Re: [Freesurfer] Error first step FS-FAST

[Douglas N Greve]

You can get that program from here

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/5.3.0-patch/lion/3dvolreg.afni

copy it into $FREESURFER_HOME/bin

doug


On 01/07/2015 05:14 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm running FS-FAST.
>
> After this command
>
> preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -fsd rest
>
> I obtain this error:
>
> register-sess completed
>
> Sess01 MC -
>
> mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA -fsd rest -per-run 
> -update
>
> Logfile is 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/mc-Sess01-rest.log
>
> ---
>
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01
>
> RunList: 001 002 003
>
> --- ** ---
>
> --- Motion Correcting Run 001 ---
>
> --- ** ---
>
> sess = Sess01
>
> Wed Jan  7 11:07:02 CET 2015
>
> mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz 
> --mcdat 001/fmcpr.mcdat
>
> ERROR: cannot find AFNI command 3dvolreg.afni
>
>
> What is 3dvolreg.afni? Where it should be placed?
>
>
>
> Thanks in advanced
>
>
>
> Stefano
>
>
>
>
>
> _______
> 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
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Re: [Freesurfer] R: Error first step FS-FAST

[Douglas N Greve]

did you rehash?
On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
>
> Thank you very much.
>
> I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but 
> the error persist.
>
> Stefano
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 7-gen-2015 11.14
> A: 
> Ogg: [Freesurfer] Error first step FS-FAST
>
> Hi list,
>
> I'm running FS-FAST.
>
> After this command
>
> preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -fsd rest
>
> I obtain this error:
>
> register-sess completed
>
> Sess01 MC -
>
> mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA -fsd rest -per-run 
> -update
>
> Logfile is 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/mc-Sess01-rest.log
>
> ---
>
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01
>
> RunList: 001 002 003
>
> --- ** ---
>
> --- Motion Correcting Run 001 ---
>
> --- ** ---
>
> sess = Sess01
>
> Wed Jan  7 11:07:02 CET 2015
>
> mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz 
> --mcdat 001/fmcpr.mcdat
>
> ERROR: cannot find AFNI command 3dvolreg.afni
>
>
> What is 3dvolreg.afni? Where it should be placed?
>
>
>
> Thanks in advanced
>
>
>
> Stefano
>
>
>
>
>
>
>
> ___
> 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
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Re: [Freesurfer] R: Error first step FS-FAST

[Douglas N Greve]

And is it executable?
On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
>
> Thank you very much.
>
> I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but 
> the error persist.
>
> Stefano
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 7-gen-2015 11.14
> A: 
> Ogg: [Freesurfer] Error first step FS-FAST
>
> Hi list,
>
> I'm running FS-FAST.
>
> After this command
>
> preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -fsd rest
>
> I obtain this error:
>
> register-sess completed
>
> Sess01 MC -
>
> mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA -fsd rest -per-run 
> -update
>
> Logfile is 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/mc-Sess01-rest.log
>
> ---
>
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01
>
> RunList: 001 002 003
>
> --- ** ---
>
> --- Motion Correcting Run 001 ---
>
> --- ** ---
>
> sess = Sess01
>
> Wed Jan  7 11:07:02 CET 2015
>
> mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz 
> --mcdat 001/fmcpr.mcdat
>
> ERROR: cannot find AFNI command 3dvolreg.afni
>
>
> What is 3dvolreg.afni? Where it should be placed?
>
>
>
> Thanks in advanced
>
>
>
> Stefano
>
>
>
>
>
>
>
> ___
> 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/

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Re: [Freesurfer] R: Re: R: Re: R: Error first step FS-FAST

[Douglas N Greve]

Try
chmod a+x 3dvolreg.afni
rehash

then run it again

On 01/07/2015 06:25 PM, std...@virgilio.it wrote:
>
> -rwxr-xr-x 1 root wheel 60776 Jan 29  2013 #trac-all#
>
> -rw-r--r--@ 1 Stefano  staff   3985520 Jan  7 21:21 3dvolreg.afni
>
>
>
> ls -l mris_register mris_register.c
>
> ls: mris_register.c: No such file or directory
>
> -rwxr-xr-x 1 root  wheel  7351544 May 14  2013 mris_register
>
>
> Thanks,
>
>
>
> Stefano
>
>
> Messaggio originale
> Da: fis...@nmr.mgh.harvard.edu
> Data: 7-gen-2015 23.09
> A: , "Freesurfer support 
> list"
> Ogg: Re: [Freesurfer] R: Re:  R:  Error first step FS-FAST
>
> ls -l and see if the 'x' bit is set. For example:
>
> ls -l mris_register mris_register.c
> -rwxrwxr-x 1 fischl fsdev 21563282 Jan  6 17:02 mris_register
> -rw-rwxrw- 1 fischl fsdev37035 Jan  6 17:02 mris_register.c
>
>
> mris_register.c is not and mris_register is executable
>
> cheers
> Bruce
>
> On Wed, 7
> Jan
> 2015,
> std...@virgilio.it wrote:
>
> > How can I check whether it is executable?
> > Thanks,
> >
> >
> > Setafno
> >
> > Messaggio originale
> > Da: gr...@nmr.mgh.harvard.edu
> > Data: 7-gen-2015 22.51
> > A: 
> > Ogg: Re: [Freesurfer] R:  Error first step FS-FAST
> >
> > And is it executable?
> > On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
> > >
> > > Thank you very much.
> > >
> > > I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but
> > > the error persist.
> > >
> > > Stefano
> > >
> > >
> > >
> > > Messaggio originale
> > > Da: std...@virgilio.it
> > > Data: 7-gen-2015 11.14
> > > A: 
> > > Ogg: [Freesurfer] Error first step FS-FAST
> > >
> > > Hi list,
> > >
> > > I'm running FS-FAST.
> > >
> > > After this command
> > >
> > > preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5
> > > -per-run -fsd rest
> > >
> > > I obtain this error:
> > >
> > > register-sess completed
> > >
> > > Sess01 MC -
> > >
> > > mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d
> > > /Applications/freesurfer/subjects/FUNCTIONAL_DATA -fsd rest -per-run
> > > -update
> > >
> > > Logfile is
> > > 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/mc-Sess01-rest.log
> > >
> > > ---
> > >
> > > /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01
> > >
> > > RunList: 001 002 003
> > >
> > > --- ** ---
> > >
> > > --- Motion Correcting Run 001 ---
> > >
> > > --- ** ---
> > >
> > > sess = Sess01
> > >
> > > Wed Jan  7 11:07:02 CET 2015
> > >
> > > mc-afni2 --i 001/f.nii --t 001/template.nii.gz --o 001/fmcpr.nii.gz
> > > --mcdat 001/fmcpr.mcdat
> > >
> > > ERROR: cannot find AFNI command 3dvolreg.afni
> > >
> > >
> > > What is 3dvolreg.afni? Where it should be placed?
> > >
> > >
> > >
> > > Thanks in advanced
> > >
> > >
> > >
> > > Stefano
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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
&g

Re: [Freesurfer] Possible to generate table of statistics for specific label?

[Douglas N Greve]

Yep, you can use somehting like

mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1 
--sum table.dat

doug


On 01/08/2015 08:50 AM, Salil Soman wrote:
> Dear List Members,
>
> Is it possible to generate tables of volume / area / thickness 
> information for a specific label that is not included in aparcstats or 
> asegstats using command line code in freesurfer (e.g. the broadman 
> areas)? If so, could someone point me to the instructions?
>
> Thank you for your time and consideration.
>
> Best wishes,
>
> Sal
>
>
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-- 
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] Problem about vol2surf

[Douglas N Greve]

Hi Kai, we'll need more information. Please consult
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

for how to report a problem or request help. Thanks!
doug

On 01/08/2015 02:42 AM, LiuKai wrote:
> Dear FS experts,
>
> I got into a trouble when used the command of mri_vol2surf.
> I planned to project a volume file (left hemisphere) onto the surface 
> (lh) of the same subject. While i got nothing (value=0 for nearly all 
> the vertexes except for a few valued vertexes on the medial surface). 
> However, i tried to project this volume (lh) file onto the surface of 
> rh, some vertexes were valued, but the dimension seems abnormal.
>
> I guess there may be something wrong with the coordinate system of 
> this volume file. This volume file was initially generated from the 
> command of mri_surf2vol as a mask (which can be projected to the 
> surface correctly), and i assigned some values to this mask volume 
> then generated this problematic volume file (as attached). So where is 
> the problem?
>
> Thank you so much for any help!!!
>
> Best Regards,
>
> kai
>
> The Chinese University of Hong Kong
>
>
> ___
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-- 
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
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Re: [Freesurfer] error unpack dicom

[Douglas N Greve]

On 01/08/2015 12:12 PM, Jan Willem Koten wrote:
>
> Dear ladies and gentlemen,
>
> I have tried to pre process my EPI dicom data using your unpacksdcmdir 
> command. My data have been obtained on a Siemens 
> skyra.  We used parallel imaging which resulted in 
> a very large number of volumes. I get 2 error messages
>
> 1) fMRI_Aging_Fage_2 err 64 64 23 1167 
> Fage_P031b0901030001000100010001.DCM
>
This means that the total expected number of frames did not match the 
number that were actually there. This can happen if a run was terminated 
prematurely.
>
> 2) INFO: this run has an error, but trying anyway
>
Is this the same run as above?

In either case, if the data look ok I would not worry about it
doug

> I have opened the resulting nifti files in freeview. This worked. But 
> I am skeptical. Should I ignore the error message?
>
> Here follows the full data output:
>
> $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
>
> /server/data/data14/fwf/FUNC/fMRI_Aging_Fage_1
>
> -src 
> /server/data/data14/fwf/Rohdaten/Fage_P031b/20121214_12.12.14-13_54_00-STD-1.3.12.2.1107.5.2.19.45250_1/fMRI_Aging_Fage_2/
>  
> -targ /server/data/data14/fwf/FUNC/Fage_P031/bold -generic -run 9 02 
> nii f2.nii
>
> Thu Jan 8 15:59:44 CET 2015
>
> mri_convert -all-info
>
> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: 
> $Name: stable5 $ TimeStamp: 2015/01/08-14:59:44-GMT BuildTimeStamp: 
> May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 
> 21:55:16 mreuter Exp $ User: jan Machine: synapse11 Platform: Linux 
> PlatformVersion: 3.11.10-17-desktop CompilerName: GCC CompilerVersion: 
> 40400
>
> synapse11
>
> Linux synapse11 3.11.10-17-desktop #1 SMP PREEMPT Mon Jun 16 15:28:13 
> UTC 2014 (fba7c1f) x86_64 x86_64 x86_64 GNU/Linux
>
> Thu Jan 8 15:59:44 CET 2015
>
> Log File is /server/data/data14/fwf/FUNC/Fage_P031/bold/unpack.log
>
> INFO: Logfile is /server/data/data14/fwf/FUNC/Fage_P031/bold/unpack.log
>
> SkipMoCo 0
>
> Scanning source directory ...
>
> INFO: summary file is 
> /server/data/data14/fwf/FUNC/Fage_P031/bold/dicomdir.sumfile
>
> INFO: status file is 
> /server/data/data14/fwf/FUNC/Fage_P031/bold/parse.status
>
> Scanning directory Thu Jan 8 15:59:44 CET 2015
>
> mri_parse_sdcmdir --sortbyrun --d 
> /server/data/data14/fwf/Rohdaten/Fage_P031b/20121214_12.12.14-13_54_00-STD-1.3.12.2.1107.5.2.19.45250_1/fMRI_Aging_Fage_2/
>  
> --o /server/data/data14/fwf/FUNC/Fage_P031/bold/dicomdir.sumfile 
> --status /server/data/data14/fwf/FUNC/Fage_P031/bold/parse.status
>
> 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 
> 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 
> 96 98 100
>
> Done scanning Thu Jan 8 16:01:06 CET 2015
>
> --
>
> 9 fMRI_Aging_Fage_2 err 64 64 23 1167 Fage_P031b0901030001000100010001.DCM
>
> unpacking config --
>
> {9 02 nii f2.nii}
>
> ---
>
> -
>
> Run 9 -
>
> Thu Jan 8 16:01:06 CET 2015
>
> 9 02 nii f2.nii
>
> INFO: this run has an error, but trying anyway
>
> mri_convert 
> /server/data/data14/fwf/Rohdaten/Fage_P031b/20121214_12.12.14-13_54_00-STD-1.3.12.2.1107.5.2.19.45250_1/fMRI_Aging_Fage_2//Fage_P031b0901030001000100010001.DCM
>  
> /server/data/data14/fwf/FUNC/Fage_P031/bold/02/f2.nii --sdcmlist 
> /server/data/data14/fwf/FUNC/Fage_P031/bold/02/flf -ot nii 
> --nspmzeropad 3 --in_type siemens_dicom
>
>
>
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-- 
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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
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Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 131, Issue 13

[Douglas N Greve]

Try giving it the full path to the label

On 01/08/2015 02:17 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email. I am running into trouble using mri_segstats 
> - the command you sent (mri_segstats --i lh.thickness --slabel subject 
> lh lh.BA3a.label --id 1
> --sum table.dat) gave me the error:
>
> "No such file or directory
> mri_segstats: could not open label file lh.BA3a.label"
>
> I tried substituting a single subject in place of "subject" in the 
> command you sent I get the same error.
> I confirmed that the lh.BA3a.label file is in the label subfolder for 
> the individual subject.
>
> I would like to output the volume, thickness, and area for all the 
> broadman areas (especially 35). Any advice you can provide on how to 
> do this would be a great help.
>
> Thank you for all your help.
>
> Sal
>
> Date: Thu, 08 Jan 2015 11:37:11 -0500
> From: Douglas N Greve  <mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Possible to generate table of statistics for
> specific label?
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <54aeb237.9010...@nmr.mgh.harvard.edu 
> <mailto:54aeb237.9010...@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
> Yep, you can use somehting like
>
> mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1
> --sum table.dat
>
> doug
>
>
> On 01/08/2015 08:50 AM, Salil Soman wrote:
> > Dear List Members,
> >
> > Is it possible to generate tables of volume / area / thickness
> > information for a specific label that is not included in aparcstats or
> > asegstats using command line code in freesurfer (e.g. the broadman
> > areas)? If so, could someone point me to the instructions?
> >
> > Thank you for your time and consideration.
> >
> > Best wishes,
> >
> > Sal

-- 
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
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Re: [Freesurfer] fcseed-sess - segmentation fault

[Douglas N Greve]

Use 10 for thalamus and not 9. Not sure why there is a difference.
doug

On 01/08/2015 02:57 PM, std...@virgilio.it wrote:
>
> Hi list,
>
>
> I'm running FAST on resting state data.
>
>
> After
>
>
> fcseed-config -segid 9 -fcname L_Thalamus.dat -fsd rest -mean -cfg 
> mean.L_Thalamus.config
>
>
> and
>
>
> fcseed-sess -s Sess01 -cfg mean.L_Thalamus.config
>
>
> gives this error:
>
>
>
> Loading 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/mask.nii.gz
>
> Loading 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.nii.gz
>
> Voxel Volume is 64.5752 mm^3
>
> Generating list of segmentation ids
>
> Found   1 segmentations
>
> Computing statistics for each segmentation
>
>   0   1  0   0.000
>
> MRIalloc(0, 1, 1): bad parm
>
>
> Reporting on   0 segmentations
>
> Computing spatial average of each frame
>
>
> Writing to 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/avgwf.mgh
>
> Segmentation fault
>
>
>
> Thanks in advance,
>
>
>
> Stefano
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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[Freesurfer] Fwd: fcseed-sess - segmentation fault

[Douglas N Greve]

Having both Thalamus and Thalamus-Proper creates all kinds of confusion. 
Is there a reason to have both?


