Re: [Freesurfer] R: Re: isxconcat-sess problem

2015-04-02 Thread Douglas Greve 

do you have another double dash (--s) in the command line?

On 4/3/15 1:00 AM, std...@virgilio.it wrote:
Thank you very much. I have resolved Sess49 (--s) error but the 
"ERROR: Flag —s unrecognized" is still remained.



Stefano

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-mar-2015 18.07
A: 
Ogg: Re: [Freesurfer] isxconcat-sess problem

Not sure what is going wrong with the 1st cmd, but the 2nd has a double
dash just before Sess49 (--s) that is causing the problem

doug

On 03/31/2015 07:55 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing the FS-FAST analysis.
>
> Some months ago, I have already preformed this analysis on some
> subjects without problem.
>
> Now, I have added some subjects. When I rerun the analysis i have
> these error:
>
> for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_thal_LH
>
> ERROR: finding sessions
>
> Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50
>
> [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano%
>
>
> and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s
> Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s
> Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s
> Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s
> Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s
> Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_THAL_LEFT
>
> ERROR: Flag —s unrecognized.
>
>
> FUNCTIONAL_DATA directory contains:
>
>
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/
> file:///Applications/free

[Freesurfer] R: Re: isxconcat-sess problem

2015-04-02 Thread stdp82 
Thank you very much. I have resolved Sess49 (--s) error but the "ERROR: Flag —s 
unrecognized" is still remained.

Stefano



Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-mar-2015 18.07
A: 
Ogg: Re: [Freesurfer] isxconcat-sess problem

Not sure what is going wrong with the 1st cmd, but the 2nd has a double 
dash just before Sess49 (--s) that is causing the problem

doug

On 03/31/2015 07:55 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing the FS-FAST analysis.
>
> Some months ago, I have already preformed this analysis on some 
> subjects without problem.
>
> Now, I have added some subjects. When I rerun the analysis i have 
> these error:
>
> for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh 
> -contrast L_Thalamus -o my-group_thal_LH
>
> ERROR: finding sessions
>
> Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50
>
> [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano%
>
>
> and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s 
> Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s 
> Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s 
> Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s 
> Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s 
> Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh 
> -contrast L_Thalamus -o my-group_THAL_LEFT
>
> ERROR: Flag —s unrecognized.
>
>
> FUNCTIONAL_DATA directory contains:
>
>
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess46/

Re: [Freesurfer] hello freesurfer developer~

2015-04-02 Thread A-reum Min 
Hi doug

dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)

I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these

dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory

always error in tmp file(x signed root.tmp.decompressed.dcm.000).

so, fix the x signed root.tmp.decompressed files... and i have no
libdcmjpeg.so.3.6.. i need it.



2015-04-03 7:02 GMT+09:00 Douglas N Greve :

> Is dcmdjpeg.fs in your path? What are the contents of the file
> /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?
>
>
> On 04/02/2015 04:53 PM, A-reum Min wrote:
> > Hi doug.
> > I try this as a test.
> > (here is a my terminal)
> >
> ***
> > [areum@localhost ~]$ su
> > Password:
> > [root@localhost areum]# tcsh
> > [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer
> > [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer
> > FSFAST_HOME   /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
> > MNI_DIR   /usr/local/freesurfer/mni
> > [areum@localhost areum]# setenv SUBJECTS_DIR
> > /usr/local/freesurfer/subjects/PISA_SPGR/1
> > [areum@localhost areum]# setenv FS_LOAD_DWI 0
> > [areum@localhost areum]# mri_convert
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh
> > mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > junk.mgh
> > $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $
> > reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm...
> > Starting DICOMRead2()
> > dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1
> > Ref Series No = 3
> > Found 246 files, checking for dicoms
> > Found 244 dicom files in series.
> > First Sorting
> > Computing Slice Direction
> > Vs: -0.8 0 0
> > Vs: -1 0 0
> > Second Sorting
> > Counting frames
> > nframes = 1
> > nslices = 244
> > ndcmfiles = 244
> > IsDWI = 0
> > PE Dir = ROW (dicom read)
> > Loading pixel data
> > JPEG compressed, decompressing
> > cd /home/areum
> > dcmdjpeg.fs +te
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > /tmp/root.tmp.decompressed.dcm.QGcfri >&
> > /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
> > ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
> > for more details
> >
> **
> > error occured again.. ㅜㅜ
> > when i type the  source $FREESURFER_HOME/SetUpFreeSurfer.csh, then
> > show up these
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer
> > FSFAST_HOME   /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
> > MNI_DIR   /usr/local/freesurfer/mni
> > But... my own data directory is
> /usr/local/freesurfer/subjects/PISA_SPGR/1
> > so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1
> > is it okay...?
> > and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ
> > 2015-04-03 5:02 GMT+09:00 Douglas N Greve  > >:
> >
> > Can you send me
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> > ? I might not be able to get to it until after the 13th.
> >
> > Also, try this as a test:
> >
> > setenv FS_LOAD_DWI 0
> > mri_convert
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh
> >
> > If that works, you can set that environment variable and run
> > recon-all.
> > But if you can send me the dicom above I'd appreciate it.
> >
> > doug
> >
> >
> > On 04/02/2015 01:40 AM, A-reum Min wrote:
> > > hi doug
> > >
> > > recon is still not working...
> > >
> > > if i type the
> > > recon-all -i
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > > -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all
> > -s subj001
> > >
> > > then error occured
> > >
> >
>  ++
> > >
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /us

