subject:"\[Freesurfer\] freesurfer@nmr.mgh.harvard.edu"

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-11-08 Thread Douglas Greve


On the first one, you have to add -all, otherwise it won't do anything


On 11/8/17 11:51 AM, aurelie ponz wrote:

Thank you Douglas for your quick response !
I used the *recon-all -i ' -subjid *

Since it wasnt working I tried *recon-all -autorecon1 -i ' 
-subjid * and it worked for _SOME_ files (including the T1) 
but I don't get the hl/rl.pial files.

Then I tried the *autorecon2* on the sa;e data and it does'nt work.
Here is the bug I got.

fsuser@xubuntu-VirtualBox:/media/sf_T1_Groove/Groove_010$ recon-all 
-autorecon2 -i leo2014_19_anat01.nii -subjid Groove_010_2


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

/usr/local/freesurfer/subjects/Groove_010_2

 mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii 
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz


mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii 
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii...
TR=945000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, -0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz...
#-
#@# EM Registration Wed Nov  8 11:42:54 EST 2017
/usr/local/freesurfer/subjects/Groove_010_2/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz 
/usr/local/freesurfer/average/RB_all_2008-03-26.gca 
transforms/talairach.lta


aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/usr/local/freesurfer/subjects/Groove_010_2/mri/nu.mgz, -1): 
could not open file

mri_em_register: could not open input volume nu.mgz.

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


recon-all -s Groove_010_2 exited with ERRORS at Wed Nov  8 11:42:56 
EST 2017


For more details, see the log file 
/usr/local/freesurfer/subjects/Groove_010_2/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 




THANK YOU very much in advance
Aurelie





On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve 
> wrote:


what is your command line? Please send the recon-all.log file


On 11/8/17 5:24 AM, aurelie ponz wrote:

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer
VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr
10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_009

 mri_convert
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

mri_convert
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any
solutions but I didnt found a solution,

Many thanks in advance,

Aurelie






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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-11-08 Thread aurelie ponz

Thank you Douglas for your quick response !
I used the *recon-all -i ' -subjid *

Since it wasnt working I tried *recon-all -autorecon1 -i '
-subjid * and it worked for *SOME* files (including the T1) but I
don't get the hl/rl.pial files.
Then I tried the *autorecon2* on the sa;e data and it does'nt work.
Here is the bug I got.

fsuser@xubuntu-VirtualBox:/media/sf_T1_Groove/Groove_010$ recon-all
-autorecon2 -i leo2014_19_anat01.nii -subjid Groove_010_2

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_010_2

 mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii...
TR=945000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, -0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz...
#-
#@# EM Registration Wed Nov  8 11:42:54 EST 2017
/usr/local/freesurfer/subjects/Groove_010_2/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta

aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/usr/local/freesurfer/subjects/Groove_010_2/mri/nu.mgz, -1): could
not open file
mri_em_register: could not open input volume nu.mgz.

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

recon-all -s Groove_010_2 exited with ERRORS at Wed Nov  8 11:42:56 EST 2017

For more details, see the log file /usr/local/freesurfer/
subjects/Groove_010_2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting


THANK YOU very much in advance
Aurelie





On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve 
wrote:

> what is your command line? Please send the recon-all.log file
>
> On 11/8/17 5:24 AM, aurelie ponz wrote:
>
> Dear Freesurfer users,
>
> I have big issues performing recon-all into the freesurfer VirtualBox.
> I dont get any error but no files are created except the 0001.mgz.
> Here is what I get.
>
> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>
> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
> 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
> /usr/local/freesurfer/subjects/Groove_009
>
>  mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
> /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
>
> mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
> /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
> INFO: using NIfTI-1 qform
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w
> .nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0.0603182, -0.982945, 0.173726)
> j_ras = (-0.125291, 0.16521, 0.978268)
> k_ras = (0.990285, 0.0807736, 0.113189)
> writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...
>
> Could you please help me I read ;ost threads and tried ;any solutions but
> I didnt found a solution,
>
> Many thanks in advance,
>
> Aurelie
>
>
>
> 
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
>
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> Freesurfer mailing list
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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,

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-11-08 Thread Douglas Greve


what is your command line? Please send the recon-all.log file


On 11/8/17 5:24 AM, aurelie ponz wrote:

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

/usr/local/freesurfer/subjects/Groove_009

 mri_convert 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii 
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz


mri_convert 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii 
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any solutions 
but I didnt found a solution,


Many thanks in advance,

Aurelie






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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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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[Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-11-08 Thread aurelie ponz

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_009

 mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w
.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any solutions but I
didnt found a solution,

Many thanks in advance,

Aurelie




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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
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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-07-05 Thread Douglas Greve

The orientation flag was not found. This is an important piece of 
infomation that should be in the header. Have these dicoms been 
anonymized? Alternatively, is this may be a newer version of dicom that 
we are not reading properly yet.