9   Left-Thalamus   0   118 14  0
10  Left-Thalamus-Proper0   118 14  0

 Forwarded Message 
Subject:[Freesurfer] fcseed-sess - segmentation fault
Date:   Thu, 8 Jan 2015 20:57:46 +0100 (CET)
From:   std...@virgilio.it
Reply-To: 	std...@virgilio.it, Freesurfer support list 


To: freesurfer@nmr.mgh.harvard.edu



Hi list,


I'm running FAST on resting state data.


After


fcseed-config -segid 9 -fcname L_Thalamus.dat -fsd rest -mean -cfg 
mean.L_Thalamus.config



and


fcseed-sess -s Sess01 -cfg mean.L_Thalamus.config


gives this error:



Loading 
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/mask.nii.gz


Loading 
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.nii.gz


Voxel Volume is 64.5752 mm^3

Generating list of segmentation ids

Found   1 segmentations

Computing statistics for each segmentation

  0   1  0   0.000

MRIalloc(0, 1, 1): bad parm


Reporting on   0 segmentations

Computing spatial average of each frame


Writing to 
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/avgwf.mgh


Segmentation fault



Thanks in advance,



Stefano



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Re: [Freesurfer] vol2surf problem

[Douglas N Greve]

)
>  Input registration matrix (computed) 
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> ---
>  Input registration matrix 
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Determinant 1
> subject = sub_100307_T1
> RegMat ---
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> srcvol = ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz
> srcreg = ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Loading label 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/lh.cortex.label
> Reading surface 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 79833
> Masking with 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/lh.cortex.label
> Writing to ./fs_HCP_40unrelated/sub_100307_T1/lh.merged_vol2surf.mgh
> Dim: 128476 1 1
> srcvol = ./fs_HCP_40unrelated/sub_100307_T1/merged_diff2fs.mgz
> srcreg = ./fs_HCP_40unrelated/sub_100307_T1/register_vol2surf.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Loading label 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/rh.cortex.label
> Reading surface 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/surf/rh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 79447
> Masking with 
> /home/fsl/Desktop/SCD/fs_HCP_40unrelated/sub_100307_T1/label/rh.cortex.label
> Writing to ./fs_HCP_40unrelated/sub_100307_T1/rh.merged_vol2surf.mgh
> Dim: 126700 1 1
>
> 4)recon-all.log: not attached
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Eccentricity ring start?

[Douglas N Greve]

The assumption is that it starts at the center/fovea. It will affect 
some things but not others. It will not affect the p-values. When you 
look at the eccentricity maps, they will be shifted in angle. I'm not 
sure how this will affect the field sign maps.

doug


On 01/09/2015 11:32 AM, Jackie Lam wrote:
> Hello,
>
> For retinotopy, what does Freesurfer assume to be the start position for the 
> expanding and contracting rings? Currently, my stimulus is such that it 
> starts some where in the middle between fully contracted and fully expanded 
> for both the expanding and contracting runs. Will it affect the analysis?
>
> Thanks,
>
> Jack
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>

-- 
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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
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Re: [Freesurfer] Eccentricity ring start?

[Douglas N Greve]

btw, it is possible to shift the angle of the eccen when you compute the 
field sign, but you'll have to run mri_fieldsign directly and not 
through fieldsign-sess.

doug

On 01/09/2015 11:42 AM, Douglas N Greve wrote:
> The assumption is that it starts at the center/fovea. It will affect
> some things but not others. It will not affect the p-values. When you
> look at the eccentricity maps, they will be shifted in angle. I'm not
> sure how this will affect the field sign maps.
>
> doug
>
>
> On 01/09/2015 11:32 AM, Jackie Lam wrote:
>> Hello,
>>
>> For retinotopy, what does Freesurfer assume to be the start position for the 
>> expanding and contracting rings? Currently, my stimulus is such that it 
>> starts some where in the middle between fully contracted and fully expanded 
>> for both the expanding and contracting runs. Will it affect the analysis?
>>
>> Thanks,
>>
>> Jack
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
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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
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Re: [Freesurfer] Error Message

[Douglas N Greve]

; > > Muhammad Naveed Iqbal Qureshi
> > > > > > > P please don't print this e-mail unless you really need to
> > > > > > >
> > > > > > > ?
> > > > > > >
> > > > > > >
> > > > > > > ___
> > > > > > > Freesurfer mailing list
> > > > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > > > > Message: 5
> > > > > > Date: Mon, 5 Jan 2015 09:52:58 +0100
> > > > > > From: maaike rive 
> > > > > > Subject: [Freesurfer] Extracting vertexvalues
> > > > > > To: "freesurfer@nmr.mgh.harvard.edu"
> > > 
> > > > > > Message-ID: 
> > > > > > Content-Type: text/plain; charset="iso-8859-1"
> > > > > >
> > > > > > Dear Freesurfer experts,
> > > > > >
> > > > > >
> > > > > >
> > > > > > I have a question about extracting vertex values of VtxMax 
> for each
> > > > > subject (for surface eara, in this case).
> > > > > >
> > > > > > Based on earlier postings, I used the command mri_segstats 
>

Re: [Freesurfer] selxavg3-sess

[Douglas N Greve]

You need to have matlab in your path to run selxavg3-sess (octave should 
work as well)

On 01/10/2015 07:08 PM, std...@virgilio.it wrote:
> Hi list,
>
> the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis 
> produces this error.
>
>
> rawfunc2surf-sess completed
>
> 
>
> Started at Sun Jan 11 00:50:53 CET 2015
>
> Ended   at Sun Jan 11 00:50:54 CET 2015
>
> preproc-sess done
>
> ---
>
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01
>
> Sun Jan 11 00:50:54 CET 2015
>
> anadir = 
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/fc.lpccseed.surf.lh
>
> DoGLMFit = 1
>
> DoContrasts = 1
>
> UpdateNeeded = 1
>
> --
>
> --- matlab output 
>
> matlab: Command not found.
>
> --
>
> ERROR: fast_selxavg3() failed\n
>
>
>
> Thanks in advance,
>
>
> Regards
>
>
>
> Stefano
>
>
>
> ___________
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> Freesurfer@nmr.mgh.harvard.edu
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Error Message

[Douglas N Greve]

t; > > > > > ?mri_nu_correct.mni --debug --n 1 --proto-iters 1000
> > > --distance 50
> > > > > > > > > --no-rescale --i orig.mgz --o orig_nu.mgz |& tee dng.log
> > > > > > > > >
> > > > > > > > > and send me dng.log
> > > > > > > > >
> > > > > > > > > doug
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On 1/4/15 7:56 PM, Muhammad Naveed Iqbal Qureshi wrote:
> > > > > > > > > Dear community,
> > > > > > > > > ?
> > > > > > > > > I execute the following command:
> > > > > > > > > ?
> > > > > > > > > recon-all
> > > > > > >
> > > > >
> > > 
> -i/media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1/scans/anat_1-a
> > > > > > > > > nat/resources/NIfTI/files/rest.nii.gz
> > > > > > >
> > > > >
> > > 
> -subject/media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1/scans/anat_1-a
> > > > > > > > > nat/resources/NIfTI/files/Processed/ -all
> > > > > > > > >
> > > > > > > > > ?
> > > > > > > > > it return with the following error message. Where am I
> > > making a
> > > > > > > > > mistake.
> > > > > > > > > ?
> > > > > > > > > ?
> > > > > > > > > Writing to 
> /media/sf_Dataset/ADHD200/Processed/mri/orig.mgz...
> > > > > > > > > ?mri_add_xform_to_header -c
> > > > > > > > >
> > > /media/sf_Dataset/ADHD200/Processed/mri/transforms/talairach.xfm
> > > > > > > > > /media/sf_Dataset/ADHD200/Processed/mri/orig.mgz
> > > > > > > > > /media/sf_Dataset/ADHD200/Processed/mri/orig.mgz
> > > > > > > > > INFO: extension is mgz
> > > > > > > > > #
> > > > > > > > > #@# Talairach Mon Jan? 5 09:51:46 KST 2015
> > > > > > > > > /media/sf_Dataset/ADHD200/Processed/mri
> > > > > > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
> > > > > > > > > --no-rescale --i orig.mgz --o orig_nu.mg

Re: [Freesurfer] mask volume with mri_segstats

[Douglas N Greve]

Can you send mask_registered.nii.gz through our filedrop?

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



On 01/09/2015 08:58 PM, Eunice Yang wrote:
> Hello- I am trying to compute the proportion of different tissue types within 
> an ROI using a mask:
> mri_segstats --seg aseg.auto.mgz --mask mask_registered.nii.gz --sum results
>
> While mri_segstats is running, the terminal will show:
> "There were 26526 voxels in the original mask
> Voxel Volume is 1 mm^3"
>
> However,  fslstats -V produces a different number of voxels in the mask. 
> Which one is correct? Also, is there a way to write out the number of voxels 
> in the mask with mri_segstats?
>
> Thanks,
> Eunice
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mask volume with mri_segstats

[Douglas N Greve]

The problem is that your mask is not a mask. A mask should have binary 
values (ie, either 0 or 1). Yours has values in-between. mri_segstats 
sets the threshold to 0.5 which gives 26526 voxels. FSL is probably 
using a threshold very close to 0.

doug


On 01/12/2015 04:25 PM, Eunice Yang wrote:
> Hi Doug- I uploaded an example mask. According to fslstats it has 
> 29016 voxels whereas mri_segstats suggests it has 26182 voxels.
> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6sthhn0ld2p
>
> Thanks!
> Eunice
>
> On Jan 12, 2015, at 8:19 AM, Douglas N Greve wrote:
>
>>
>> Can you send mask_registered.nii.gz through our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>>
>>
>> On 01/09/2015 08:58 PM, Eunice Yang wrote:
>>> Hello- I am trying to compute the proportion of different tissue 
>>> types within an ROI using a mask:
>>> mri_segstats --seg aseg.auto.mgz --mask mask_registered.nii.gz --sum 
>>> results
>>>
>>> While mri_segstats is running, the terminal will show:
>>> "There were 26526 voxels in the original mask
>>> Voxel Volume is 1 mm^3"
>>>
>>> However,  fslstats -V produces a different number of voxels in the 
>>> mask. Which one is correct? Also, is there a way to write out the 
>>> number of voxels in the mask with mri_segstats?
>>>
>>> Thanks,
>>> Eunice
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>>>
>>>
>>
>> -- 
>> 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
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Re: [Freesurfer] functional connectivity analysis

[Douglas N Greve]

Mostly looks ok to me, except that you are using the left isthmus 
cingulate (1010) instead of thalamus (10). If you want to use motion 
correction parameters as nuisance regressors, use -mcextreg
Where did you see -mcreg ?
Step 7 is group level preprocessing
Step 8 is group analysis
Step 9 is correction for multiple comparisons (mri_glmfit-sim)





On 01/13/2015 02:36 PM, std...@virgilio.it wrote:
> Hi list,
> I'd like to perform functional connectivity analysis between thalamus 
> and whole cortex.
> I have two groups (control and disease) and I' d like also to assess 
> between groups differences.
> I'm performing these steps. Please, could you check if these are 
> corrected and could you respond to some questions?
>
> Thanks,
>
> Stefano
>
> 1.Analyze anatomicals in FreeSurfer (recon-all)
> 2.Create subjectname file.
> 3.Preprocessing
> preproc-sess -s sessionid -fwhm 5 -surface fsaverage lhrh -mni305-2mm
>
> 4.Parameters configuration to creates a text file describing the FC 
> seed for an individual.
> fcseed-config -segid 1010 -fcname L_Thalamus.dat -fsd bold -mean -cfg 
> mean.L_Thalamus.config
>
> Create nuisance variables:
> fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
> fcseed-sess -s sessionid -cfg wm.config
> fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config
> fcseed-sess -s sessionid -cfg vcsf.config
>
> 5.Configure analyses
> mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh 
> -fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg 
> wm.dat 5 -polyfit 5 -nskip 4 -fsd bold -TR 1.1
>
> -mcreg was not found! Why?
>
> 6.First Level Analysis
> selxavg3-sess -s sessionid -a fc.lpccseed.surf.lh
>
> ces.mgz - contrast effect size (contrast matrix * regression coef)
> cesvar.mgz - variance of contrast effect size
> sig.mgz - significance map (-log10(p))
> pcc.mgz - partial correlation coefficient map
>
> 7.Group-level analysiss - Higher Level Analysis (isxconcat-sess, 
> mri_glmfit)
> isxconcat-sess -sf sessidlist -analysis workmem.sm05.lh -contrast 
> encode-v-base -o my-group
>
> 8.Correction for Multiple Comparisons (mri_glmfit-sim)
> mri_glmfit  --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage lh 
> --glmdir my-glm.wls --nii.gz  --fsgd group1.fsgd --C group.diff.mtx 
> --C group1.mtx --C g1g2.intercept.mtx
>
> Is it corrected?
>
> 9. Multiple correction
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] qdec group analysis error

[Douglas N Greve]

You still cannot use 3 levels. You will have to use the "manual" stream, 
ie, use mris_preproc, mri_surf2surf (smoothing), mri_glmfit, and 
mri_glmfit-sim. See the wiki for more info
doug

On 01/14/2015 02:14 PM, Hirsch, Gabriella wrote:
> Hello there,
>
> I am trying to run an analysis in qdec with 25 subjects, 1 factor 
> (diagnosis) with three levels (e.g control, diag1, diag2) in order to 
> compare cortical thickness in these diagnostic groups. I am coming 
> across two main errors;
>
> 1. The first one I get upon clicking "analyze" in the qdec GUI I get 
> the error:
>
> Error in Analyze: Couldn't open 
> /subject_directory/subject/surf/lh.thickness.fwhm10.fsaverage.mgz or 
> .mgh file.
>
> This makes sense since the subject in question did not have that file 
> in that path. Having googled the issue, one answer pointed out that I 
> may have needed to run
> recon-all -s  -qcache
>
> However, when I run this, nothing happens and 
> thelh.thickness.fwhm10.fsaverage.mgzfile was not
> created.
>
> 2. Secondly, I read on an old version of the wiki that qdec does not support 
> more than two levels in a factor.
> Is this still the case?
>
> If this is not possible, can you suggest a freesurfer processing stream that 
> might suit this type of analysis?
>
> Thank you!
> Gabriella
>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Viewing QDEC results in tksurfer

[Douglas N Greve]

what is your tksurfer command line?

On 01/13/2015 07:12 AM, Worker, Amanda wrote:
>
> Hi,
>
>
> Is it possible to view the results of a qdec analysis (correlation 
> with a single continuous group) in tksurfer? I am currently unable to 
> open it and I'm getting an error saying  "could not open 
> file */mri/transforms/talairach.xfm ..no such file or directory" . Is 
> this a file that is not created with qdec?
>
>
> I'm also trying to visualise group mean thickness' in different 
> colours to allow difference between groups, that are not significant 
> in the analysis to be visualised. I cannot find any advice on how to 
> do this, is this something it's possible to do using either freeview 
> of tksurfer?
>
>
> Thanks,
>
>
> Amanda
>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

[Douglas N Greve]

Try demeaning each covariate. Do so with respect to the mean across all 
subjects and not within group.
doug

On 01/15/2015 08:02 AM, 이현아 wrote:
> /Hello/
> /I’m trying to do an group analysis using mir_glmfit but I met this error./
> ERROR: matrix is ill-conditioned or badly scaled, condno = 165279
>
> 1. my command line was
>
> mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd --C 
> C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir
>
> 2. I attached the fsgd file, which was made in edit. It contains 1 
> class (2 levels) and 2 variables (age & education)
>
> 3. contrast is ‘-1 1 0 0 0 0’
> 4. design matrix is like below
> Design matrix --
>  1.000   0.000   74.000   0.000 14.000   0.000;
>  1.000   0.000   70.000   0.000 12.000   0.000;
>  1.000   0.000   73.000   0.000 6.000   0.000;
>  1.000   0.000   84.000   0.000 15.000   0.000;
>  0.000   1.000   0.000   60.000 0.000   12.000;
>  0.000   1.000   0.000   59.000 0.000   12.000;
>  0.000   1.000   0.000   63.000 0.000   9.000;
>  0.000   1.000   0.000   60.000 0.000   12.000;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 164365
>
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd 
> --C C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir
>   2. The FSGD file (if using one)
>   3. And the design matrix above
>
>
>
> thanks,
>
> H.A. LEE
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Apply alignment transformation to a surface?