Re: [Freesurfer] hello freesurfer developer~

2015-04-02 Thread A-reum Min 
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these

dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory

dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1
-->SUBJECTS_DIR

2015-04-03 10:50 GMT+09:00 A-reum Min :

> I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
> then show up these
>
> dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
> cannot open shared object file: No such file or directory
>
> dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
> and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1
> -->SUBJECTS_DIR
>
>
>
>
>
> 2015-04-03 7:02 GMT+09:00 Douglas N Greve :
>
>> Is dcmdjpeg.fs in your path? What are the contents of the file
>> /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?
>>
>>
>> On 04/02/2015 04:53 PM, A-reum Min wrote:
>> > Hi doug.
>> > I try this as a test.
>> > (here is a my terminal)
>> >
>> ***
>> > [areum@localhost ~]$ su
>> > Password:
>> > [root@localhost areum]# tcsh
>> > [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer
>> > [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
>> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> > FREESURFER_HOME   /usr/local/freesurfer
>> > FSFAST_HOME   /usr/local/freesurfer/fsfast
>> > FSF_OUTPUT_FORMAT nii.gz
>> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
>> > MNI_DIR   /usr/local/freesurfer/mni
>> > [areum@localhost areum]# setenv SUBJECTS_DIR
>> > /usr/local/freesurfer/subjects/PISA_SPGR/1
>> > [areum@localhost areum]# setenv FS_LOAD_DWI 0
>> > [areum@localhost areum]# mri_convert
>> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh
>> > mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
>> > junk.mgh
>> > $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $
>> > reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm...
>> > Starting DICOMRead2()
>> > dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
>> > dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1
>> > Ref Series No = 3
>> > Found 246 files, checking for dicoms
>> > Found 244 dicom files in series.
>> > First Sorting
>> > Computing Slice Direction
>> > Vs: -0.8 0 0
>> > Vs: -1 0 0
>> > Second Sorting
>> > Counting frames
>> > nframes = 1
>> > nslices = 244
>> > ndcmfiles = 244
>> > IsDWI = 0
>> > PE Dir = ROW (dicom read)
>> > Loading pixel data
>> > JPEG compressed, decompressing
>> > cd /home/areum
>> > dcmdjpeg.fs +te
>> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
>> > /tmp/root.tmp.decompressed.dcm.QGcfri >&
>> > /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
>> > ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
>> > for more details
>> >
>> **
>> > error occured again.. ㅜㅜ
>> > when i type the  source $FREESURFER_HOME/SetUpFreeSurfer.csh, then
>> > show up these
>> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> > FREESURFER_HOME   /usr/local/freesurfer
>> > FSFAST_HOME   /usr/local/freesurfer/fsfast
>> > FSF_OUTPUT_FORMAT nii.gz
>> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
>> > MNI_DIR   /usr/local/freesurfer/mni
>> > But... my own data directory is
>> /usr/local/freesurfer/subjects/PISA_SPGR/1
>> > so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1
>> > is it okay...?
>> > and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ
>> > 2015-04-03 5:02 GMT+09:00 Douglas N Greve > > >:
>> >
>> > Can you send me
>> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
>> > ? I might not be able to get to it until after the 13th.
>> >
>> > Also, try this as a test:
>> >
>> > setenv FS_LOAD_DWI 0
>> > mri_convert
>> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh
>> >
>> > If that works, you can set that environment variable and run
>> > recon-all.
>> > But if you can send me the dicom above I'd appreciate it.
>> >
>> > doug
>> >
>> >
>> > On 04/02/2015 01:40 AM, A-reum Min wrote:
>> > > hi doug
>> > >
>> > > recon is still not working...
>> > >
>> > > if i type the
>> > > recon-all -i
>> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
>> > > -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all
>> > -s subj001
>> > >
>>

Re: [Freesurfer] hello freesurfer developer~

2015-04-02 Thread A-reum Min 
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and
then show up these

dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6:
cannot open shared object file: No such file or directory

dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin)
and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1
-->SUBJECTS_DIR





2015-04-03 7:02 GMT+09:00 Douglas N Greve :

