5.3 in regard to skull stripping, although it is probably a bit better
>
> Bruce
>
>
> On Fri, 17 Nov 2017, Michelle VanTieghem wrote:
>
> Hello,
>> I have posted several times about problems with skull-stripping with our
>> dataset. We have tried gcut
>> and multiple other options in other packages (AFNI, FSL, ANTS) to remove
>> skull from structural
>> images in our dataset with little success.
>>
>> Recently, a colleague suggested this may be due to versions: that 6.0
>> deals with skull stripping
>> much better than 5.3.
>>
>>  I wanted to ask if indeed this could be the case before I go install 6.0
>> and re-run everything in
>> my study.
>>
>> Thank you,
>> Michelle
>>
>> --
>> Michelle VanTieghem
>> PhD student in Psychology
>> Developmental Affective Neuroscience Lab
>> Columbia University
>> mrv2...@columbia.edu
>>
>>
>>
>
> 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.
>



-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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Re: [Freesurfer] cuda compile help

2017-11-18 Thread Meij, Henk 
And that ofcourse was the partial answer, as listed on wiki page, I need to 
apply a data dir,, these links are pointing to missing files. Will retry Monday.


-Henk


[hmeij@n78 freesurfer-gpu.git]$ find . -name *glnxa64* -exec ls -l {} \;
lrwxrwxrwx 1 hmeij its 195 Nov 17 08:14 ./scripts/fs_spmreg.glnxa64 -> 
../.git/annex/objects/9g/2q/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a
lrwxrwxrwx 1 hmeij its 196 Nov 17 08:14 ./fsfast/bin/fast_selxavg3b.glnxa64 -> 
../../.git/annex/objects/5P/qx/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce
lrwxrwxrwx 1 hmeij its 194 Nov 17 08:14 ./fsfast/bin/mkcontrast2m.glnxa64 -> 
../../.git/annex/objects/P7/77/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Meij, Henk 

Sent: Friday, November 17, 2017 6:35:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cuda compile help

I should have mentioned, i did not do any data dirs step, confused on this, 
just hoping to compile gpu code

-Henk



- Reply message -
From: "Meij, Henk" 
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] cuda compile help
Date: Fri, Nov 17, 2017 6:24 PM


cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env 
recap:


  999  cd /usr/local/freesurfer-gpu.git/
 1001  export PATH=/usr/local/cuda-8.0/bin:$PATH
 1002  export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64
 1004  make clean
 1008  ./setup_configure | tee -a setup_configure.log
 1011  ./configure --disable-Werror 
--with-pkgs-dir=/usr/local/centos6-x86_64-packages 
--prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda-8.0 | tee -a 
configure.log
 1012  time make -j4 | tee -a make.log
 1013  make install


[hmeij@n78 freesurfer-gpu.git]$ grep nvcc Makefile
NVCC = /usr/local/cuda-8.0/bin/nvcc


Q1 what causes this and how to fix, make install fails
/bin/install -c fs_spmreg.glnxa64 irepifitvol.glnx64 
/usr/local/freesurfer-6.0.0/bin
/bin/install: cannot stat â_spmreg.glnxa64âNo such file or directory
/bin/install: cannot stat âepifitvol.glnx64âNo such file or directory
make[2]: *** [install-data-local] Error 1
make[2]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts'
make: *** [install-recursive] Error 1



Q2 no cuda packages, maybe related to Q1

[hmeij@n78 freesurfer-gpu.git]$ ls /usr/local/freesurfer-6.0.0/bin/*cuda*
/usr/local/freesurfer-6.0.0/bin/cuda_setup


Thanks for any help.
-Henk

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Re: [Freesurfer] % overlap of multiple labels

2017-11-18 Thread Bruce Fischl 
Hi Idil

I think you can use --label-list for multiple labels, or stuff them into 
annot files and it should do everything it finds.

cheers
Bruce
On Fri, 17 Nov 2017, 
Yagmur Ozdemir 19 wrote:

> Hello Freesurfer experts,
> 
> I am using the mris_compute_parc_overlap command to compute the % overlap of 
> two labels of the same
> region. Is there a way to do this for multiple labels?
> 
> Best
> Idil
> 
> 
>
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Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

2017-11-18 Thread Bruce Fischl 

Hi Michelle

are you doing anything out of the ordinary? Do you want to send us a 
dataset and we will take a look? I don't think 6.0 is very different from 
5.3 in regard to skull stripping, although it is probably a bit better


Bruce

On Fri, 17 Nov 2017, Michelle VanTieghem wrote:


Hello, 
I have posted several times about problems with skull-stripping with our 
dataset. We have tried gcut
and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull 
from structural
images in our dataset with little success.

Recently, a colleague suggested this may be due to versions: that 6.0 deals 
with skull stripping
much better than 5.3. 

 I wanted to ask if indeed this could be the case before I go install 6.0 and 
re-run everything in
my study.

Thank you, 
Michelle 

--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu

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Re: [Freesurfer]  hippocampus subfields

2017-11-18 Thread Bruce Fischl 

Hi Zheng

no difference between what and what?

cheers
Bruce
On Fri, 17 Nov 2017, 郑凤莲 wrote:


Hi professor,

    I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was
an obvious difference in left hippocampus, but no difference in right 
hippocampus. Then, I run
segmentation of hippocampus subfields. The result showed there is no difference 
in total left or
right hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is
there inconsistent result in two means? 
    Thank you very much.

Sincerely,
Zheng



 


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