[Douglas N Greve]

use mri_surf2surf. If you run it with --help you will see several 
examples. See example 4. You will need a registration which you should 
already have if can map the volumes.

doug

On 01/15/2015 11:08 AM, Andrea Grant wrote:
> Hello,
>
> I am comparing segmentations from subjects who have been scanned at 7T 
> and 3T. I'd like to be able to view the T1 image collected at 3T with 
> the surfaces from both the 3T and 7T segmentations.
>
> For a given subject, I know how to align the 3T and 7T volume images 
> (e.g., brainmask or T1) and apply the transformation matrix to the 
> cortical and subcortical volume labels (e.g., wmparc.mgz), but I can't 
> figure out how to apply that transformation to the surface files. Do I 
> need to convert the surface files to volume with mri_surf2vol, 
> transform that, and then convert back? I'm interested in ?h.pial, 
> ?h.white in particular, and I use FSL flirt to align the volumes.
>
> Thanks,
>
> Andrea
>
> -
> Andrea Grant
> Visual Neuroimaging Technologist
> Center for Magnetic Resonance Research, University of Minnesota
> 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948
> gran0...@umn.edu <mailto:gran0...@umn.edu>
> umn.edu/~gran0260 <http://umn.edu/%7Egran0260>
>
>
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] incomplete preprocessing

[Douglas N Greve]

You can try
recon-all -s subject -make all

It may or may not work depending upon how things were left



On 01/15/2015 08:08 PM, Muhammad Naveed Iqbal Qureshi wrote:
>
> Hi,
>
> How can I execute recon-all on an incomplete preprocessed file in 
> freesurfer.
>
> My Pc was accidently shut down during the process.
>
> Thank you.
>
> Best Regards
>
> Naveed
>
>
>
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-- 
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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
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Re: [Freesurfer] Viewing QDEC results in tksurfer

[Douglas N Greve]

QDEC will not produce mean maps for each group. If this is something you 
want to do, you will need to do it in the command-line group analysis 
stream. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis




On 01/15/2015 05:25 AM, Worker, Amanda wrote:
> Hi,
>
> I am currently only able to open a thickness map for a single subject using 
> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, but 
> I'd really like to plot the mean thickness for a particular group to compare 
> to others visually. Is this possible?
>
> Thanks,
>
> Amanda
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: 14 January 2015 23:46
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>
> what is your tksurfer command line?
>
> On 01/13/2015 07:12 AM, Worker, Amanda wrote:
>> Hi,
>>
>>
>> Is it possible to view the results of a qdec analysis (correlation
>> with a single continuous group) in tksurfer? I am currently unable to
>> open it and I'm getting an error saying  "could not open
>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is
>> this a file that is not created with qdec?
>>
>>
>> I'm also trying to visualise group mean thickness' in different
>> colours to allow difference between groups, that are not significant
>> in the analysis to be visualised. I cannot find any advice on how to
>> do this, is this something it's possible to do using either freeview
>> of tksurfer?
>>
>>
>> Thanks,
>>
>>
>> Amanda
>>
>>
>>
>> ___
>> 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
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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
> 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.
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>

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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] Convert volume index to vertex number in surface

[Douglas N Greve]

You can create a label with your coordinates in them and then use the 
--paint feature of mri_label2label
doug

On 01/16/2015 01:52 PM, Bruce Fischl wrote:
> Hi Meiling
>
> to go from volume points to the surface you pretty much have to 
> search. We speed this up internally by compiling the surface into a 
> spatial lookup table then only searching through the vertices that are 
> in each bin, but there is no easy external interface to that code 
> (although you are welcome to write such a thing).
>
> cheers
> Bruce
>
>
> On Sat, 17 Jan 2015, Meiling Li wrote:
>
>> hello
>> I have some points defined in volume (RAS coordination) and now I 
>> want to
>> see these locations (vertex number) on surface. I don't know how to 
>> do it.
>> I can see one point using tkmedit, input the coordination and save 
>> point and
>> then in tksurfer, go to saved point, so I can get the vertex number.
>> However, now i have so many subjects, and so many points defined in 
>> volume,
>> how can i find these vertex numbers soon?
>> Thanks in advance!
>>
>> Meiling
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> ___
> 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
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Re: [Freesurfer] Viewing QDEC results in tksurfer

[Douglas N Greve]

what is your command line?

On 01/16/2015 11:02 AM, Worker, Amanda wrote:
> Hi Doug,
>
> I have set up and run the usual Group Analysis through the command line. I 
> have then run " mri_concat output-of-preproc.mgh --mean --o 
> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects 
> included in the preprocessing.
>
> I'm now having a problem with visualising this with tksurfer, getting  ERROR: 
> could not read header info from T1 or orig in 
> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri
>
> Presumably this is because all of the T1/orig are stored in each subjects 
> data file and I'm not trying to look at a specific subject. Is there a way to 
> get around this problem?
>
> Best wishes,
>
> Amanda
>
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: 15 January 2015 16:56
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>
> QDEC will not produce mean maps for each group. If this is something you
> want to do, you will need to do it in the command-line group analysis
> stream. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
>
>
>
> On 01/15/2015 05:25 AM, Worker, Amanda wrote:
>> Hi,
>>
>> I am currently only able to open a thickness map for a single subject using 
>> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, 
>> but I'd really like to plot the mean thickness for a particular group to 
>> compare to others visually. Is this possible?
>>
>> Thanks,
>>
>> Amanda
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: 14 January 2015 23:46
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>>
>> what is your tksurfer command line?
>>
>> On 01/13/2015 07:12 AM, Worker, Amanda wrote:
>>> Hi,
>>>
>>>
>>> Is it possible to view the results of a qdec analysis (correlation
>>> with a single continuous group) in tksurfer? I am currently unable to
>>> open it and I'm getting an error saying  "could not open
>>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is
>>> this a file that is not created with qdec?
>>>
>>>
>>> I'm also trying to visualise group mean thickness' in different
>>> colours to allow difference between groups, that are not significant
>>> in the analysis to be visualised. I cannot find any advice on how to
>>> do this, is this something it's possible to do using either freeview
>>> of tksurfer?
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Amanda
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>>
>> ___
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>> 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: su

Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area

[Douglas N Greve]

I don't have a core paper on the area mapping (which is more complicated 
than mapping thickness). Anderson Winkler wrote a paper on the subject, 
but we are not using his method. Our method is relatively simple. Each 
vertex in fsaverage is mapped back to the individual to find the closest 
vertex. The thickness or area at this vertex is then assigned to the 
vertex in fsaverage. There will be some fsaverage vertices that map to 
the same vertex in the individual. For thickness, this is not a problem. 
For area or volume, we divide the value by the number of fsaverage 
vertices that share the individual vertex to preserve the total. This 
may leave some vertices in the individual that were never a closest 
vertex. We loop through these vertices and do a reverse map back to 
fsaverage to find the closest vertex. These fsaverage vertices will then 
have multiple vertices from the individual.  For thickness, we compute 
the mean of the source vertices. For area or volume we compute the sum 
(must preserve the total).

make sense?
doug



On 01/16/2015 12:00 AM, Bronwyn Overs wrote:
> I meant that as well as the mapping of the area to the average space.
>
> 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 <http://neura.edu.au>
>
> Follow @neuraustralia on twitter 
> <https://twitter.com/neuraustralia>Follow NeuRA on facebook 
> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
>
> On 16/01/2015 3:58 pm, Douglas Greve wrote:
>>
>> The computation is pretty simple, it is just the average of the area 
>> of the surrounding triangle. Is that what you mean or do you mean the 
>> mapping of said area to the average space?
>> doug
>>
>>
>>
>> On 1/15/15 11:37 PM, Bronwyn Overs wrote:
>>> Dear Mailing List,
>>>
>>> I would like to understand how freesurfer calculates the surface 
>>> area at each voxel to be used in the GLM procedure. Is there a key 
>>> methods paper that describes this process, and can this method be 
>>> explained in simple terms?
>>> -- 
>>>
>>> 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 <http://neura.edu.au>
>>>
>>> Follow @neuraustralia on twitter 
>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook 
>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
>>> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
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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
>> 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.
>
>
>
> ___
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-- 
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
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Re: [Freesurfer] converting .nii to .mgz

[Douglas N Greve]

Does that file exist?

On 01/19/2015 11:30 PM, Borzello, Mia wrote:
> Hi Bruce,
>
> Thanks for getting back to me so quickly!
> I just tried that and got the following error:
> reading from ct.anat.nii...
> niiRead(): error opening file 
> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
> I'm wondering if the nifti file is possibly corrupted. Is there a way to 
> check this?
>
> Thanks so much,
> Mia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 19, 2015 10:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> Hi Mia
> If all you want to do is convert try
>
> mri_convert ct.anat.nii ct.anat.mgz
>
> Cheers
> Bruce
>
>
>
>> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>>
>> Hi Freesurfers,
>>
>> I'm looking at Freesurfer files from are from years ago trying to look at 
>> the ct.anat file. Unfortunately, i have the nifti file and not the mgz file, 
>> so I'm wondering if there is a way to create it. In trying to find an answer 
>> online, I found this: 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
>> I tried that but got an error. It may be a syntax error; this was my command 
>> line: recon-all -i 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>>
>>
>> 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
>>
>>   ssh huygens
>>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>>   cd /autofs/space/huygens_001/users/mia/subjects
>>
>>
>> 1) MG17
>> 2) recon-all -i 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>> 3) ERROR: Flag 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  unrecognized.
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015
>>
>> For more details, see the log file
>> To report a problem, see 
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>> Thanks so much,
>> Mia
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
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> 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
>
>

-- 
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
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Viewing QDEC results in tksurfer

[Douglas N Greve]

Use View->Configure->Overlay


On 01/20/2015 08:48 AM, Worker, Amanda wrote:
> Hi Bruce,
>
> Thanks for your help. Is there a way that I can now change the colour bar, 
> it's currently red to yellow meaning pretty much the whole brain is red. I'd 
> like several different colours to illustrate different thickness'.
>
> I don't seem to be able to edit Mid or Slope.
>
> Thanks,
>
> Amanda
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 20 January 2015 12:47
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>
> Hi Amanda,
> click the "truncate" button.
>
> cheers
> Bruce
> On Tue, 20 Jan 2015, Worker, Amanda wrote:
>
>> My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" 
>> d- which is when I got the error.
>>
>> I have now tried loading fsaverage first with "tksurfer fsaverage lh 
>> inflated" and it seems to be working fine.
>>
>> The problem now is changing the colour scale to display only positive 
>> values. I have played around with the Min, Max and Slope and can't seem to 
>> remove values below zero. What I'm after is a scale showing thickness in mm 
>> ranging from something like 1mm-3.5mm (or if it's easier whatever the min 
>> and max thickness' are for the group)
>>
>> Best wishes,
>>
>> Amanda
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: 16 January 2015 19:52
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>>
>> what is your command line?
>>
>> On 01/16/2015 11:02 AM, Worker, Amanda wrote:
>>> Hi Doug,
>>>
>>> I have set up and run the usual Group Analysis through the command line. I 
>>> have then run " mri_concat output-of-preproc.mgh --mean --o 
>>> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects 
>>> included in the preprocessing.
>>>
>>> I'm now having a problem with visualising this with tksurfer, getting  
>>> ERROR: could not read header info from T1 or orig in 
>>> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri
>>>
>>> Presumably this is because all of the T1/orig are stored in each subjects 
>>> data file and I'm not trying to look at a specific subject. Is there a way 
>>> to get around this problem?
>>>
>>> Best wishes,
>>>
>>> Amanda
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: 15 January 2015 16:56
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>>>
>>> QDEC will not produce mean maps for each group. If this is something you
>>> want to do, you will need to do it in the command-line group analysis
>>> stream. See
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>
>>>
>>>
>>>
>>> On 01/15/2015 05:25 AM, Worker, Amanda wrote:
>>>> Hi,
>>>>
>>>> I am currently only able to open a thickness map for a single subject 
>>>> using "tksurfer SUBJECT lh inflated". I can use the analysis figures from 
>>>> qdec, but I'd really like to plot the mean thickness for a particular 
>>>> group to compare to others visually. Is this possible?
>>>>
>>>> Thanks,
>>>>
>>>> Amanda
>>>>
>>>> 
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>>  on behalf of Douglas N Greve 
>>>> 
>>>> Sent: 14 January 2015 23:46
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer
>>>>
>>>> what is your tksurfer command line?
>>>>
>>>> On 01/13/2015 07:12 AM, Worker, Amanda wrote:
>>>>> Hi,
>>>>>
>>>>>
>>>>> Is it possible to view the results of a qdec analysis (correlation
>>>>> with a single continuous group) in tksurfer? I am currently unable to
>>>>> open it and I'm getting an error sayin

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

[Douglas N Greve]

If that is the model you want, then you will have to create your own 
design matrix. The FSGD format does not allow for some covariates 
(Score) to have interaction terms and others (Age) to not.

doug


On 01/18/2015 04:08 PM, lindsay hanford wrote:
> Dear Freesurfer Community,
>
> I'm running into the issue of how to deal with testing the interaction 
> effects of a model with multiple categorical variables. I have tried 
> bypassing this issue by running multiple separate FSGD analyses, 
> however, I wonder if this is the best mention to do this
>
> To put it into statistical terms, I am interested in creating a model 
> that looks at group differences (2: HC vs Dx), and its interaction 
> with test score (2: High vs Low) while still controlling for nuisance 
> variables (sex, age).
> in other words:
>
> Cortical Thickness ~ Group + Group*Score + Score + Sex + Age
> Group*Score = interaction term
>
> I am mostly confused with how to appropriately create a contrast file 
> that can show the interaction between Group and Score (two categorical 
> variables) and STILL regress out the effects of sex. Is this even 
> possible using fsgd?
>
> Thank you in advance!
>
> Lindsay
>
>
>
> -- 
> Lindsay Hanford, BSc, PhD Candidate
> McMaster Integrative Neuroscience Discovery & Study| *Department of 
> Psychology, Neuroscience & Behaviour *
> McMaster University *|* 1280 Main Street West, PC329 Psychology 
> Building *|* Hamilton, ON, L8S 4L8
> 905 525 9140 x24784***|*lindsay.hanf...@gmail.com 
> <mailto:lindsay.hanf...@gmail.com>
>
>
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-- 
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
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Re: [Freesurfer] converting .nii to .mgz

[Douglas N Greve]

Can you put this on our file drop?