> Is dcmdjpeg.fs in your path? What are the contents of the file
> /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?
>
>
> On 04/02/2015 04:53 PM, A-reum Min wrote:
> > Hi doug.
> > I try this as a test.
> > (here is a my terminal)
> >
> ***
> > [areum@localhost ~]$ su
> > Password:
> > [root@localhost areum]# tcsh
> > [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer
> > [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer
> > FSFAST_HOME   /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
> > MNI_DIR   /usr/local/freesurfer/mni
> > [areum@localhost areum]# setenv SUBJECTS_DIR
> > /usr/local/freesurfer/subjects/PISA_SPGR/1
> > [areum@localhost areum]# setenv FS_LOAD_DWI 0
> > [areum@localhost areum]# mri_convert
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh
> > mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > junk.mgh
> > $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $
> > reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm...
> > Starting DICOMRead2()
> > dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1
> > Ref Series No = 3
> > Found 246 files, checking for dicoms
> > Found 244 dicom files in series.
> > First Sorting
> > Computing Slice Direction
> > Vs: -0.8 0 0
> > Vs: -1 0 0
> > Second Sorting
> > Counting frames
> > nframes = 1
> > nslices = 244
> > ndcmfiles = 244
> > IsDWI = 0
> > PE Dir = ROW (dicom read)
> > Loading pixel data
> > JPEG compressed, decompressing
> > cd /home/areum
> > dcmdjpeg.fs +te
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > /tmp/root.tmp.decompressed.dcm.QGcfri >&
> > /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
> > ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
> > for more details
> >
> **
> > error occured again.. ㅜㅜ
> > when i type the  source $FREESURFER_HOME/SetUpFreeSurfer.csh, then
> > show up these
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer
> > FSFAST_HOME   /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer/subjects
> > MNI_DIR   /usr/local/freesurfer/mni
> > But... my own data directory is
> /usr/local/freesurfer/subjects/PISA_SPGR/1
> > so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1
> > is it okay...?
> > and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ
> > 2015-04-03 5:02 GMT+09:00 Douglas N Greve  > >:
> >
> > Can you send me
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> > ? I might not be able to get to it until after the 13th.
> >
> > Also, try this as a test:
> >
> > setenv FS_LOAD_DWI 0
> > mri_convert
> > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh
> >
> > If that works, you can set that environment variable and run
> > recon-all.
> > But if you can send me the dicom above I'd appreciate it.
> >
> > doug
> >
> >
> > On 04/02/2015 01:40 AM, A-reum Min wrote:
> > > hi doug
> > >
> > > recon is still not working...
> > >
> > > if i type the
> > > recon-all -i
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > > -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all
> > -s subj001
> > >
> > > then error occured
> > >
> >
>  ++
> > >
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm
> > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm
> > > ERROR: GetDICOMInfo(

Re: [Freesurfer] hello freesurfer developer~

2015-04-02 Thread Douglas N Greve 
Is dcmdjpeg.fs in your path? What are the contents of the file 
/tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ?


On 04/02/2015 04:53 PM, A-reum Min wrote:
> Hi doug.
> I try this as a test.
> (here is a my terminal)
> ***
> [areum@localhost ~]$ su
> Password:
> [root@localhost areum]# tcsh
> [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer
> [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME   /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer/subjects
> MNI_DIR   /usr/local/freesurfer/mni
> [areum@localhost areum]# setenv SUBJECTS_DIR 
> /usr/local/freesurfer/subjects/PISA_SPGR/1
> [areum@localhost areum]# setenv FS_LOAD_DWI 0
> [areum@localhost areum]# mri_convert 
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh
> mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm 
> junk.mgh
> $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $
> reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm...
> Starting DICOMRead2()
> dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1
> Ref Series No = 3
> Found 246 files, checking for dicoms
> Found 244 dicom files in series.
> First Sorting
> Computing Slice Direction
> Vs: -0.8 0 0
> Vs: -1 0 0
> Second Sorting
> Counting frames
> nframes = 1
> nslices = 244
> ndcmfiles = 244
> IsDWI = 0
> PE Dir = ROW (dicom read)
> Loading pixel data
> JPEG compressed, decompressing
> cd /home/areum
> dcmdjpeg.fs +te 
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm 
> /tmp/root.tmp.decompressed.dcm.QGcfri >& 
> /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out
> ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out 
> for more details
> **
> error occured again.. ㅜㅜ
> when i type the  source $FREESURFER_HOME/SetUpFreeSurfer.csh, then 
> show up these
>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME   /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer/subjects
> MNI_DIR   /usr/local/freesurfer/mni
> But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1
> so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1
> is it okay...?
> and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ
> 2015-04-03 5:02 GMT+09:00 Douglas N Greve  >:
>
> Can you send me
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> ? I might not be able to get to it until after the 13th.
>
> Also, try this as a test:
>
> setenv FS_LOAD_DWI 0
> mri_convert
> /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh
>
> If that works, you can set that environment variable and run
> recon-all.
> But if you can send me the dicom above I'd appreciate it.
>
> doug
>
>
> On 04/02/2015 01:40 AM, A-reum Min wrote:
> > hi doug
> >
> > recon is still not working...
> >
> > if i type the
> > recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm
> > -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all
> -s subj001
> >
> > then error occured
> >
> ++
> >
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071584.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071585.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071586.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> > DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071587.dcm
> > ERROR: GetDICOMInfo(): dcmGetDWIPa

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-04-02 Thread Ani Varjabedian 

Hello Edgar,

I am going to be looking at your case and seeing if I can replicate the 
error. I have your .nii file and will run it through our processing 
stream here, but could you send me your subject folder so that I can 
look through your files/logs to give me some more information?