On 6/25/17 9:45 PM, 糜超 wrote:

Hi,
I am preprocessing my fMRI data acquired with Philips. when I using 
the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .'

The error occurred likes below:
Found 31 total files.
Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201
Subject xxx
Date xxx
Time 110223
Institution x.
0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002
101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003
301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004
401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007
501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008
601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011
701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013
801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016
901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018
1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019
1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022
1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024
mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./XX_0003...
Starting DICOMRead2()
dcmfile = ./XX_0003
dcmdir = .
WARNING: tag image orientation not found in ./XX_0003
Ref Series No = 101
ERROR: bits = 0 not supported.

My os is Linux 16.04 and the Freesurfer's version is 5.3.







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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-06-25 Thread 糜超

Hi,
I am preprocessing my fMRI data acquired with Philips. when I using the command 
'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .'
The error occurred likes below:
Found 31 total files.
Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201
Subject xxx
Date xxx
Time 110223
Institution x.
0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002
101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003
301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004
401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007
501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008
601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011
701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013
801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016
901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018
1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019
1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022
1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024
mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./XX_0003...
Starting DICOMRead2()
dcmfile = ./XX_0003
dcmdir = .
WARNING: tag image orientation not found in ./XX_0003
Ref Series No = 101
ERROR: bits = 0 not supported.


My os is Linux 16.04 and the Freesurfer's version is 5.3.





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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

2015-11-12 Thread Douglas N Greve

/
really? So if you run

ls -l 
/Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz/

what do you get?

On 11/11/2015 07:59 PM, Heidi Foo wrote:
> Hi Dr Greve,
>
> Yes it does, for all base templates, there 
> are lh(rh).long.thickness-avg(pc1, rate, and 
> spc).fwhm0(5,10,20,25).fsaverage.mgh files.
>
> I did the following steps in preprocessing:
>
> 1. recon-all -all -s  -i path_to_tpN_dc m
> 2. recon-all -base  -tp  -tp  ... -all
> 3. recon-all -long   -all
> 4. long_mris_slopes --qdec 
> /Users/nnidementia/Documents/PDFS/long.qdec.table.txt --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
> --time years --qcache fsaverage --sd /Users/nnidementia/Documents/PDFS
> 5. long_mris_slopes --qdec 
> /Users/nnidementia/Documents/PDFS/QDEC/long.qdec.table.txt --meas 
> thickness --hemi lh --sd /Users/nnidementia/Documents/PDFS --do-pc1 
> --do-label --generic-time --fwhm 10 --qcache fsaverage --stack-pc1 
> /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.thickness-pc1.stack.mgh
>  
> --isec-labels 
> /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.fsaverage.cortex.label
>
> Thanks.
>
> Regards,
> Heidi Foo
>
>
>
>
> On Wed, Nov 11, 2015 at 11:57 PM, Douglas Greve 
> > wrote:
>
> does that file exist? Did you run recon-all -qcache ?
>
>
> On 11/11/15 7:54 AM, Heidi Foo wrote:
>> Apologies, the error message should be /Error in
>> analyze: couldn't open
>> 
>> /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file./
>>
>> On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo > > wrote:
>>
>> Hi Dr Greve,
>>
>> Thank you for your advice, it is deeply appreciated. I
>> removed the blank lines of wmh.levels and included a carriage
>> return at the end of the long.qdec.table.txt.
>>
>> However, there is still /error in analyze: Couldn't open
>> 
>> /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file./
>> /
>> /
>> I checked my qdec.table.txt (both cross and long) but I did
>> not see any fsaverage included in the list of subjects. Am I
>> missing something?
>>
>> Thank you.
>>
>> Regards,
>> Heidi Foo
>> /
>> /
>>
>> On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve
>> > > wrote:
>>
>> Also, try removing the blank line at the end of
>> wmh.levels, and make sure you have a carriage return at
>> the end of long.qdec.table.txt. This may fix the 2nd error
>>
>> On 11/09/2015 10:38 PM, Heidi Foo wrote:
>>
>> Dear Dr Greve,
>>
>> Thanks for your reply. I have already linked
>> fsaverage to my SUBJECTS_DIR but the error still
>> persists.
>>
>> Attached is my qdec (long and cross) files.
>>
>> Thanks.
>>
>> Regards,
>> Heidi Foo
>>
>>
>>
>> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve
>> > 
>> > >> wrote:
>>
>>
>>
>> On 11/06/2015 09:35 PM, Heidi Foo wrote:
>>
>> Dear FreeSurfer experts,
>>
>> I am trying to compare between stable WMH
>> group and rapid
>> progressed WMH group in regards to the
>> cortical thickness as
>> well as volume changes in the gray matter.
>> The nuisance
>> variable in my case is age. I ran my analysis
>> using QDEC but
>> encountered a few problems:
>>
>> 1. There is error in analyze: couldn't open file
>>
>> It looks like it cannot find fsaverage. Link it
>> to your
>> SUBJECTS_DIR if you have not already.
>>
>> 2. If this error doesn't appear, another one
>> does.
>> QdecGlmDesign::Create: zero factors!
>> (Attached the screenshot of the errors for
>> your perusal)
>>
>> please send the qdec file
>>
>>
>> I am hoping that you could give me a solution
>> to my problems.
>>
>> Thank you so much.
>>
>> Regards,
>> Heidi
>>
>>
>>