On 01/20/2015 11:26 AM, mborze...@partners.org wrote:
> *
> You have received 1 secure file from mborze...@partners.org.
> *
> Use the secure link below to download.
> Here is the ct.anat.nii file
> Secure File Downloads:
> Available until: **30 January 2015**
> Click link to download:
> *ct.anat.nii* 
> <https://transfer.partners.org/seos/1000/mpd/ui31012015928325bc47f437adc56d49b2dc7b3b9a>
> 31,744.34 KB
> You have received attachment(s) within this email. To download the 
> attachment(s), please click on the link(s) above. This service is 
> provided by Partners Research Computing.
>
> http://rc.partners.org/
> mailto:r...@partners.org
>
> Secured by Accellion <http://www.accellion.com>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] converting .nii to .mgz

[Douglas N Greve]

use my email

On 01/20/2015 02:29 PM, Borzello, Mia wrote:
> yes, definitely. I just tried to upload to this email: 
> freesurfer@nmr.mgh.harvard.edu
> and it says "Server Error! User 'freesurfer' is not a valid NMR Account 
> holder"
> I have a feeling this is a user error- sorry about that.
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 20, 2015 11:34 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> Can you put this on our file drop?
>
>
> On 01/20/2015 11:26 AM, mborze...@partners.org wrote:
>> *
>> You have received 1 secure file from mborze...@partners.org.
>> *
>> Use the secure link below to download.
>> Here is the ct.anat.nii file
>> Secure File Downloads:
>> Available until: **30 January 2015**
>> Click link to download:
>> *ct.anat.nii*
>> <https://transfer.partners.org/seos/1000/mpd/ui31012015928325bc47f437adc56d49b2dc7b3b9a>
>> 31,744.34 KB
>> You have received attachment(s) within this email. To download the
>> attachment(s), please click on the link(s) above. This service is
>> provided by Partners Research Computing.
>>
>> http://rc.partners.org/
>> mailto:r...@partners.org
>>
>> Secured by Accellion <http://www.accellion.com>
>>
>>
>>
>> ___
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> --
> 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
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>

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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
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Re: [Freesurfer] converting .nii to .mgz

[Douglas N Greve]

details, see the log file
>>> To report a problem, see 
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>> Thanks so much,
>>> Mia
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>>
>>
>>
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>
>

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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
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Re: [Freesurfer] converting .nii to .mgz

[Douglas N Greve]

does
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
exist?

On 01/20/2015 03:40 PM, Borzello, Mia wrote:
> Okay, cool, I just tried with the full path to the .nii file and it worked. 
> However, when I tried to load the ct.anat.mgz using tkmedit i get an error in 
> loading the volume.
>
> 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
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd /autofs/space/huygens_001/users/mia/subjects
>
> 1) MG17
> 2) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz
> 3) this is the error:
> mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz,
>  -1): could not open file
> Converting main surface: 100% done.
> Converting main surface: 100% done.
> Converting original surface: 100% done.
> Converting pial surface: 100% done.
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl
>
> and the grey box pops up saying it couldn't load the volume.
>
> (not sure if I should start a new thread for this or not). Thanks again for 
> all your help,
> m
>
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 20, 2015 2:57 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> I was able to convert your file without problem. When you run mri_convert, 
> you have to give a path to a file that exists. Below, the error says that it 
> cannot find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
> Does this file exist? It is different than the one you have below, ie
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>
>
>
>
> On 01/20/2015 11:26 AM, Borzello, Mia wrote:
>> Hi guys,
>> full command line: mri_convert ct.anat.nii ct.anat.mgz
>>
>> command line: ls -l 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>> -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>
>> I had to send the ct.anat.nii file separately because it was too large of a 
>> file for this email.
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 20, 2015 7:43 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] converting .nii to .mgz
>>
>> Hi Mia
>>
>> can you please send us the full command line? And also do an ls -l of
>> that file and include it?
>>
>> thanks
>> Bruce
>> On Tue, 20 Jan 2015, Borzello, Mia wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for getting back to me so quickly!
>>> I just tried that and got the following error:
>>> reading from ct.anat.nii...
>>> niiRead(): error opening file 
>>> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>>>
>>> I'm wondering if the nifti file is possibly corrupted. Is there a way to 
>>> check this?
>>>
>>> Thanks so much,
>>> Mia
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, January 19, 2015 10:38 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] converting .nii to .mgz
>>>
>>> Hi Mia
>>> If all you want to do is convert try
>>>
>>> mri_convert ct.anat.nii ct.anat.mgz
>>>
>>> Cheers
>>> Bruce
>>>
>>>
>>>
>>>> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>>&

Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

[Douglas N Greve]

You will need a 4 group FSGD. The interaction would be contrast 7 on the 
4G web page
doug

On 01/21/2015 09:38 AM, lindsay hanford wrote:
> Hello Doug,
>
> Thank you for your reply. I misused the word contrast, when I should 
> have said design matrix. It looks at though I should be able to look 
> at an interaction effect between two variables but ignore another. In 
> the case of the example
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V you could be able 
> to look at the interaction between Group and Age while ignoring (or 
> controlling) for the effects of weight.
> But maybe this is not possible to do with a categorical variable?
>
> I have also considered using a four group design as shown in
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, where you 
> concatenate two categorical variables however, I dont think you can 
> look at interaction effects between those variables anymore.
>
> So I'm still wondering if it is possible to look at the interaction 
> between two categorical variables using fsgd?
>
> GroupDescriptorFile 1
> #Title SZ vs HC
> Class HC
> Class SZ
> Variables Score Sex Age
> Input 130 HC high m 50
> Input 277 HC low f 53
> Input 190 HC low m 25
> Input 201 SZ high f 29
> Input 250 SZ high f 52
> ...
>
> Group difference.mtx
> 1 -1 0 0 0 0 0 0
>
> Group by Score interaction .mtx
> 0 0 1 -1 0 0 0 0
>
> But this doesn't and should work. How should I proceed?
>
>
> Thanks again,
>
>
> Lindsay
>
>
> -- 
> Lindsay Hanford, BSc, PhD Candidate
> McMaster Integrative Neuroscience Discovery & Study| *Department of 
> Psychology, Neuroscience & Behaviour *
> McMaster University *|* 1280 Main Street West, PC329 Psychology 
> Building *|* Hamilton, ON, L8S 4L8
> 905 525 9140 x24784***|*lindsay.hanf...@gmail.com 
> <mailto:lindsay.hanf...@gmail.com>
>
>
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-- 
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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
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Re: [Freesurfer] mri_cnr and bash

[Douglas N Greve]

how do you want to define CNR?

On 01/21/2015 06:21 AM, Jacek Manko wrote:
> Dear All,
>
> I have been wondering if there is a way (already implemented in the 
> FreeSurfer) to export CNR measurement outputs to seperate file, like a table 
> or someting. If not, it will possible only via some pretty advanced bash 
> scripting, am I right? If so, has anyone some experience with that matter?
>
> Thanks.
>
> Cheers,
> Jacek Manko
>
>
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>

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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
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Re: [Freesurfer] Parcellated regions as masks?

[Douglas N Greve]

establish a registration between the functional and anatomical with 
bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the 
function space.

On 01/21/2015 01:52 PM, sabin khadka wrote:
> Hi FS users,
>
> We've T1 and EPI images collected. For my analysis I want to use FS 
> parcellated regions (both cortical/sub-cortical regions) as ROIs 
> (Masks) for my functional images. Would anyone kindly let me know what 
> is the best way to proceed.
> Cheers,
> Sabin Khadka
>
>
> ___
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-- 
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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
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Re: [Freesurfer] Correspondence between label vertex number and time course

[Douglas N Greve]

You are correct. Note that if you want to compute an average inside of a 
label, that you may want to use fMRI data that is unsmoothed (even on 
the surface) as this will cause false correlations between labels.

doug

On 01/21/2015 01:16 PM, Jan Willem Koten wrote:
> Dear experts
> I have created a larger number of labels on the FS_average surface and
> performed an FS_FAST analysis. The main goal is to obtain a functional
> connectome that contains all the possible correlations between 50 Rois 
> in 100 subjects.
> The FS_fast analysis resulted in a 'fmcpr.sm5.subject.lh.nii.gz' file.
> I assume that this file has been mapped to the FS_average surface
> using spherical alignment. Therefore the vertex numbers reported in
> the FS_average label may directly correspond with the column position 
> of the
> time course in the two dimensional lh.nii.gz for any given subject*.*
> *Is this correct?*
> *Or do I need to transform the lh.nii.gz with a spherical coreg file? *
> >
> > Thanks in advance
> >
> > Cheers Jan
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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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
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Re: [Freesurfer] Parcellated regions as masks?

[Douglas N Greve]

If you run it with --help you'll see several examples.

On 01/21/2015 03:21 PM, sabin khadka wrote:
> Hi Doug- Thanks for the reply. Would you mind elaborating on how 
> exactly to use mri_label2vol to map the aparc+aseg.mgz into the
> function space ( I could not find the correct syntax that should be 
> used)? Also, what should i do if I want individual masks for each ROI?
> Cheers,
> Sabin Khadka
>
> ------------
> *From:* Douglas N Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Wednesday, January 21, 2015 1:59 PM
> *Subject:* Re: [Freesurfer] Parcellated regions as masks?
>
> establish a registration between the functional and anatomical with
> bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the
> function space.
>
> On 01/21/2015 01:52 PM, sabin khadka wrote:
> > Hi FS users,
> >
> > We've T1 and EPI images collected. For my analysis I want to use FS
> > parcellated regions (both cortical/sub-cortical regions) as ROIs
> > (Masks) for my functional images. Would anyone kindly let me know what
> > is the best way to proceed.
> > Cheers,
> > Sabin Khadka
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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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> 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 
> <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.
>
>
>
>
>
> ___
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-- 
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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
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Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model

[Douglas N Greve]

The Group by Score interaction.mtx is indeed

0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0




On 01/21/2015 03:26 PM, lindsay hanford wrote:
> Thank you for you help! Yes the contrast 7 in the group 4 example 
> makes complete sense. However, I am still left with not being able to 
> control for the effects of another categorical variable.
> For example I can look at the interaction of Group X Score, but for 
> this I need to remove the categorical variable sex (M/F):
> GroupDescriptorFile 1
> > #Title SZ vs HC
> > Class HChigh
> > Class HClow
> > Class SZhigh
> > Class SZlow
> > Variables Score Age
> > Input 130 HChigh 50
> > Input 277 HClow 53
> > Input 190 HClow 25
> > Input 201 SZhigh 29
> > Input 250 SZhigh 52
> > ...
> >
> > Group difference.mtx
> > 0.5 -0.5 -0.5 0.5 0 0 0 0
>
> However, I understand how important it is to control for the effects of sex. 
> Am I better to try 8 groups?
>
> GroupDescriptorFile 1
> #Title SZ vs HC
> Class HCmhigh
> Class HCfhigh
> Class HCmlow
> Class HCflow
> Class SZmhigh
> Class SZfhigh
> Class SZmlow
> Class SZflow
> Variables Age
> Input 130 HCmhigh 50
> Input 277 HCflow 53
> Input 190 HCmlow 25
> Input 201 SZfhigh 29
> Input 250 SZfhigh 52
> ...
>
> Group difference.mtx
> 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0
>
> Heres where I am confused:
> Group by Score interaction.mtx
> could either be:
>
> 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0
>
> or perhaps?
>
> 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0
> 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0
>
>
> Once again, thank you in advance!!
>
>
> Lindsay
> -- 
> Lindsay Hanford, BSc, PhD Candidate
> McMaster Integrative Neuroscience Discovery & Study| *Department of 
> Psychology, Neuroscience & Behaviour *
> McMaster University *|* 1280 Main Street West, PC329 Psychology 
> Building *|* Hamilton, ON, L8S 4L8
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> <mailto:lindsay.hanf...@gmail.com>
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Re: [Freesurfer] mri_cnr and bash

[Douglas N Greve]

would something like this work?

set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf 
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr > yourfile




On 01/21/2015 02:46 PM, Jacek Manko wrote:
> My desirable output would be then a .txt file that consists of merely two 
> columns. The first column is the subject's ID and the second is the CNR value 
> only, for example:
>
> bruce 1.602
> bert 1.555
> john_doe 1.666
>
> Thanks in advance.
>
> Cheers,
> Jacek
>
> Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
>> Hi Jacek
>>
>> if you give us an example of what the desired output would be for you it
>> would just be a couple of minutes to put it in the code. Or maybe someone
>> can post some sed code (or some easy alternative) to parse the CNR out of
>> the output.
>>
>> Bruce
>>
>>
>> On Wed,
>> 21 Jan 2015, Jacek Manko wrote:
>>
>>> Oh, I thought it was already defined. I am referring actually to this
>> thread...
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
>>>
>>> ...and, allowing myself to specify my problem, when I type the command
>> 'mri_cnr' what I become in my terminal is something more or less like
>> that:
>>> "
>>>>> mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz
>>>>> processing MRI volume
>>>> /homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
>>>>>  white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
>>>>>  gray/white CNR = 2.241, gray/csf CNR = 1.026
>>>>> lh CNR = 1.633
>>>>>  white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
>>>>>  gray/white CNR = 2.205, gray/csf CNR = 0.937
>>>>> rh CNR = 1.571
>>>>> total CNR = 1.602
>>> "
>>>
>>> My question is, if there is a way to export the CNR value, that is
>> 1.602, to a seperate file alongside with the subject's ID. I suppose
>> there are no such bulit-in commands in FreeSurfer, is that right?
>>> Thanks.
>>>
>>>
>>> Cheers,
>>> Jacek Manko
>>>
>>>
>>>
>>> Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
>>>> how do you want to define CNR?
>>>>
>>>> On 01/21/2015 06:21 AM, Jacek Manko wrote:
>>>>> Dear All,
>>>>>
>>>>> I have been wondering if there is a way (already implemented in the
>>>> FreeSurfer) to export CNR measurement outputs to seperate file, like a
>>>> table or someting. If not, it will possible only via some pretty
>>>> advanced bash scripting, am I right? If so, has anyone some experience
>>>> with that matter?
>>>>> Thanks.
>>>>>
>>>>> Cheers,
>>>>> Jacek Manko
>>>>>
>>>>>
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>>>>>
>>>>>
>>>> --
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
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Re: [Freesurfer] QDEC group comparisons

[Douglas N Greve]

No, sorry.
doug

On 01/21/2015 01:02 PM, Leyden, Kelly wrote:
> Hi Everyone,
>
> I have been using both tksurfer and QDEC to view group comparisons of 
> cortical thickness maps. One advantage of using tksurfer has been the 
> ability to view various measures such as mean, tval, and stderr. Is 
> there any way of viewing maps other than just the mean 
> thickness/volume/etc. on QDEC?
>
> Thanks for your help,
> Kelly
>
>
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Re: [Freesurfer] using -cw256 as default is good?

[Douglas N Greve]

I think it should be ok, but I have not tested it extensively. On one 
data set the two commands gave the same result.
doug

On 01/22/2015 12:48 PM, Daniel Ferreira wrote:
> Dear experts,
>
> Could you please help me with my previous comment (see below)?
>
> Thanks so much
>
> Daniel Ferreira
>
>
>
> Dear experts,
>
> We are processing a dataset that gives us this error  quite often:
> ERROR! FOV=300.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
>
> Is it ok if I use -cw256 by default to all my scans even for those with
> FOV=256 that do not need such flag?
>
> Thanks
>
> Best regards
>
> Dani
>
>
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Re: [Freesurfer] average values per cluster

[Douglas N Greve]

We get these kind of reports occasionally. When I ask people to confirm 
that they use exactly the same design matrix in SPSS, I never hear back, 
so I assume that it gets resolved. So please check. The other thing you 
can do is to run in matlab, something like

cd glmdir/contrast
X = load('Xg.dat');
y = load('ocn.dat');
C = load('C.dat');
[beta rvar] = fast_glmfit(y,X);
[F p] = fast_fratio(beta,X,rvar,C);
p will be the p-value

If you used an unsigned cluster-forming threshold (ie, abs), then it is 
possible that some of the voxels are pos and some are neg so that they 
average out

doug




On 01/26/2015 09:03 AM, maaike rive wrote:
> Dear Freesurfer experts,
>
> Sorry to bother you again, but I have two more questions about 
> extracting (thickness/surface/GI) values from a certain cluster.
>
> As I understood, the abs.y.ocn.dat file gives the average values for a 
> given significant cluster (e.g. a cluster where there is a significant 
> AxB interaction).
>
> I may be completely misunderstanding things, but if I use these values 
> in SPSS for further statistics and test the same interaction (AxB), 
> than according to SPSS this interaction is /not /significant 
> (corrected for the same covariates as in the FSGD file).
>
> Could you tell me what is going wrong here? I do not trust my results now.
>
> Furthermore, is it possible (and if so, how?) to extract the average 
> values of exactly the same cluster, but in an independent group not 
> used in the analysis, for post-hoc comparisons in SPSS?
>
> Thanks,
>
> Maaike
>
>
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Re: [Freesurfer] Some questions about fsaverage

[Douglas N Greve]

You'll need to get a copy of mri_surf2surf.{linux,mac}. It was there all 
the time I just did not put it on the installation page. I've updated 
the page with this link

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_surf2surf.{linux,mac}


When you re-run delete the xhemi folder if it exists.