You can upload the subject folder through filedrop2.0 which is a bit 
easier to use, as long as your folder is under 2GB!

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thank you,
Ani Varjabedian

On 04/02/2015 11:23 AM, Edgar Busovaca wrote:

Hello Bruce,

I just wanted to touch base regarding the "Indices_oob.nii" subject I 
had sent to MGH.  Were you by any chance able to detect the issue with 
running recon-all on this subject.  Thanks in advance for taking a 
look at this.


Best regards,
Edgar Busovaca


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


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer

2015-04-02 Thread Douglas N Greve 
I think it is just that tksurfer reports coordinates from the orig 
surface whereas the cluster summary reports coordinates from the white 
surface. We some how never got around to fixing this in tksurfer.

doug

On 04/02/2015 10:18 AM, Alexandra Tanner wrote:
> Hi Doug and Freesurfers,
>
> I ran mri_surfcluster to generate coordinates for cluster maxima from a
> functional surface analysis. The summary text file generated by
> mri_surfcluster lists a bunch of information about the clusters, including
> talairach coordinates for each cluster peak (see example below). I
> visualized these max vertices in tksurfer by entering the "VtxMax" given
> in the summary file into the "Vertex Index" field in the tksurfer tools
> window. I'm noticing, however, that the talairach coordinates given in the
> tksurfer tools window ("Vertex Talairach") after entering the vertex index
> are not the same as the coordinates listed in the summary file. Seems the
> coordinates are off by .5 - 1 millimeter or so, which I know is not much,
> but I'm curious if anyone knows the reason for this discrepancy?
> Additionally, if we want to use the peaks for seeds in a functional
> connectivity analysis which set of coordinates is more accurate?
>
> Any insight would be greatly appreciated!
>
> Best,
> Alex
>
> Ex. Summary text file:
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
> 1   33.019  124877   1219.98 30.7   21.1   -1.4  2841
> 2   27.538  116676   1406.49  7.6   23.7   38.1  2923
> 3   25.380  109387   3977.58 41.9   31.2   26.7  7023
> 4   24.404   86863   3241.21 31.5  -60.2   39.0  7288
> 5  -20.441  104109   1903.13  5.5   20.5   -7.4  3923
> 6   18.118  141781600.75  5.5  -23.0   26.4  1553
>
> Cluster 1 Vertex Talairach coordinates from tksurfer tools: (29.88  20.79
> -1.32)
>
>
>
>

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

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

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?

2015-04-02 Thread Douglas N Greve 

You can draw ROIs in tksurfer, save them as a label, then use 
mri_label2vol to map the label into a nifti volume. Why do you need a 
color wheel for this?


On 04/02/2015 06:57 AM, Kaule, Falko wrote:
> I want to draw a ROI on a surface and save it as nifti (or which type is 
> needed to get there).
>
> My original input data is a nifti. For extracting/drawing the visual areas I 
> project the data on a surface.
>
>> my aim:
> In the end I want to have nifti from different visual areas to use them as 
> masks for further analysis,
>   i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of 
> sub001.
>
>> my current, unspecific way:
> At the moment I take V1 from the Juelich histological atlas and save it as 
> nifti (using fslview), and align it into subject space.
> This is quite unspecific, especially since I have the phasemaps for the 
> subjects from retinotopic mapping.
>
>> the problems (just need to solve one of them):
> - can't draw and save ROI on inflated in freeview
> - don't get a colorwheel like colorcode in tksurfer
> - can't get the nifti aligned to the rtview surface
>
>
> Thank you very much,
> Falko
> 
> Date: Wed, 01 Apr 2015 12:43:08 -0400
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer
>  generated Phasemaps?
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <551c201c.5080...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Falko, I'm not sure what you mean by extract the visual areas as an
> ROI. Do you want the mean over the ROI? Or each of the time courses? Is
> your input data a surface or a volume?
>
> On 04/01/2015 11:25 AM, Kaule, Falko wrote:
>> Dear all,
>> having phasemaps, generated with AFNI, I would like to extract the visual 
>> areas as ROI from a surface view (infalted, flatmap or sth. like this).
>>
>>> Steps I've tried:
>> As I'm already familar with freeview and a bit with tksurfer I tried to use 
>> them to do that. After reading through the freesurfer-mailinglist and wiki, 
>> it seems not possible to extract ROI from surface view. Right?
>>
>> tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set 
>> colorwheel alike.
>>
>> rtview can be used to extract ROI and can have a colorwheel colorcode but 
>> expects radian values (sin, cos, and kind of significance values). I 
>> converted the phasemaps to sin and cos values. Loading these niftis shows, 
>> that the alignment in rtview is wrong. It seems some kind of rotated.
>>
>>
>>> The code:
>> # coregister (gives identity matrix because it is already coregistered to 
>> anatomy)
>> mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz
>> ref=/sub001/templates/t1w/brain.nii.gz
>> reg=new_coreg.dat
>> tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg
>>
>> # alignment is wrong but colorcode looks as expected
>> rtview --s sub001 --reg $reg --rh --polar --real 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz  --imag 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz
>>
>> # gives proper alignment
>> #
>> tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz 
>> -overlay-reg-identity
>>
>> freeview -v sub001/templates/t1w/brain.nii.gz 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg&
>>
>>> The coregistration matrix new_coreg.dat
>> sub001
>> 0.699928
>> 0.67
>> 0.15
>> 9.99403953552e-01 0.000e+00 1.862645149230957e-09 
>> -1.340251287729188e-06
>> 0.000e+00 9.99403953552e-01 0.000e+00 
>> 2.139647040166892e-05
>> 0.000e+00 1.490116119384766e-08 1.000e+00 
>> -2.403078542556614e-05
>> 0 0 0 1
>> round
>>
>> Thanks,
>> Falko
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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/