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

2015-11-11 Thread Douglas Greve

does that file exist? Did you run recon-all -qcache ?

On 11/11/15 7:54 AM, Heidi Foo wrote:
Apologies, the error message should be /Error in analyze: couldn't 
open 
/Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz 
or .mgh file./

On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo > wrote:

Hi Dr Greve,

Thank you for your advice, it is deeply appreciated. I removed the
blank lines of wmh.levels and included a carriage return at the
end of the long.qdec.table.txt.

However, there is still /error in analyze: Couldn't open

/Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file./
/
/
I checked my qdec.table.txt (both cross and long) but I did not
see any fsaverage included in the list of subjects. Am I missing
something?

Thank you.

Regards,
Heidi Foo
/
/

On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve
> wrote:

Also, try removing the blank line at the end of wmh.levels,
and make sure you have a carriage return at the end of
long.qdec.table.txt. This may fix the 2nd error

On 11/09/2015 10:38 PM, Heidi Foo wrote:

Dear Dr Greve,

Thanks for your reply. I have already linked fsaverage to
my SUBJECTS_DIR but the error still persists.

Attached is my qdec (long and cross) files.

Thanks.

Regards,
Heidi Foo

On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve

>> wrote:

On 11/06/2015 09:35 PM, Heidi Foo wrote:

Dear FreeSurfer experts,

I am trying to compare between stable WMH group
and rapid
progressed WMH group in regards to the cortical
thickness as
well as volume changes in the gray matter. The
nuisance
variable in my case is age. I ran my analysis
using QDEC but
encountered a few problems:

1. There is error in analyze: couldn't open file

It looks like it cannot find fsaverage. Link it to your
SUBJECTS_DIR if you have not already.

2. If this error doesn't appear, another one does.
QdecGlmDesign::Create: zero factors!
(Attached the screenshot of the errors for your
perusal)

please send the qdec file

I am hoping that you could give me a solution to
my problems.

Thank you so much.

Regards,
Heidi

-- 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/

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.

-- 
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:

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

2015-11-10 Thread Douglas N Greve

Also, try removing the blank line at the end of wmh.levels, and make 
sure you have a carriage return at the end of long.qdec.table.txt. This 
may fix the 2nd error

On 11/09/2015 10:38 PM, Heidi Foo wrote:
> Dear Dr Greve,
>
> Thanks for your reply. I have already linked fsaverage to my 
> SUBJECTS_DIR but the error still persists.
>
> Attached is my qdec (long and cross) files.
>
> Thanks.
>
> Regards,
> Heidi Foo
>
>
>
> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve 
> > wrote:
>
>
>
> On 11/06/2015 09:35 PM, Heidi Foo wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to compare between stable WMH group and rapid
> progressed WMH group in regards to the cortical thickness as
> well as volume changes in the gray matter. The nuisance
> variable in my case is age. I ran my analysis using QDEC but
> encountered a few problems:
>
> 1. There is error in analyze: couldn't open file
>
> It looks like it cannot find fsaverage. Link it to your
> SUBJECTS_DIR if you have not already.
>
> 2. If this error doesn't appear, another one does.
> QdecGlmDesign::Create: zero factors!
> (Attached the screenshot of the errors for your perusal)
>
> please send the qdec file
>
>
> I am hoping that you could give me a solution to my problems.
>
> Thank you so much.
>
> Regards,
> Heidi
>
>
> -- 
> 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/
>
>
>
> 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.
>
>