On 01/23/2015 12:32 PM, Alexandre Routier wrote:
> Hello everyone,
>
> I have a new question concerning fsaverage: I would like to perform 
> some asymmetry analyses but I noticed that the left and right 
> hemispheres were not symmetric.
>
> I found here ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi ) how 
> to register a subject to fsaverage_sym but I have some issues.
> "surfreg --s $subject --t fsaverage_sym --lh" worked fine (see first 
> log file)  and the ${subject}/xhemi/surf/ folder is empty.
> Then "surfreg --s $subject --t fsaverage_sym --lh --xhemi" (see second 
> log file) didn't work because ${subject}/xhemi/surf/lh.sphere was not 
> found. Did I miss something ? I modified FS 5.1 thanks to the section 
> "Installation" concerning my configuration.
>
> Moreover, I cannot test yet but I would like to know if the following 
> commands will work for a single subject:
> mris_preproc --target fsaverage_sym --hemi lh \
>   --xhemi --paired-diff \
>   --srcsurfreg fsaverage_sym.sphere.reg \
>   --meas thickness \
>   --out lh.lh-rh.thickness.sm00.mgh \
>   --s ${name_subject}
>
> # Smooth e.g. 10mm of the surface
> mris_fwhm --s ${name_subject} --hemi lh --cortex --smooth-only --fwhm 
> 10 --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm10.mgh
>
> # Analyze
> mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir 
> glm.lh.lh-rh.thickness.sm10 --osgm --surf ${name_subject} lh
>
> I slightly modified the commands on the tutorial for my needs but I 
> can't check for the moment.
>
> Thanks in advance for your help.
>
> Best regards,
> Alexandre
>
>
> 2014-12-05 12:09 GMT+01:00 Alexandre Routier 
> mailto:alexandre.rout...@gmail.com>>:
>
> Hello,
>
> Thanks for your answers :)
>
> mri_annotation2label enabled me to convert the ROI of Desikan
> Atlas as I wanted and the Brodmann were indeed in
> $FREESURFER_HOME/subjects/fsaverage/label .
>
> Have a nice day,
> Alexandre
>
>
> 2014-12-04 23:01 GMT+01:00 Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>:
>
> Hi Alexandre
>
> I'm not entirely sure what you are asking, but the fsaverage
> Brodmann areas and parcellations should all be stored in the
> directory:
>
> $FREESURFER_HOME/subjects/fsaverage/label
>
> cheers
> Bruce
>
>
>
> On Thu, 4 Dec 2014, Alexandre Routier wrote:
>
> Hello,
>
> I am currently working with cortical thickness and more
> particularly with
> the fsaverage. Since the thickness has the same number of
> voxel, I would
> like to correspond the voxels with some ROI, for instance the
> Desikan-Killiany Atlas or the Brodmann area.
>
> Are they any label or text files which correspond a ROI
> with the indices of
> the voxels in fsaverage ?
>
> Thanks in advance for you help,
> Alexandre
>
>
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Re: [Freesurfer] cortical thickness analysis

[Douglas N Greve]

what is your mri_glmfit-sim command line? Try running it with --cwp 1 to 
get all clusters regardless of their p-value
doug

On 01/23/2015 04:01 PM, Hirsch, Gabriella wrote:
>
> Hi freesurfer experts,
>
> I have a question I was hoping someone could help me with;
>
> I am currently analysing the cortical thickness of two subject 
> populations (patient and control) using the group analysis tutorial 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng).
>
> However, when I ran the processing stream for the clusterwise 
> correction for multiple comparisons, all my visualized clusters all 
> disappeared (using tksurfer or freeview) and no clusters showed to be 
> significant in the CWP column of the cluster summary txt file 
> (NClusters=0). I have played around with the thresholds but it doesn't 
> seem to make much of a difference. For what it's worth, I'm using a 
> simple t-test contrast.
>
> Any thoughts as to what is going on?
>
> Similarly, is there any way of accessing p-values of uncorrected clusters?
>
> Thanks so much for your help.
>
> Best,
>
> Gabriella
>
>
>
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Re: [Freesurfer] vertex-wise covariate for gyrification index

[Douglas N Greve]

QDEC does not allow it, but you can do it with mri_glmfit with the --pvr 
option. Run mri_glmfit with --help to get more info.
doug

On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote:
> Hi all,
> I wrote a paper about gyrification in a sample of malnourished patients. I
> found only little overlap between maps of significantly rediced cortical
> thickness and maps of significantly reduced gyrification index (in
> comparison to a group of healthy controls).
> One of the reviewer raised the question that this is not sufficient to
> demonstrate that reduced gyrification is not due to reduced cortical
> thickness (or GM volume) and suggest to perform a between group analysis
> using cortical thickness (or volume) maps as vertex-wise covariates.
> Is it possible to perform this type of analysis? I believe that QDEC does
> not allow it
>
> Thank you
>
> Angela
>
>
>
>
>
>> Hi Maria
>>
>> it's really hard to say - you'll need to try it out. There aren't strong
>> prior constraints on skull shape, but if the shape of the brain is too
>> different, things may degrade
>>
>> Bruce
>>
>>
>> On Fri, 23 Jan 2015, Maria Holland wrote:
>>
>>> Hi all,
>>> I am starting a project analyzing patients with cranial deformities.
>>> How
>>> robust is the automatic cortical reconstruction process - i.e., would it
>>> be
>>> able to handle deformed skulls?  Similar to this picture:
>>>
>>> http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis
>>> .png
>>>
>>> I am also wondering about the possibility of getting information about
>>> the
>>> intermediate steps of the local gyrification calculation.  Like, could
>>> we
>>> get information on the pial and outer pial surface paths on each
>>> individual
>>> slice, before that information is turned into a 3D surface?
>>>
>>> Thanks for your help!
>>>
>>> ~ Maria
>>>
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Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

[Douglas N Greve]

Try demeaning your covariates. Do so on a sample-wise basis (ie, compute 
the mean age across all subjects, then subtract that mean from all ages)
doug

On 01/14/2015 07:30 PM, i_geschwind2013 wrote:
> /Hello/
> /I’m trying to do an group analysis using mir_glmfit but I met this error./
> ERROR: matrix is ill-conditioned or badly scaled, condno = 165279
>
> 1. my command line was
>
> mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd --C 
> C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir
>
> 2. I attached the fsgd file, which was made in edit. It contains 1 
> class (2 levels) and 2 variables (age & education)
>
> 3. contrast is ‘-1 1 0 0 0 0’
> 4. design matrix is like below
> Design matrix --
>  1.000   0.000   74.000 0.000   14.000   0.000;
>  1.000   0.000   70.000 0.000   12.000   0.000;
>  1.000   0.000   73.000 0.000   6.000   0.000;
>  1.000   0.000   84.000 0.000   15.000   0.000;
>  0.000   1.000   0.000 60.000   0.000   12.000;
>  0.000   1.000   0.000 59.000   0.000   12.000;
>  0.000   1.000   0.000 63.000   0.000   9.000;
>  0.000   1.000   0.000 60.000   0.000   12.000;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 164365
>
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd 
> --C C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir
>   2. The FSGD file (if using one)
>   3. And the design matrix above
>
>
>
> thanks,
>
> H.A. LEE
>
>
>
>
> ___________
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Re: [Freesurfer] retinotopy in subject volumetric space

[Douglas N Greve]

This is a bug in 5.3. I've put a new version for you here. Let me know 
if that works
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol

On 01/27/2015 01:26 PM, Benjamin Zimmerman wrote:
> Hello,
>
> When I try your recommended code, I am able to get the data back into 
> volumetric space, but one hemisphere's cortex is significantly thinner 
> than the other. If I do mri_surf2vol separately on each hemisphere, I 
> don't have this problem. It seems to occur only if I try merging the 
> two files. I assume that this is because I am using the volume that I 
> am merging to as a template instead of inputting the template 
> directly. Do you have any ideas how to solve this problem?
>
> Thanks for your help,
>
> Ben
>
>
>
>
>
>
>
> On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> I don't think we have a tool to display the color wheel in a
> volume. FreeView might be able to do it. For the color wheel in
> tksurfer, you are looking at the angle file (one for eccen and one
> for polar), so you would map them. You can run mri_surf2vol
> something like
>
> mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject
> --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz
> mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject
> --hemi rh  --fillribbon --merge vol.angle.mgz --o vol.angle.mgz
>
> doug
>
>
> On 12/18/14 1:24 PM, Benjamin Zimmerman wrote:
>> I mean the individual's anatomical volumetric space.
>>
>> On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>>
>> wrote:
>>
>>
>> What do you mean by the individual's volumetric space? The
>> anatomical
>> space or the functional space?
>>
>>
>> On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:
>> > Thanks for the advice. I thought I would like to use
>> mri_surf2vol, but
>> > I am a little confused about the parameters and how they
>> relate to
>> > what the retinotopy analysis outputs.
>> >
>> > To be explicit, I want to view the real.nii.gz and
>> imag.nii.gz files
>> > in an individual's volumetric space. I can load these as
>> overlays to
>> > the inflated surface using tksurfer  
>> inflated.
>> > Then I can configure the overlay to use a color wheel color
>> scale and
>> > display as complex to see the retinotopic mapping.
>> >
>> > I'm not sure how I would go about using mri_surf2vol to
>> recreate this
>> > map in volumetric space. Should I just use real.nii.gz and
>> imag.nii.gz
>> > as surfval? Where is the registration file outputted in a
>> retinotopy
>> > analysis?
>> >
>> > Thank you for any more help that you can provide,
>> >
>> > Ben
>> >
>> > On Mon, Dec 15, 2014 at 3:26 PM, dgw > <mailto:dgwake...@gmail.com>
>> > <mailto:dgwake...@gmail.com <mailto:dgwake...@gmail.com>>> wrote:
>> >
>> > Hi Ben,
>> >
>> > You should be able to map it back with mri_surf2vol. I
>> haven't done
>> > this, but the wiki page looks fairly detailed:
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
>> >
>> > HTH
>> > D
>> >
>> > On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman
>> > > <mailto:benjamin.zimmerm...@gmail.com>
>> > <mailto:benjamin.zimmerm...@gmail.com
>> <mailto:benjamin.zimmerm...@gmail.com>>> wrote:
>> > > Hi all,
>> > >
>> > > FsFast has an excellent individual retinotopy
>> analysis that
>> > allows me to see
>> > > phase data on the inflated surface of the brain. Is
>> there a way
>> > to view the
>> > > results of the retinotopy analysis in the subject's
>> original
>> > volumetric
>> > > space rathe

Re: [Freesurfer] MNI to RAS?

[Douglas N Greve]

Depends on what you mean by easy:). Check out this web page

http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems


On 01/27/2015 03:27 PM, Chu, Catherine,M.D. wrote:
>
> Hi,
>
> Is there an easy way to convert MNI coordinates to Freesurfer RAS 
> coordinate space?
>
> Thanks!
>
> Cat
>
>
>
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MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] average values per cluster

[Douglas N Greve]

The t is correct. When the contrast matrix only has one row, then the F 
is just an unsigned t. I don't know anything about SPSS so I can't tell 
from what you have sent whether it is the same model or not. Try to get 
SPSS to output the design matrix. Did you try the matlab code below?

On 01/29/2015 01:40 PM, maaike rive wrote:
> Hi Douglas,
>
> I checked but as far as I see it I used the same models. I attached 
> the SPSS model and output as wel as the FSGD file and contrast file 
> (to test a diagnosis x age interaction). Now that I come to think of 
> it, I think the reason for the discrepant findings is that I used a 
> t-contrast instead of an F-contrast for the interaction in Freesurfer. 
> Apologies I did not think about this earlier. But maybe there is 
> something else I did completely wrong.
>
> What do you think?
>
> If it is indeed the t vs F contrast, than how should I specify that 
> the contrast is an F-contrast? Is it ok to just add another line to 
> the contrastfile (so
> 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
>
> Thanks again,
>
> Maaike
>
> > Date: Mon, 26 Jan 2015 11:23:59 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] average values per cluster
> >
> >
> > We get these kind of reports occasionally. When I ask people to confirm
> > that they use exactly the same design matrix in SPSS, I never hear 
> back,
> > so I assume that it gets resolved. So please check. The other thing you
> > can do is to run in matlab, something like
> >
> > cd glmdir/contrast
> > X = load('Xg.dat');
> > y = load('ocn.dat');
> > C = load('C.dat');
> > [beta rvar] = fast_glmfit(y,X);
> > [F p] = fast_fratio(beta,X,rvar,C);
> > p will be the p-value
> >
> > If you used an unsigned cluster-forming threshold (ie, abs), then it is
> > possible that some of the voxels are pos and some are neg so that they
> > average out
> >
> > doug
> >
> >
> >
> >
> > On 01/26/2015 09:03 AM, maaike rive wrote:
> > > Dear Freesurfer experts,
> > >
> > > Sorry to bother you again, but I have two more questions about
> > > extracting (thickness/surface/GI) values from a certain cluster.
> > >
> > > As I understood, the abs.y.ocn.dat file gives the average values 
> for a
> > > given significant cluster (e.g. a cluster where there is a 
> significant
> > > AxB interaction).
> > >
> > > I may be completely misunderstanding things, but if I use these 
> values
> > > in SPSS for further statistics and test the same interaction (AxB),
> > > than according to SPSS this interaction is /not /significant
> > > (corrected for the same covariates as in the FSGD file).
> > >
> > > Could you tell me what is going wrong here? I do not trust my 
> results now.
> > >
> > > Furthermore, is it possible (and if so, how?) to extract the average
> > > values of exactly the same cluster, but in an independent group not
> > > used in the analysis, for post-hoc comparisons in SPSS?
> > >
> > > Thanks,
> > >
> > > Maaike
> > >
> > >
> > > ___
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> > > 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
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> >
> > ___
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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
> > http://www.partners.org/complianceline . If the e-mail was sent to 
> you in error
> > but does not contain patient information, please contact the sender 
> and properly
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> >
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Re: [Freesurfer] extracting pvalues

[Douglas N Greve]

On 01/26/2015 05:30 PM, Douglas Greve wrote:
>
> what do you mean? Just a list of values? the column, row, slice as well?
>
> On 1/26/15 4:02 PM, Hirsch, Gabriella wrote:
>>
>> Hi FreeSurfer experts,
>>
>> Is there a way to extract significant pvalues from sig.mgh files 
>> (Obtained from the  GroupAnalysisDng tutorial)?
>>
>> I’ve looked online but having trouble. Somehow mris_covert isn’t 
>> working.
>>
>> Thanks!
>>
>> Gabriella
>>
>>
>>
>> ___
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas N Greve]

t;>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe 
>>>>>>>>>>> to the NeuRA Magazine 
>>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ___
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ___
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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
>>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ___
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>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>>
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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
>>>>>>>> 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.
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>
>>>>>> ___
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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
>>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>> ___
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>>>>
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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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>>>> error
>>>> but does not contain patient information, please contact the sender and 
>>>> properly
>>>> dispose of the e-mail.
>>>
>>>
>>>
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>>
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>>
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>
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Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas N Greve]

How sure are you that you are using the exact same model? Can you output 
the design matrix from SPSS? Can you input the FS design matrix into 
SPSS? Are you sure you are using the exact same input data?