___

Re: [Freesurfer] mri_glmfit skipping .mtx files

2015-04-02 Thread Douglas N Greve 
The limit should be 100. If you run mri_glmfit a 2nd time just with the 
missing contrasts, do they appear?

On 04/02/2015 02:34 AM, Bronwyn Overs wrote:
> Dear freesurfer mailing list,
>
> Is there a limit to the number of .mtx files you can feed to 
> mri_glmfit? I am running an anlysis with 25 different .mtx files, and 
> when the analysis runs it just skips the 22nd and 23rd .mtx file. This 
> means these contrasts are also missing from the glmdir. Do you know 
> how I can fix this?
> -- 
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter 
> Follow NeuRA on facebook 
> Subscribe to 
> the NeuRA Magazine 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hello freesurfer developer~

2015-04-02 Thread Douglas N Greve 
Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm 
? I might not be able to get to it until after the 13th.

Also, try this as a test:

setenv FS_LOAD_DWI 0
mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh

If that works, you can set that environment variable and run recon-all. 
But if you can send me the dicom above I'd appreciate it.

doug


On 04/02/2015 01:40 AM, A-reum Min wrote:
> hi doug
>
> recon is still not working...
>
> if i type the
> recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm 
> -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001
>
> then error occured
> ++
>
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071584.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071585.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071586.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071587.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071588.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071589.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071590.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071591.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071592.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071593.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071594.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071595.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071596.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071597.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071598.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071599.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071600.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071601.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071602.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071603.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071604.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071605.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071606.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071607.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071608.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071609.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071610.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071611.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071612.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071613.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071614.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071615.dcm
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
> DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I00716

Re: [Freesurfer] Label to Nii Conversion

2015-04-02 Thread Douglas N Greve 
You can use mri_label2label and use the --outmask option. If you are 
going to use mri_segstats to do the extraction, you can skip the 
mri_label2label step and specify the label with --slabel (and add --id 1 
otherwise it will give you two ROI results, one in the label, the other 
outside the label)

On 04/01/2015 10:50 PM, MCLAREN, Donald wrote:
> I have a label file on the surface, but want to be able to use it to 
> extract surface data that is already in nifti format (dimensions: 
> [2737 1 6]).
>
> Is there a way to convert a label to nifti?
>
> Best Regards, Donald McLaren
> =
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General 
> Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren 
> 
> Office: (773) 406-2464
> =
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or 
> agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking 
> of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at 
> (773)
> 406-2464 or email.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri glmfit-sim (group analysis tutorial question)

2015-04-02 Thread Douglas N Greve 
Did you run mri_glmfit before that to create lh.gender_age.glmdir ?

On 04/02/2015 12:08 PM, Özlem Ece Demir wrote:
> Dear all,
>
> I am following the tutorial for group analysis. I successfully ran all 
> the steps up until the simulation for clusterwise correction. When I 
> attempted to run the mri_glmfit-sim using the following command in the 
> tutorial:
>
> mri_glmfit-sim \
>   --glmdir lh.gender_age.glmdir \
>   --cache 4 neg \
>   --cwp  0.05\
>   --2spaces
>
> I receive the following error:
> ERROR: cannot find 
> /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm
>
> Do you know how can I go about addressing this issue?
> Thank you.
> Best regards,
> Ece
>
> -- 
> Özlem Ece Demir, Ph.D.
> Research Director
> Language Development Project
> Department of Psychology
> University of Chicago
> 5848 South University Avenue
> Chicago, IL  60637
>
> Telephone: 773-732-7144
> Fax:  773-834-5261
> Email: e...@uchicago.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How to extract thickness value of each cluster showed groups difference