-- 
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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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

2015-11-10 Thread Douglas N Greve

Are those the qdec files that generate the first error? That error 
implies that fsaverage is included as a subject in the qdec file. Is 
this possible?


On 11/09/2015 10:38 PM, Heidi Foo wrote:
> Dear Dr Greve,
>
> Thanks for your reply. I have already linked fsaverage to my 
> SUBJECTS_DIR but the error still persists.
>
> Attached is my qdec (long and cross) files.
>
> Thanks.
>
> Regards,
> Heidi Foo
>
>
>
> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve 
> > wrote:
>
>
>
> On 11/06/2015 09:35 PM, Heidi Foo wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to compare between stable WMH group and rapid
> progressed WMH group in regards to the cortical thickness as
> well as volume changes in the gray matter. The nuisance
> variable in my case is age. I ran my analysis using QDEC but
> encountered a few problems:
>
> 1. There is error in analyze: couldn't open file
>
> It looks like it cannot find fsaverage. Link it to your
> SUBJECTS_DIR if you have not already.
>
> 2. If this error doesn't appear, another one does.
> QdecGlmDesign::Create: zero factors!
> (Attached the screenshot of the errors for your perusal)
>
> please send the qdec file
>
>
> I am hoping that you could give me a solution to my problems.
>
> Thank you so much.
>
> Regards,
> Heidi
>
>
> -- 
> 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/
>
>
>
> 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.
>
>

-- 
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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[Freesurfer] freesurfer@nmr.mgh.harvard.edu

2013-01-22 Thread Nicola Toschi


Hello list,

is there a quick way to decimate an overlay /while respecting surface 
geomery)? I am looking to downsample by about a factor 100.


Alternatively, I know I can use mris_decimate to downsample a surface, 
but I would have to project my highres overlays onto the downsampled 
surface (which may not be straightforward).


Thanks a lot in advance,

Nicola
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[Freesurfer] freesurfer@nmr.mgh.harvard.edu

2012-11-21 Thread Gabriel Gonzalez Escamilla

Dear DougI'm looking for making the interhemispheric registration procedure of FS, I was just gertting familiar with it by reading the:http://surfer.nmr.mgh.harvard.edu/fswiki/XhemiI found that in the step # Correct for MC say that this need a new version of mri_glmfit-sim, is this version somehow available now? or it does refeer to the FS v5.1 version?I have two doubs about the whole procedure:which are the main differences between using the FS average and creating my own average?and second: if I decide to create my own atlas, after all the 1.3 procedure, should I then run the 1.2 steps subtituing the FSaverage_sym for mine?Many thanks in advanced,Gabriel
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

2012-11-21 Thread Douglas N Greve



On 11/21/2012 05:48 AM, Gabriel Gonzalez Escamilla wrote:
 Dear Doug

 I'm looking for making the interhemispheric registration procedure of 
 FS, I was just gertting familiar with it by reading the:
 http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
 I found that in the step # Correct for MC say that this need a new 
 version of mri_glmfit-sim, is this version somehow available now? or 
 it does refeer to the FS v5.1 version?
Actually, you don't need the new version anymore. Just run it without 
the --subject-override fsaverage argument. I'll change it on the wiki.

 I have two doubs about the whole procedure:
 which are the main differences between using the FS average and 
 creating my own average?
Your own atlas might allow for a better fit to the data.
 and second: if I decide to create my own atlas, after all the 1.3 
 procedure, should I then run the 1.2 steps subtituing the 
 FSaverage_sym for mine?
Yes.
I would try it with the default fsaverage_sym. I had to go through 35 
iterations to make sure fsaverage_sym was really symmetrical. This takes 
a very long time, so if your results are satisfactory with 
fsaverage_sym, I would use that.
doug

 Many thanks in advanced,
 Gabriel

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

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