On 02/04/2015 06:32 PM, Bronwyn Overs wrote:
> Ahh right. I have just understood which part of the output I needed to 
> look at. However, for the ROI GLM there are only 1-2 regions that were 
> significantly different between groups, while the SPSS ANCOVA showed 
> significant group differences for the majority of parcellated regions. 
> I have confirmed that I am using the exact same model for each, so it 
> is only the analysis method that differs. Do you know why these two 
> methods would produce such disparate results?
>
>
> 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 <http://neura.edu.au>
>
> Follow @neuraustralia on twitter 
> <https://twitter.com/neuraustralia>Follow NeuRA on facebook 
> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
>
> On 5/02/2015 3:16 am, Douglas N Greve wrote:
>> I'm not sure that I understand what I'm looking at. If it is an ROI
>> analysis, then there is no surface, it should be about 40 numbers, one
>> for each ROI.
>>
>> On 02/03/2015 06:26 PM, Bronwyn Overs wrote:
>>> Hi Doug,
>>>
>>> Thanks for your correction.
>>>
>>> I have now completed the FDR for my case-control comparisons, and it
>>> appears that none of the regions survived. This is again quite
>>> confusing given the large number of parcellated regions that survived
>>> FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the
>>> sig.mgh file from ROI analysis looks as you would expect (it looks
>>> very strange to me):
>>>
>>>
>>>
>>> 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<http://neura.edu.au>
>>>
>>> Follow @neuraustralia on twitter
>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>
>>> On 4/02/2015 9:35 am, Douglas Greve wrote:
>>>> Yes, it should be .^
>>>>
>>>> On 2/3/15 5:33 PM, Bronwyn Overs wrote:
>>>>> Hi Doug,
>>>>>
>>>>> I am having a problem with the line in Matlab 2014b:
>>>>> p = 10^-abs(sigmat);
>>>>> I keep getting the following error:
>>>>> Error using  ^
>>>>> Inputs must be a scalar and a square matrix.
>>>>> To compute elementwise POWER, use POWER (.^)
>>>>> instead.
>>>>>
>>>>> Do you know why this would be?
>>>>>
>>>>> 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<http://neura.edu.au>
>>>>>
>>>>> Follow @neuraustralia on twitter
>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>>>
>>>>> On 4/02/2015 2:22 am, Douglas Greve wrote:
>>>>>> There is not a way to do it from the command line. You can do it in
>>>>>> matlab, something like
>>>>>>
>>>>>> sig = MRIread('sig.mgh');
>>>>>> sigmat = f

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas N Greve]

It should be 10^-abs(sig)


On 02/06/2015 12:53 AM, Bronwyn Overs wrote:
> Hi Doug,
>
> Thanks for all of your help. I am investigating the differences 
> between the design matrices now.
>
> I have one more query about the sig.table.dat file put out by the GLM 
> using the parcellated ROIs. When I transform each of the values in 
> this file to p values using 10^"value", some of the resulting p-value 
> are >1. Do you know why this would be happening? Here is an example of 
> one of my sig.table.dat files, where 10^.799 = 6.295:
>
> lh.aparc.thicknessme_gender_ageRem me_group_ageRem
> lh_bankssts_thickness   0.107  -2.752
> lh_caudalanteriorcingulate_thickness  -2.616  -0.190
> lh_caudalmiddlefrontal_thickness   -0.701  -4.258
> lh_cuneus_thickness 0.799  -1.178
> lh_entorhinal_thickness 1.669  -4.129
> lh_fusiform_thickness  -0.088  -6.808
> lh_inferiorparietal_thickness  -0.665  -1.477
> lh_inferiortemporal_thickness   0.149  -7.985
> lh_isthmuscingulate_thickness  -0.476  -2.393
> lh_lateraloccipital_thickness   0.212  -1.189
> lh_lateralorbitofrontal_thickness   0.288  -7.657
> lh_lingual_thickness1.148  -1.594
> lh_medialorbitofrontal_thickness1.405  -4.461
> lh_middletemporal_thickness 0.727  -7.215
> lh_parahippocampal_thickness   -1.059  -2.854
> lh_paracentral_thickness   -0.514  -0.282
> lh_parsopercularis_thickness0.444  -3.541
> lh_parsorbitalis_thickness -0.110  -7.075
> lh_parstriangularis_thickness   0.244  -4.769
> lh_pericalcarine_thickness  0.376  -0.218
> lh_postcentral_thickness   -0.485  -0.832
> lh_posteriorcingulate_thickness-0.135  -1.241
> lh_precentral_thickness 0.196  -2.102
> lh_precuneus_thickness  0.018  -1.361
> lh_rostralanteriorcingulate_thickness  -1.208  -2.073
> lh_rostralmiddlefrontal_thickness   0.437  -4.470
> lh_superiorfrontal_thickness   -0.141  -2.743
> lh_superiorparietal_thickness  -0.288  -0.365
> lh_superiortemporal_thickness   0.227  -4.646
> lh_supramarginal_thickness -1.185  -1.354
> lh_frontalpole_thickness   -0.325  -0.521
> lh_temporalpole_thickness  -0.067  -4.074
> lh_transversetemporal_thickness-0.009  -1.618
> lh_insula_thickness 0.553  -6.063
>
> 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 <http://neura.edu.au>
>
> Follow @neuraustralia on twitter 
> <https://twitter.com/neuraustralia>Follow NeuRA on facebook 
> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
>
> On 5/02/2015 10:46 am, Douglas N Greve wrote:
>> How sure are you that you are using the exact same model? Can you output
>> the design matrix from SPSS? Can you input the FS design matrix into
>> SPSS? Are you sure you are using the exact same input data?
>>
>> On 02/04/2015 06:32 PM, Bronwyn Overs wrote:
>>> Ahh right. I have just understood which part of the output I needed to
>>> look at. However, for the ROI GLM there are only 1-2 regions that were
>>> significantly different between groups, while the SPSS ANCOVA showed
>>> significant group differences for the majority of parcellated regions.
>>> I have confirmed that I am using the exact same model for each, so it
>>> is only the analysis method that differs. Do you know why these two
>>> methods would produce such disparate results?
>>>
>>>
>>> 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<http://neura.edu.au>
>>>
>>> Follow @neuraustralia on twitter
>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>
>>> On 5/02/2015 3:16 am, Douglas N Greve wrote:
>>>> I'm not sure that I understand

Re: [Freesurfer] V1 masking

[Douglas N Greve]

Try using the --label-stat statvol option


On 02/06/2015 04:12 AM, David Soto wrote:
> Hi,
> I have been succesfully using mri_label2vol on the V1.labels to get a 
> nii file
> (i.e. mri_label2vol --label rh.V1.label  --temp 
> $SUBJECTS_DIR/$i/mri/orig/001 --identity --o rV1.nii --subject $i 
> --hemi rh --proj frac 0 1 0.01)
>
>
> but now I would like to use the "v1.prob.label" to get a .nii file 
> that  includes the probabilities of a voxel being on V1.
>
> is this possible?
>
> many thanks!
> david
>
>
>
> ___
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> 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
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Re: [Freesurfer] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

[Douglas N Greve]

Look here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
and get the appropriate mri_segstats for your system. Copy it to 
$FREESURFER_HOME/bin, rehash, and rerun

doug

On 02/06/2015 08:07 AM, Roberto Medeiros de Souza wrote:
> Hi,
> I'm knew to FreeSurfer. I am using the stable v5.3 and I am having the 
> known issue about
> "Creation of the aseg.stats table fails when only running -autorecon1 
> or -autorecon2 because ribbon.mgz is not present." The FreeSurfer page 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) says that 
> this problem has been solved and that I should ask for a patch. Does 
> anyone knows where I can get this patch?
>
>
> Thanks in advance!
>
> Roberto Medeiros de Souza
>
>
>
> ___
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-- 
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
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Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

[Douglas N Greve]

It sounds like the voxel size is wrong. Where did you get the input 
volume from? If you load the input volume into tkmedit or freeview, how 
does it look? If you run mri_info on the input, what voxel size does it 
give?

On 02/06/2015 11:21 AM, Liu Y wrote:
> Hi Bruce,
> The full recon-all command line is "recon-all -cw256 -s T8_1 -all" and 
> the input format is mgz. The mgz file is created by running 
> recon-all -i. The 001.mgz under /mri/orig looks just normal, but when 
> complete the  "recon-all -cw256 -s T8_1 -all",  the orig.mgz was 
> re-scaled (stretched) in left-right direction, and could not see the 
> left and right boundaries of the brain.
> Thanks,
> Yawu
>
> On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Yawu
>
> what was the full recon-all command line? What is your input
> format? If
> all else fails you can mri_convert your input volume nifti or mgz and
> override what is in the header (e.g. mri_convert -iks 1 ...)
>
> cheers
> Bruce
> On Fri, 6 Feb
> 2015, Liu Y wrote:
>
> > Dear Experts,
> > When I run recon-all -cw256 -s problemcase -all, the program
> seems not able
> > accurately to recognize the voxel size in this problematic case,
> in other
> > cases there is no problem. The program gave a warning like this:
> >
> >
> 
> WARNING===
> > ==
> > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which
> cannot fit
> > in 256^3 mm^3 volume.
> > The resulting volume will have 338 slices.
> > If you find problems, please let us know
> (freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>).
> >
> 
> ===
> > ==
> >
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from
> /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
> > TR=8.08, 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)
> > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels.
> > Data is conformed to 1 mm size and 338 voxels for all directions
> > changing data type from float to uchar (noscale = 0)...
> > MRIchangeType: Building histogram
> > Reslicing using trilinear interpolation
> > writing to
> /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
> >
> > 
> > ERROR! FOV=338.000 > 256
> > Include the flag -cw256 with recon-all!
> > Inspect orig.mgz to ensure the head is fully visible.
> > 
> >
> > Then I checked the orig.mgz, the image was re-scaled (stretched) in
> > left-right direction, and could not see the left and right
> boundaries of the
> > brain. The program said that the Original Data has (1, 1, 2) mm
> size, but
> > actually the voxel size is 1*1*1 mm3.
> >
> > The freesurfer version 5.3, Ubuntu 12.04
> >
> > Thanks,
> >
> > Yawu
> >
> >
> >
> >
> ___
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>
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> The information in this e-mail is intended only for the person to
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> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
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> but does not contain patient information, please contact the
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-- 
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
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Re: [Freesurfer] average values per cluster

[Douglas N Greve]

I) values from
> a certain cluster.
> > > > >
> > > > > As I understood, the abs.y.ocn.dat file gives
> the average values
> > > for a
> > > > > given significant cluster (e.g. a cluster
> where there is a
> > > significant
> > > > > AxB interaction).
> > > > >
> > > > > I may be completely misunderstanding things,
> but if I use these
> > > values
> > > > > in SPSS for further statistics and test the
> same interaction (AxB),
> > > > > than according to SPSS this interaction is
> /not /significant
> > > > > (corrected for the same covariates as in the
> FSGD file).
> > > > >
> > > > > Could you tell me what is going wrong here? I
> do not trust my
> > > results now.
> > > > >
> > > > > Furthermore, is it possible (and if so, how?)
> to extract the average
> > > > > values of exactly the same cluster, but in an
> independent group not
> > > > > used in the analysis, for post-hoc comparisons
> in SPSS?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Maaike
> > > > >
> > > > >
> > > > > ___
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto: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
> <mailto: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
> <http://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
> <mailto: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.
> > > >
> > >
> > >
> > > ___
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> > > 

Re: [Freesurfer] bbregister error [Was: TRACULA mask error]

[Douglas N Greve]

t it over to your email
>>>>>>>> address - hopefully you have received this.
>>>>>>>>
>>>>>>>> I've had a look at the segmentations and they look ok, so I 
>>>>>>>> think there
>>>>>>>> may be an issue with registrating between the T1 and diffusion. 
>>>>>>>> Anyway I
>>>>>>>> have sent an example over, hopefully this will give you some 
>>>>>>>> idea of
>>>>>>>> what has gone wrong.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Amanda
>>>>>>>>
>>>>>>>> 
>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>>>>>>  on behalf of Anastasia 
>>>>>>>> Yendiki 
>>>>>>>> Sent: 11 December 2014 19:37
>>>>>>>> To: Freesurfer support list
>>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>>>>
>>>>>>>> Hi Amanda - The final masks used by tracula are derived from the
>>>>>>>> structural and not the diffusion data, i.e., they are the 
>>>>>>>> whole-brain
>>>>>>>> FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto 
>>>>>>>> diffusion
>>>>>>>> space and dilated slightly. It may be that there was something 
>>>>>>>> wrong with
>>>>>>>> the FreeSurfer reconstructions of those subjects (if, for 
>>>>>>>> example, the T1
>>>>>>>> contrast was poorer in part of the brain and the part was not 
>>>>>>>> included in
>>>>>>>> the brain mask), or that there was misregistration between the 
>>>>>>>> T1 and
>>>>>>>> diffusion. You can troubleshoot this by looking at the 
>>>>>>>> aparc+aseg in
>>>>>>>> diffusion space (from the dlabel/diff directory, over the FA 
>>>>>>>> map (from the
>>>>>>>> dmri directory).
>>>>>>>>
>>>>>>>> If you still have trouble deciding what went wrong, you can 
>>>>>>>> upload a zip
>>>>>>>> file for me with all the directories created by trac-all (dmri, 
>>>>>>>> dlabel,
>>>>>>>> etc) for one of these subjects, here:
>>>>>>>>https://gate.nmr.mgh.harvard.edu/filedrop2/
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> a.y
>>>>>>>>
>>>>>>>> On Thu, 27 Nov 2014, Worker, Amanda wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Dear All,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I have run all of the pre-processing steps on my DTI data and 
>>>>>>>>> as I am
>>>>>>>>> checking my nodif_brain_mask I have realised that some of the 
>>>>>>>>> masks have
>>>>>>>>> become distorted and twisted in some way. I have attached 
>>>>>>>>> screenshots of
>>>>>>>>> both the raw data (which looks fine) and the white mask (which is
>>>>>>>>> distorted). In addition, as I have read that it is important 
>>>>>>>>> to check the
>>>>>>>>> dtifit_V1 and dtifit_FA I have also included these in the word 
>>>>>>>>> document,
>>>>>>>>> incase this helps.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> This distortion has occured for approximately a quarter of the 
>>>>>>>>> subjects that
>>>>>>>>> I have processed and the rest look good. Please can you let me 
>>>>>>>>> know if you
>>>>>>>>> have any ideas about what has gone wrong and how to fix this?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks in advance for your help,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Amanda
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> ___
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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
>>>>>>>> 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.
>>>>>>>>
>>>>>>>>
>>>>>>>> ___
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>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> ___
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ___
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Re: [Freesurfer] DTI question

[Douglas N Greve]

You can add something like --mul 1000 to the mri_segstats command line 
to multiply the values by 1000 to get 3 more decimal places
doug