2015-04-02 Thread Douglas N Greve 

That data should already be there. If you run mri_glmfit-sim with 
--help, look for the description of the csdbase.y.ocn.dat file

On 04/02/2015 01:32 PM, yxin-li wrote:
> Dear Freesurfer expert:
>I am sorry to disturb you. I am a beginner using freesurfer. I 
> have calcualted the cortical thickness difference between patients and 
> control group using the command "mri_glmfit-sim". I found the 
> differences were located in three cluster: cluster1, cluster2 and 
> cluster3. Then I want to extract the thickness value in each cluster 
> and calculate the correlaton between the thickness value and the 
> behavioral performance.
>  Howere I don't know how to achieve this goal. Could anyone give me 
> the example command to produce ROI masks and extract the thickness values.
> Thanks!
> Ping Li
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Computing pial layers

2015-04-02 Thread Borzello, Mia 
Hi Freesurfers,

I'm having some trouble computing the pial layers. Below are the details.

Thanks!

Here is the output from "bugr":
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

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

RedHat release: CentOS release 6.5 (Final)

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

NMR Center info (/space/freesurfer exists):

  machine: huygens

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

  PWD: /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf


1) MG82
2) mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 60
3) Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!



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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] How to extract thickness value of each cluster showed groups difference

2015-04-02 Thread yxin-li 
Dear Freesurfer expert:
   I am sorry to disturb you. I am a beginner using freesurfer. I have 
calcualted the cortical thickness difference between patients and control group 
using the command "mri_glmfit-sim". I found the differences were located in 
three cluster: cluster1, cluster2 and cluster3. Then I want to extract the 
thickness value in each cluster and calculate the correlaton between the 
thickness value and the behavioral performance. 
 Howere I don't know how to achieve this goal. Could anyone give me the example 
command to produce ROI masks and extract the thickness values.
Thanks!
Ping Li___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Brain Imaging, Built Better: The HCP Course in Hawaii

2015-04-02 Thread Matt Glasser 
To advance the field of brain imaging, the HCP was given the unusual NIH
mandate to devote its first two years to rethinking data acquisition and
analysis methods prior to collecting its core dataset.  The HCP course
provides an excellent opportunity for brain imagers to profit from this
experience by interacting with key HCP investigators in an accessible and
approachable setting.  Among the speakers are David Van Essen (HCP¹s PI),
Steve Smith (FSL), Tom Nichols (brain imaging statistician), Dan Marcus
(XNAT and ConnectomeDB), Robert Oostenveld (FieldTrip), and many others.

We¹ve designed the HCP Course both for folks with considerable brain
imaging experience and for those who are just starting out.  Attendees
will learn how to take advantage of HCP-related advances in data
acquisition, preprocessing, and analysis methods, enhancing their
prospects in an increasingly competitive neuroimaging field.  Highlighted
topics include:

*How to acquire high quality MRI data for use with the HCP¹s cutting-edge
analysis tools.
*How to better answer the question ³Where am I in the brain?² by using the
HCP¹s new standard space and analysis approach‹CIFTI grayordinates‹that
substantially improves spatial localization across subjects and studies.
*How to avoid the erosion of neuroanatomical fidelity caused by
conventional brain imaging analysis methods, instead accurately aligning
cortical areas across subjects and studies and minimizing blurring.
*The first public unveiling of the HCP¹s group average multi-modal
cortical parcellation together with methods for automatically defining
these parcels in individual subjects‹even those with atypical cortical
organization.
*How to perform novel analyses by integrating very high temporal
resolution electrophysiological data (MEG) together with high spatial
resolution MRI in a common analysis framework built around parcellation.

Note that space is limited‹and who doesn¹t want an excuse join us in
Hawaii for an extra week before OHBM? (June 8-12)

See the HCP course website for more details and let us know if you have
any questions (hcpcou...@humanconnectome.org):

http://humanconnectome.org/course-registration/2015/exploring-the-human-con
nectome.php 

Hope to see you in Honolulu,

Matt Glasser.



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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri glmfit-sim (group analysis tutorial question)

2015-04-02 Thread Özlem Ece Demir 
Dear all,

I am following the tutorial for group analysis. I successfully ran all the
steps up until the simulation for clusterwise correction. When I attempted
to run the mri_glmfit-sim using the following command in the tutorial:

mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --cache 4 neg \
  --cwp  0.05\
  --2spaces

I receive the following error:
ERROR: cannot find
/autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm

Do you know how can I go about addressing this issue?
Thank you.
Best regards,
Ece

-- 
Özlem Ece Demir, Ph.D.
Research Director
Language Development Project
Department of Psychology
University of Chicago
5848 South University Avenue
Chicago, IL  60637

Telephone: 773-732-7144
Fax:  773-834-5261
Email:  e...@uchicago.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-04-02 Thread Edgar Busovaca 
Hello Bruce,

I just wanted to touch base regarding the "Indices_oob.nii" subject I had
sent to MGH.  Were you by any chance able to detect the issue with running
recon-all on this subject.  Thanks in advance for taking a look at this.