On 02/12/2015 02:06 AM, Thomas Potrusil wrote:
> Hi Anastasia,
> you´re right, the values are reasonable! The problem is that I cannot 
> read out all the decimal places that I can see in FreeView as 
> described! When I save the values of distinct ROIs to a .stats file, I 
> can only see e.g. 0.0007 but I need 0.000770333 for further 
> processing. Do you have any suggestions how I can get more decimal 
> places on a .stats file?
> Thanks a lot, Tom
> *Gesendet:* Mittwoch, 11. Februar 2015 um 17:39 Uhr
> *Von:* "Anastasia Yendiki" 
> *An:* "Freesurfer support list" 
> *Betreff:* Re: [Freesurfer] DTI question
> Hi Tom - These are reasonable values for mean diffusivity (a.k.a. 
> ADC). Only FA is normalized to take values in the 0-1 range. a.y On 
> Wed, 11 Feb 2015, Thomas Potrusil wrote: > Dear FreeSurfers! > A 
> question concerning DTI analysis came up: >   > I already run dt_recon 
> on my dataset which works very well. I also used the output to extract 
> FA-values of distinct ROIs - no Problem. Now I want to do the same for 
> ADC but I only get > values in my .stats files like 0.0007 or 0.0008. 
> > I use the following code: >   > dt_recon --i $dcmfile --b bvals 
> bvecs --s $subj --o $outdir_dt_recon >   > mri_vol2vol --mov 
> $outdir_dt_recon/adc.nii \   --reg $outdir_dt_recon/register.dat \   
> --fstarg --interp nearest \   --o $outdir_dt_recon/adc.anat.mgh > > 
> mri_segstats \   --seg $SUBJECTS_DIR/$subj/mri/wmparc.mgz \   --ctab 
> $FREESURFER_HOME/FreeSurferColorLUT.txt \   --id 12 --id 51 --id 2 
> --id 41 --id 16 --id 13 --id 52 --id 27 --id 59\   > --i 
> $outdir_dt_recon/adc.anat.mgh --seg-erode 1 --sum 
> $outdir_dt_recon/adc.stats >   > When I load adc.anat.mgh into 
> FreeView and scroll to a ROI, I can see a value like 0.000770333! This 
> means (for me) that the value is 'there' but has to be multiplied by 
> 10^3?! Do you > have any suggestions how I can get these values to a 
> .stats file? >   > Thanks a lot, > Tom > 
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Re: [Freesurfer] V1 masking

[Douglas N Greve]

Yes
On 02/13/2015 08:59 AM, David Soto wrote:
> Hi, thanks for your advise, very useful
>
> to create my V1 masks in the end I used mri_label2vol  with 
> --stat-thresh thresh .99
>
> just to confirm, am I right to say that the mask contains voxels with 
> a .99 probability of
> being V1?
>
> (the mask does look more constrained in the borders)
>
> thanks!
> ds
>
> On Fri, Feb 6, 2015 at 9:12 AM, David Soto  <mailto:d.sot...@gmail.com>> wrote:
>
> Hi,
>
> I have been succesfully using mri_label2vol on the V1.labels to
> get a nii file
> (i.e. mri_label2vol --label rh.V1.label  --temp
> $SUBJECTS_DIR/$i/mri/orig/001 --identity --o rV1.nii --subject $i
> --hemi rh --proj frac 0 1 0.01)
>
>
> but now I would like to use the "v1.prob.label" to get a .nii file
> that  includes the probabilities of a voxel being on V1.
>
> is this possible?
>
> many thanks!
> david
>
>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] freeview registration

[Douglas N Greve]

I know that Ruopeng was fixing it a few months ago. Ruopeng, did you 
finish that fix?
doug

On 03/02/2015 10:28 AM, Xiaomin Yue wrote:
> Hi Doug,
>
> thanks for your response.  You are right that the freeview in v5.3 
> doesn't generate the registration file correctly. However, the newest 
> development version of freeview can generate a lta registration file 
> correctly with correct source and target volume.  then, a registration 
> file in reg format can be generated using lta_convert included in the 
> development version of freesurfer.  It is much easier and precise to 
> manually adjust the registration using freeview than tkregister.   It 
> might be useful to include a tool using freeview to manually adjust 
> registration in the next freesurfer release.
>
> Xiaomin
>
> 
> Date: Sun, 1 Mar 2015 13:57:52 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] freeview registration
>
>
> I think that freeview does not correctly generate the registration 
> file. You can use it to check the regsitration, but us tkregister if  
> you need to edit  it.
> doug
>
>
> On 2/27/15 10:18 AM, Xiaomin Yue wrote:
>
> Hi All,
>
> After using freeview to manually adjust the registration between a
> functional and T1.mgz generated by bbregister, I saved the
> registration file in freeview as lta format, which seems the only
> option.  However, the registration file has same file name for
> source and target volume.  So, when loading it again to freeview,
> the registration is totally wrong.   In order to avoid the
> problem, I converted the register.dof6.dat to lta formation, where
> the lta file has correct source and target volume name.  Then, I
> loaded the lta file generated from register.dof6.dat, did manual
> adjustment, and then saved adjusted registration as a lta file.
>  the final lta file has same problem.   I am using freesurfer 5.3.
>  Any suggestion is appreciated.
>
> Thanks,
> Xiaomin
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] funcroi-table-sess error, "variable must begin with a letter"

[Douglas N Greve]

The log file you sent has a different error:

ERROR: cannot find allVfix in NMASA_induction.lh


On 02/17/2015 01:40 PM, Joseph Andreano wrote:
> Hi Doug,
>
> We're having difficulty extracting signal from ROIs using
> funcroi-table-sess.  Every time we try, we get the following error
> message: "set: Variable name must begin with a letter."
>
> In an earlier discussion about this error
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39320.html)
> you asked for a debug version of the command we were having difficulty
> with.  The file is attached.
>
> Thanks,
> Joe Andreano
>
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] cluster colors

[Douglas N Greve]

I'm not sure what is going on there. Can you send me the cluster.summary 
file?
doug

On 02/18/2015 02:47 PM, Hirsch, Gabriella wrote:
>
> Yes – sorry this is probably easier with images.
>
> The files I’m visualizing are the sig.mgh (uncorrected) and 
> cache.th13.abs.sig.ocn. mgh (cluster corrected) respectively, 
>  overlayed on an fsaverage brain. I am visualizing using tksurfer.
>
> When I run mri_glmfit, I get the “example_sig” output (see attached), 
> which was expected. However, after I run the clusterwise correction 
> (mri_glmfit-sim), my clusters come out in a different color (in this 
> case red, every time, for every cluster; see “example_cluster”).
>
> The tutorial indicates the cluster color scale is arbitrary, however, 
> ALL of my clusters post-correction are always the same color, and 
> always different from the pre-corrected clusters. I found this a 
> little confusing since red is a color from the heat map, which may be 
> interpreted as an inverse of the original uncorrected output – but it 
> seems this color is in fact arbitrary. Is this correct?
>
> Gabriella
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
> Greve
> *Sent:* Wednesday, February 18, 2015 2:16 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] cluster colors
>
>
> I don't think I understand. What files are you visualizing? What is 
> your command to visualize?
>
> On 2/18/15 3:42 PM, Hirsch, Gabriella wrote:
>
> Hi FS experts,
>
> I had a quick question I was hoping someone could help me with; I
> used the group analysis tutorial
> 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools)
> to analyse two groups of subjects.
>
> I ran the mri_glmfit command, as well as the clusterwise
> correction (mri_glmfit-sim) on the same data; however upon
> visualization, the two outputs present clusters in different
> colors (before correction all clusters are blue and after
> post-correction all clusters are red - this is consistent across
> conditions). According to the tutorial, I should disregard the red
> color since it is arbitrary (and not, in fact, an inversion of
> what I see from the uncorrected data). Note that I have NOT
> changed the contrast or any other setting.
>
> Am I understanding this correctly?
>
> Thank you.
> Gabriella
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Register.dof

[Douglas N Greve]

On 02/18/2015 09:54 PM, Xiaomin Yue wrote:
> Hi Doug,
>
> Thanks for your response.  I did run bbregister to register the EPI to 
> T1, but it did not resample the EPI to T1 space, just generated a 
> register.dof6.dat file, which is expected according to the help 
> document.  Also, the help document of bbregister doesn’t indicate 
> resampling or sort, unless I missed something.
It is the --o option.
> I did try mri_vol2vol to resample the EPI to T1 space, using the 
> registration file generated by bbregister.  When I loaded the T1 and 
> EPI in freeview, the two doesn’t match well, unless I loaded the EPI 
> with the registration file.  Did I do something wrong?  Or I shouldn’t 
> expect T1 and EPI line up after mri_vol2vol?
Did you check the registration with tkregister? Look at the last line in 
the bbregister log file to get the command line. if that does not look 
ok, then vol2vol will surely not work. If it does look ok, then send the 
vol2vol command line
doug
>
> Xiaomin
>
> *From:* Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>
> *Sent:* ‎Wednesday‎, ‎February‎ ‎18‎, ‎2015 ‎1‎:‎35‎ ‎PM
> *To:* Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>
>
>
> Yes, if you've run the T1 through recon-all, then you can use 
> bbregister to create a registration between the two. It will also 
> resample to the T1 space, but you can also use mri_vol2vol to do so too.
> doug
>
>
> On 2/18/15 5:43 PM, Xiaomin Yue wrote:
>
> Hi,
>
> I like to transfer a epi file to a T1 space.  Is it possible?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> We don't have anything to do this directly. However, we do have
> this tool:
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> See if that meets your needs.
>
> doug
>
> On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> > Hello,
> > I am performing clustering ofer data sampled to the fsaverage5
> surfaces.
> > I would now like to be able to do color matchign and other
> processes that require a vertex correspondence across both surfaces.
> >
> > I have noticed that the vertices do not correspond directly
> (vertex 25 of lh is not the homologous of vertex 25 in rh)
> > As both hemispheres have the same number of vertices I guess
> this has probably already been done, but I have not been able to
> find this information.
> >
> > Is there any lookup-table or any easy method to calculate vertex
> correspondence across hamispheres for fsaverage5 surfaces?
> >
> > Thank you in advance
> >
> > David Moreno-Dominguez
> > Research Group: Neuroanatomy and Connectivity
> > Methods & Development Unit: Cortical Networks and Cognitive
> Functions
> > Max Planck Institute for Human Cognitive and Brain Sciences
> > Stephanstraße 1A, 04103 Leipzig, Germany
> > Phone: +49 341 9940-2580
> > Email: mor...@cbs.mpg.de
> > http://www.cbs.mpg.de/~moreno <http://www.cbs.mpg.de/%7Emoreno>
> >
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Re: [Freesurfer] Surface-based Interhemispheric Registration generate average surface from average subject

[Douglas N Greve]

What do you mean that no surfaces were generated? There are two things 
you have to do. One is to create the template. The second is to apply 
the template (the first set of steps).
doug

On 02/20/2015 04:15 AM, pfannmo...@uni-greifswald.de wrote:
> Hi FSexperts,
>
> I would like to compute a symmetrical template out of the anatomical images 
> in a group of subjects. I followed the description in:
>
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
>
> Afterwards I recognized that no surfaces were generated. Since the 
> computation takes quiet a while, the generation of the surfaces from the data 
> which have already been computed would be very helpfull. Is it possible to do 
> that?
>
> Yours pfannmoe
>

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Re: [Freesurfer] mris_preproc skips subjects

[Douglas N Greve]

Can you send your fsgd file?

On 02/21/2015 08:42 AM, Anders Hougaard wrote:
> Dear Freesurfers,
>
> Sorry for this newbie question:
> I'm preparing my data for a group analysis using mris_preproc:
>
> mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas
> thickness --out lh.nocov.thickness.00.mgh
>
> I have 120 subjects in total and my FSGD file simply looks like this
>
> GroupDescriptorFile 1
> Class Group1
> Class Group2
> Input pt01 Group1
> Input pt02 Group1
> [..rest of lines left out..]
> Input ct01 Group2
> Input ct02 Group2
> [..rest of lines left out..]
>
>
> When I run mris_preproc, the program only assembles the first two
> subjects in group 1 and the first subject in group 2, i.e. 3 subjects
> not 120.
>
> I have run -make all on all subjects and there is nothing to make.
> I'm running ver. 5.3.0
>
> What is wrong?
>
> All the best,
> Anders
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Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

[Douglas N Greve]

That is strange. Can you send the full terminal output from the first 
call  to mri_glmfit-sim?
doug

On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote:
> Hello Freesurfers,
>
> I use freesurfer v5.3.0
>
> When I do group analysis correction for multiple comparisons for lh as 
> follows:
>
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir 
> group.glm --nii.gz --surface fsaverage lh
>
> mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
>
> I get this error message:
>
> ERROR: cannot find 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd
>
> For the mkanalysis-sess i used fwhm = 5.
>
> When i do the same for mni305 and use:
>
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir 
> group.glm --nii.gz
>
> mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166
>
> It works well without an error.
>
> Thanks,
> Eiran
>
>
> On Monday, February 23, 2015 10:37 AM, 
> "freesurfer-requ...@nmr.mgh.harvard.edu" 
>  wrote:
>
>
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Re: [Freesurfer] Creating subject-wise functional ROIs on the cortical surface

[Douglas N Greve]

Can you use mri_surfcluster to do this? It can output a binary mask, 
annotation, or label. You just need to give it the input and a 
threshold. If you just want constrain it to a given label, then you'll 
need to create a mask.
doug

On 02/20/2015 09:14 PM, Eric Reavis wrote:
> Hello Freesurfers,
>
> I've run into issues trying to create functionally-defined ROIs on the 
> cortical surface in FreeSurfer 5.3.
>
> I processed my functional localizer data in FsFast, which produced 
> nice activation maps on the cortical surface. I would like to create 
> ROIs from those maps (i.e., freesurfer labels) for use in other 
> analyses. Specifically, I'd like to select the largest significant 
> cluster in a particular anatomical neighborhood (lateral occipital) 
> and make a label with the same boundaries.
>
> I've used tksurfer to draw labels before (e.g., to create functionally 
> defined retinotopic ROIs), so I initially planned to create the ROIs 
> by hand in tksurfer on the inflated cortical surface. However, the 
> overlay threshold requires adjustment from the default value, and in 
> both tksurfer and tksurfer-sess I encountered the "Configure Overlay 
> Display" clipping error listed as a known issue in FreeSurfer 5.1 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes). Although the 
> release notes state that the error was slated to be fixed in 5.3, I 
> can attest that it is not, at least on my machine. I tried the .tcl 
> file workaround suggested for 5.1, as well as various keyboard 
> shortcuts to try to press the invisible 'apply' button, but to no avail.
>
> Since tksurfer didn't work, I next tried to use freeview to create the 
> labels. However, as far as I can tell, freeview doesn't yet support 
> drawing labels on the cortical surface, only volumetric ROIs. Is that 
> correct?
>
> I am wondering if there might be a workaround for this -- there seems 
> to be a functionality gap since tksurfer is no longer actively 
> supported but freeview is not yet fully developed. I am considering 
> doing this part of the processing in SUMA, since I know that the 
> functionality exists there, but it would be nice to be able to do 
> everything in freesurfer.
>
> Better yet, is there a freesurfer program that I could use to 
> automatically create labels based on the largest contiguous activation 
> cluster within a particular region of the parcellated brain, bypassing 
> the need for manual intervention?
>
> Thanks in advance for any suggestions,
>
> --Eric
>
> ---
> Eric A. Reavis, Ph.D.
> Postdoctoral Scholar
> Semel Institute for Neuroscience and Human Behavior
> UCLA
> (310) 478-3711 ext. 43382 
>
>
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Re: [Freesurfer] Using -qcache command multiple times

[Douglas N Greve]

It will just recreate the files, no need to delete anything.
doug

On 02/23/2015 10:25 AM, Anne Park wrote:
> Hello,
>
> I had a question about using the -qcache command for smoothing. 
> Previously, the -qcache command was used on several subjects in my 
> dataset, and since then, these subjects have undergone some manual 
> edits (control points, edits to wm.mgz, etc.). Currently, I’d like to 
> run the -qcache command on the entire group of subjects – do I need to 
> delete any files created by the previous uses of -qcache first, or is 
> it ok just to go ahead and run the command for all subjects?
>
> Thank you,
> Anne Park
>
>
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Re: [Freesurfer] Desikan-Kilany atlas

[Douglas N Greve]

You can use $SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz (already in the 
volume), then use mri_label2vol (with --seg flag) and 
$FREESURFER_HOME/average/mni152.register.dat for the registration. The 
problem is that the cortical labels are all very thin and won't 
intersect well with your ICA volume. But that is the price you pay when 
trying to bring surface analysis into the volume space.
doug