Best regards,
Edgar Busovaca
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer

2015-04-02 Thread Alexandra Tanner 
Hi Doug and Freesurfers,

I ran mri_surfcluster to generate coordinates for cluster maxima from a
functional surface analysis. The summary text file generated by
mri_surfcluster lists a bunch of information about the clusters, including
talairach coordinates for each cluster peak (see example below). I
visualized these max vertices in tksurfer by entering the "VtxMax" given
in the summary file into the "Vertex Index" field in the tksurfer tools
window. I'm noticing, however, that the talairach coordinates given in the
tksurfer tools window ("Vertex Talairach") after entering the vertex index
are not the same as the coordinates listed in the summary file. Seems the
coordinates are off by .5 - 1 millimeter or so, which I know is not much,
but I'm curious if anyone knows the reason for this discrepancy?
Additionally, if we want to use the peaks for seeds in a functional
connectivity analysis which set of coordinates is more accurate?

Any insight would be greatly appreciated!

Best,
Alex

Ex. Summary text file:
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
   1   33.019  124877   1219.98 30.7   21.1   -1.4  2841
   2   27.538  116676   1406.49  7.6   23.7   38.1  2923
   3   25.380  109387   3977.58 41.9   31.2   26.7  7023
   4   24.404   86863   3241.21 31.5  -60.2   39.0  7288
   5  -20.441  104109   1903.13  5.5   20.5   -7.4  3923
   6   18.118  141781600.75  5.5  -23.0   26.4  1553

Cluster 1 Vertex Talairach coordinates from tksurfer tools: (29.88  20.79 
-1.32)



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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?

2015-04-02 Thread Bruce Fischl 
Hi Falko

why not use our estimates of V1/V2 instead? They are far more accurate. I 
think tksurfer has a colorwheel option, since we always used it for 
retinotopy analysis way back when. But even if not, you should be able to 
create the label in tksurfer then import it into freeview, no?

cheers
Bruce


On 
Thu, 2 Apr 2015, Kaule, Falko wrote:

> I want to draw a ROI on a surface and save it as nifti (or which type is 
> needed to get there).
>
> My original input data is a nifti. For extracting/drawing the visual areas I 
> project the data on a surface.
>
>> my aim:
> In the end I want to have nifti from different visual areas to use them as 
> masks for further analysis,
> i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of 
> sub001.
>
>> my current, unspecific way:
> At the moment I take V1 from the Juelich histological atlas and save it as 
> nifti (using fslview), and align it into subject space.
> This is quite unspecific, especially since I have the phasemaps for the 
> subjects from retinotopic mapping.
>
>> the problems (just need to solve one of them):
> - can't draw and save ROI on inflated in freeview
> - don't get a colorwheel like colorcode in tksurfer
> - can't get the nifti aligned to the rtview surface
>
>
> Thank you very much,
> Falko
> 
> Date: Wed, 01 Apr 2015 12:43:08 -0400
> From: Douglas N Greve 
> Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer
>generated Phasemaps?
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <551c201c.5080...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Falko, I'm not sure what you mean by extract the visual areas as an
> ROI. Do you want the mean over the ROI? Or each of the time courses? Is
> your input data a surface or a volume?
>
> On 04/01/2015 11:25 AM, Kaule, Falko wrote:
>> Dear all,
>> having phasemaps, generated with AFNI, I would like to extract the visual 
>> areas as ROI from a surface view (infalted, flatmap or sth. like this).
>>
>>> Steps I've tried:
>> As I'm already familar with freeview and a bit with tksurfer I tried to use 
>> them to do that. After reading through the freesurfer-mailinglist and wiki, 
>> it seems not possible to extract ROI from surface view. Right?
>>
>> tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set 
>> colorwheel alike.
>>
>> rtview can be used to extract ROI and can have a colorwheel colorcode but 
>> expects radian values (sin, cos, and kind of significance values). I 
>> converted the phasemaps to sin and cos values. Loading these niftis shows, 
>> that the alignment in rtview is wrong. It seems some kind of rotated.
>>
>>
>>> The code:
>> # coregister (gives identity matrix because it is already coregistered to 
>> anatomy)
>> mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz
>> ref=/sub001/templates/t1w/brain.nii.gz
>> reg=new_coreg.dat
>> tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg
>>
>> # alignment is wrong but colorcode looks as expected
>> rtview --s sub001 --reg $reg --rh --polar --real 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz  --imag 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz
>>
>> # gives proper alignment
>> #
>> tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz 
>> -overlay-reg-identity
>>
>> freeview -v sub001/templates/t1w/brain.nii.gz 
>> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg&
>>
>>> The coregistration matrix new_coreg.dat
>> sub001
>> 0.699928
>> 0.67
>> 0.15
>> 9.99403953552e-01 0.000e+00 1.862645149230957e-09 
>> -1.340251287729188e-06
>> 0.000e+00 9.99403953552e-01 0.000e+00 
>> 2.139647040166892e-05
>> 0.000e+00 1.490116119384766e-08 1.000e+00 
>> -2.403078542556614e-05
>> 0 0 0 1
>> round
>>
>> Thanks,
>> Falko
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the

Re: [Freesurfer] Labeling of handknob area in primary motor cortex

2015-04-02 Thread Bruce Fischl 
no, I don't think we do

sorry
Bruce
On Thu, 2 Apr 2015, Silas wrote:

> Dear freesurfer,
> 
> I was also wondering if you have an existing label of the handknob area
> located in primary motor cortex?
> 
> Best, Silas
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)

2015-04-02 Thread Bruce Fischl 
Hi Silas

sure, there are tools for drawing ROIs/labels on the surface in tksurfer. 
You can create a label on fsaverage or an individual subject, then use 
mri_label2label to map it to other subjects if you like

cheers
Bruce
On Thu, 2 Apr 2015, 
Silas wrote:

> Dear freesurfer,
> 
> Do you have an existing label of the dorsal part of the premotor cortex? If
> not, is it possible to manually label this area?
> 
> Best, Silas
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?

2015-04-02 Thread Kaule, Falko 
I want to draw a ROI on a surface and save it as nifti (or which type is needed 
to get there).

My original input data is a nifti. For extracting/drawing the visual areas I 
project the data on a surface.

> my aim:
In the end I want to have nifti from different visual areas to use them as 
masks for further analysis,
 i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of 
sub001.

> my current, unspecific way:
At the moment I take V1 from the Juelich histological atlas and save it as 
nifti (using fslview), and align it into subject space.
This is quite unspecific, especially since I have the phasemaps for the 
subjects from retinotopic mapping.

> the problems (just need to solve one of them):
- can't draw and save ROI on inflated in freeview
- don't get a colorwheel like colorcode in tksurfer
- can't get the nifti aligned to the rtview surface


Thank you very much,
Falko

Date: Wed, 01 Apr 2015 12:43:08 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer
generated Phasemaps?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <551c201c.5080...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Falko, I'm not sure what you mean by extract the visual areas as an
ROI. Do you want the mean over the ROI? Or each of the time courses? Is
your input data a surface or a volume?

On 04/01/2015 11:25 AM, Kaule, Falko wrote:
> Dear all,
> having phasemaps, generated with AFNI, I would like to extract the visual 
> areas as ROI from a surface view (infalted, flatmap or sth. like this).
>
>> Steps I've tried:
> As I'm already familar with freeview and a bit with tksurfer I tried to use 
> them to do that. After reading through the freesurfer-mailinglist and wiki, 
> it seems not possible to extract ROI from surface view. Right?
>
> tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set 
> colorwheel alike.
>
> rtview can be used to extract ROI and can have a colorwheel colorcode but 
> expects radian values (sin, cos, and kind of significance values). I 
> converted the phasemaps to sin and cos values. Loading these niftis shows, 
> that the alignment in rtview is wrong. It seems some kind of rotated.
>
>
>> The code:
> # coregister (gives identity matrix because it is already coregistered to 
> anatomy)
> mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz
> ref=/sub001/templates/t1w/brain.nii.gz
> reg=new_coreg.dat
> tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg
>
> # alignment is wrong but colorcode looks as expected
> rtview --s sub001 --reg $reg --rh --polar --real 
> sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz  --imag 
> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig 
> sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz
>
> # gives proper alignment
> #
> tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz 
> -overlay-reg-identity
>
> freeview -v sub001/templates/t1w/brain.nii.gz 
> sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg&
>
>> The coregistration matrix new_coreg.dat
> sub001
> 0.699928
> 0.67
> 0.15
> 9.99403953552e-01 0.000e+00 1.862645149230957e-09 
> -1.340251287729188e-06
> 0.000e+00 9.99403953552e-01 0.000e+00 
> 2.139647040166892e-05
> 0.000e+00 1.490116119384766e-08 1.000e+00 
> -2.403078542556614e-05
> 0 0 0 1
> round
>
> Thanks,
> Falko
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Labeling of handknob area in primary motor cortex

2015-04-02 Thread Silas 
Dear freesurfer,

I was also wondering if you have an existing label of the handknob area located 
in primary motor cortex?

Best, Silas
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)

2015-04-02 Thread Silas 
Dear freesurfer,

Do you have an existing label of the dorsal part of the premotor cortex? If 
not, is it possible to manually label this area?

Best, Silas
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.