On 02/24/2015 04:42 PM, Bruce Fischl wrote:
> I see. You could do what you want by sampling the ?h.aparc.annot into 
> the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). 
> Actually, if you do surf2vol from fsaverage I think it's already in 
> MNI coords, but Doug can confirm. The problem is going to be that the 
> mapping won't be very accurate across subjects. You would be better 
> off doing it all on the surface
>
> cheers
> Bruce
>
> On Tue, 24 Feb 2015, Norman Benbrahim wrote:
>
>> No problem,
>> I want to take certain regions and use them as masks in order to 
>> compute the joint
>> histogram between a thresholded z-score map obtained from ICA (a 
>> resting state
>> network) masked in that region, and the variance of the BOLD image. I 
>> already have
>> scripts set up to do this in matlab, so I would only need the atlas 
>> in nifti format
>> so I can pick out which regions to use (using the rich club paper, 
>> van den Heuvel et
>> al. 2011), and create masks out of those.
>>
>> On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl 
>>  wrote:
>>   Hi Norman
>>
>>   perhaps you can take a step back and tell us what you want to 
>> use it
>>   for?
>>   We might be able to suggest a better analysis strategy
>>   Bruce
>>   On Tue, 24 Feb 2015,
>>   Norman Benbrahim wrote:
>>
>>   > Hi,
>>   > I want to use the Desikan-Kilany atlas to run some analysis 
>> in some
>>   regions, however
>>   > I am very new to freesurfer. What I would like to accomplish 
>> is the
>>   following:
>>   > 1) Transform the atlas into MNI152 2mm space
>>   > 2) Convert the atlas to a binary nifti image (similarly to 
>> the way
>>   FSL's atlases are
>>   > stored)
>>   > If anyone can help me get started that would be awesome. 
>> Thank you!
>>   > -Norman
>>   >
>>   >
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

You would do the long analysis using a random effects analysis. For each 
subject you can get a slope (this won't work if the subject only has 1 
time point), then concatenate the slopes into a file and run mri_glmfit, 
then follow the procedures from the archive email you reference.
doug

On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
> Hi Doug and others,
>
> I would like apply (Monte Carlo simulation) cluster correction (as opposed to 
> the implemented vertex-wise FDR correction) on the results from a 
> longitudinal study I analyzed using the LME toolbox. The design is unbalanced 
> (different number of time points, from 1 to 4, per subject).
>
> In this thread 
> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) 
> you, Doug, suggested, if I understand correctly:
>
> - concatenating the images using `mris_preproc --paired-diff`
> - smooth with the same kernel size as used in the lme analysis
> - running `mri_glmfit` on them with an fsgd file that uses the same 
> covariates and the same contrast (excluding the interaction term with time) 
> as used in the lme analysis
> - overwriting sig.mgh with the one from the lme analysis
> - running `mri_glmfit-sim --cache`
>
> How would I extend this to my case where I don't have pairwise images, but 1 
> image for some participants, for others up to 4?
>
> Thanks a lot,
>
> Janosch
>
>
>
>

-- 
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MGH-NMR Center
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Re: [Freesurfer] What exactly was wrong with DOSS in QDEC

[Douglas N Greve]

Hi Chris, the error was very unpredicatable. If you want to see whether 
it was wrong or not, you can look at the contrast matrix it created 
(C.dat in the contrast folder).
doug

On 02/25/2015 07:11 AM, Christoph Abé wrote:
> Hello,
>
> I am dealing again with the "old" issue of using DOSS in QDEC. This 
> option was removed. I cannot find any detailed explanations of what 
> exactly was wrongly computed when selecting DOSS. I only find as 
> explanation:
>
> "that there *may be* a bug in the way that QDEC computes contrasts for 
> DOSS"
>
> "There is a bug in it that causes the contrasts to be in error *at times*"
>
> Which specific contrasts were actually affected?
> And how did it compute it instead of what?
> Did it happen all the time, or only sometimes, and why?
>
> *Most important for me: *Did it affect a group comparison using 
> (nuisance) covariates?
> Or were the other additional correlation and interaction contrasts the 
> ones which did not make sense?
>
> Would be nice to get some more insight into this.
>
> Thank you,
> Chris
>
>
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Re: [Freesurfer] Lta_convert

[Douglas N Greve]

try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert

On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson" 
> mailto:dgray...@ucdavis.edu>> wrote:
>
> ok, great.
>
> so let's say I have a linear transformation or a full warp field to go 
> between the freesurfer processed image and the unprocessed brain. is 
> there a way that I can propagate onto the unprocessed image the entire 
> freesurfer contents including the "mri" and "label" and everything 
> else, using the warp? The processed image has extensive manual edits, 
> so I basically just want to transfer everything over.
>
> Thanks Bruce!
>
> -David
>
> On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi David
>
> yes, you can use bbregister to do the rigid alignment, then use it as
> initialization for mri_nl_align. I would think you are better off
> doing the
> surface recons and using cvs though. It's only computer time
>
> cheers
> Bruce
>
> On Wed, 25 Feb 2015, David Grayson wrote:
>
> > Hey Bruce,
> > Thanks for responding. I would actually prefer nonlinear. I did
> not mention
> > it, but the aseg data that I have is on a distortion-corrected
> T1 image,
> > whereas the unprocessed image I want to warp onto is the same
> scan but not
> > corrected for distortion. The distortions are nonlinear. I was
> hoping there
> > might be a way to get a warp field to go between the two images
> without
> > running both images through the recon-all pipeline. Are there
> any other
> > possible tools?
> >
> > Thanks!
> > -David
> >
> > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> >   Is there any reason you need it to be nonlinear? I would think
> >   bbregister and mri_vol2vol would do the trick
> >   Cheers
> >   Bruce
> >
> >
> >
> >   > On Feb 25, 2015, at 11:18 PM, David Grayson
> >   mailto:dgray...@ucdavis.edu>> wrote:
> >   >
> >   > Hi freesurfers,
> >   >
> >   > I am hoping to warp an aparc+aseg.mgh file from a subject's
> >   freesurfer-processed image to a separate (unprocessed) T1
> image
> >   on the same subject. I would like to use a purely
> >   intensity-based nonlinear volumetric registration to do
> this, to
> >   save time and complication. I understand I can do this if
> I have
> >   a .m3z warp file.
> >   >
> >   > My question is, how can I get this warp file? I have tried
> >   using mri_cvs_register with the --step3 option, but that
> appears
> >   to only work after the surface-based registrations have been
> >   carried out. I haven't found another tool to do this yet.
> >   >
> >   > Are there any ideas? Thank you very much for your time.
> >   >
> >   > -David
> > > ___
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Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

[Douglas N Greve]

It looks like you'll want to use mri_mask (?)
doug


On 02/26/2015 10:12 AM, Sarah Finnegan wrote:
> Hi Bruce
>
> Thanks for your reply,
> I did use mri_vol2surf for the sampling
>
> mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi 
> {hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
>
> I don't believe that I want to average within the ROI. I want to take any 
> clusters of activity within V2 and feed this into a script i'm developing in 
> MATLAB to work out the distance between different voxel clusters and the size 
> of each cluster, but only for within my region defined as V2. Hopefully that 
> makes sense, If I average I think I will lose this spatial information?
>
> Thanks
> Sarah
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: 26 February 2015 15:04
> To: Freesurfer support list
> Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
>
> Hi Sarah
>
> have you used mri_vol2surf to sample the data onto the surface? When you
> say "extract specific regions of functional data from a flat " do you
> want to average within the ROI?
>
> cheers
> Bruce
> On Thu, 26 Feb 2015, Sarah Finnegan wrote:
>
>> I have a question about the equivalent of fslmaths -mas option in
>> freesurfer.
>> I have several manually defined labels in .label form that I want to use to
>> extract specific regions of functional data from a flat patch. Ordinarily in
>> fsl I would just use
>>
>> fslmaths -invol {functional_data} -mas {bin_label} -outvol
>> {masked_functional_data}
>>
>> but I'm a little confused about an equivalent for this in free surfer as I
>> don't want to perform any further stats on these ROI yet, extract them from
>> any surrounding data and overlay onto the flattened surface.
>>
>> I have tried using
>> mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
>> {anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
>> {func_V2_mask_out}
>> but when overlaying the output file there are no data points visible.
>>
>> Any help would be great as several other functions that I have tried seem to
>> be obsolete,
>>
>> Thanks!
>> Sarah
>>
>>
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Re: [Freesurfer] mri_surfcluster questions

[Douglas N Greve]

On 02/26/2015 01:46 PM, Janosch Linkersdörfer wrote:
> Hi all,
>
> I experimented with the different flags for mri_surfcluster and have 2 issues 
> that I don't understand, it would be great if somebody could enlighten me:
>
> 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would 
> expect, i.e., only clusters with a minimum vertex-wise p-value > thmin are 
> shown. When I use 'neg' or 'pos', I get clusters with a minimum value below 
> thmin. Why is that?
By default, the threshold
will be adjusted when the --sign is pos or neg by subtracting log10(2.0).
This assumes several things: (1) the source is a -log10(p) map, and (2)
the pvalue was computed using a two-sided t-test. Under these conditions,
subtracting log10(2.0) is like dividing the p-value by 2 (ie, changing it
from a two-tailed test to a one-tailed test). If the input map does not
meet these criteria, then run with --no-adjust.

>
> 2) The FDR correction seems to be very lenient. Using --fdr .05, for example, 
> I get a thmin of 1.158247. That is probably not correct, right?
It all depends on the data. If you have a lot of activation, it can be 
very lenient.
>
> The command I use looks somewhat like:
>
> mri_surfcluster --sd /my/subj/dir --in sig.mgh --subject fsa
> verage(_DKT) --hemi lh --annot aparcDKT40 --sum summary.txt --clabel 
> /path/to/label/lh.cortex.label [--fdr .05 | --thmin 3] --thsign [pos | neg | 
> abs]
>
> Thanks,
>
> Janosch
>
>
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Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas N Greve]

On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> Dear Doug,
>
> Thank you for helping !
>
> Yes I directly used the regheader option because in the steps before I 
> already registered ASL maps on anatomical T1.
>
> The brain.fsaverage.lh.mgh come from the projection of the T1 brain 
> mask (dilated by 1) on the fsaverage.
>
> 1) So isn't it better to project first on the anatomical subject then 
> on fsaverage than what I've done ?
This is what is done internally when you spec a target subject that is 
not the same as the source subject.
>
> 2) Smoothing with mris_fwhm is a good way with --mask option ?
Yes, though I don't think that masking will have an effect the way you 
created the mask (everything will be in the mask). I would use --cortex 
to smooth only within cortex (and so exclude the medial wall).
doug

>
> Thank you for your precious advices !
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-01 19:45 GMT+01:00 Douglas Greve  <mailto:gr...@nmr.mgh.harvard.edu>>:
>
>
> Basically looks ok. The only things that jump out at me are that
> you are using regheader (I would create a registration file with
> bbregister rather than assuming that there was no motion between
> the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come
> from?
> doug
>
>
>
> On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:
>> Dear Freesurfer's experts,
>>
>> I computed some perfusion maps from ASL data. These perfusion
>> maps were registered on anatomical T1 and I would like to make a
>> group analysis on surfaces. Please find below my actual commands
>> in order to project these volumic maps on fsaverage then smooth
>> the data projected on fsaverage :
>>
>> *Project CBF maps on fsaverage* :
>> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
>> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
>> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
>> //mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
>> fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
>> rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/
>>
>> *Smooth the data projected on fsaverage (native ASL data size
>> voxel of 3mm)* :
>> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
>> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh
>> --mask brain.fsaverage.lh.mgh//
>> //mris_fwhm --s fsaverage --hemi rh --smooth-only --i
>> rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh
>> --mask brain.fsaverage.rh.mgh/
>>
>> Could you advise me on these two steps and tell me first if this
>> is the best way to project CBF maps on fsaverage, then to smooth
>> the data on surfaces ? Is my process could be improved ?
>>
>> Best regards,
>> -- 
>> -
>> Matthieu Vanhoutte, MSc
>> Research Engineer - Department of Neuroradiology
>> Regional University Hospital, Lille, France
>>
>>
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Re: [Freesurfer] Regression coefficient qdec

[Douglas N Greve]

r-values are not produced. The coefficients are regression coefficients, 
not correlation coefficients. If you want correlation coefficinets, I 
would do it in matlab. download this

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit_pcc.m

copy it to $FREESURFER_HOME/matlab

The use tksurfer or freeview to view the resulting pcc maps

doug


On 03/02/2015 06:07 AM, Erik Lindberg wrote:
> Dear Freesurfers,
>
> I am trying to display the regional regresssion coefficent for age in 
> qdec. However the colorbar still gives me the traditional 0, 1.3 etc
>
> is there anyway to change the colorbar. I would like to be able to 
> display only regions that have more than say 0.3 correlation with age 
> - so it would be god if I can get the colorbar to display the 
> r-values. Is that possible?
>
> best
> Eric
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Bad design matrix

[Douglas N Greve]

000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
>   0.000   1.000   0.000  -0.900   0.000  -9.138;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
>
> 2015-03-01 19:41 GMT+01:00 Douglas Greve :
>> Try demeaning your covariates. By demeaning, I mean to compute the mean
>> across all subjects, then subtract the mean from all values (for each
>> covariate).
>> doug
>>
>>
>>
>> On 3/1/15 2:40 AM, Anders Hougaard wrote:
>>
>> Dear all,
>>
>> I'm comparing cortical thickness of a group of patients to a group of
>> controls.
>> I want to regress out the effects of gender, age, disease severity and
>> disease duration.
>> For the controls, the last two parameters equals zero.
>>
>> When running mri_glmfit, i get ERROR: matrix is ill-conditioned or
>> badly scaled, condno = 1e+08
>> See the design matrix attached. My contrasts are set as
>> 1 -1 0 0 0 0 0 0 0 0
>> and
>> -1 1 0 0 0 0 0 0 0 0
>>
>> What should I do to improve this?
>>
>> All the best,
>> Anders
>>
>>
>>
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Re: [Freesurfer] Monte Carlo Simulation

[Douglas N Greve]

Hi Rick, in the future please post to the list and not to us personally. 
Thanks! When you did the volume-based analysis, it should have masked 
out anything anything that was not subcortical. Did it not? If not, then 
when you run mri_glmfit you can add --mask 
$SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.

doug

On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote:
> Hi Doug,
>
> I was running the following command in launchpad in order to correct 
> for multiple comparison (using a output file from a PASL FS analysis):
>
> pbsubmit -m riwohoy -q extended -c "mri_glmfit-sim --glmdir 
> tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0 
> cbf.talairach_p01_abs_montecarlo"
>
>
> When I looked for the surviving clusters, I just found clusters in the 
> cortical area but not in sub-cortical areas (the cortical clusters 
> where consistent with the clusters I found in the cortical analyses 
> though). Is there a way I can limit the Monte Carlo Simulation to 
> sub-cortical areas only so that I'll also see the most sgn. clusters 
> in the sub-cortical areas? Please let me know if you have any 
> additional questions!
>
> Thanks,
> Rick

-- 
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Fax: 617-726-7422

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Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

[Douglas N Greve]

Hi Antonin, please remember to send responses to the list. Thanks! I've 
put a new version of cluster-sess in that same location. Let me know if 
that works.

for the mri_mcsim command, make sure to pass it a fwhm that is an 
integer. Also, I would probably just run it with --fwhm-max so that it 
does all the fwhms below the max. There is virtually no time penalty for 
this and it may be useful in other cases where the fwhm is not exactly 
the same.

doug

On 03/03/2015 08:42 AM, Antonin Skoch wrote:
> Dear Douglas,
>
> thank you very much for the file. It seems, that the -cache-dir 
> parameter is not parsed properly in this script.
> By -cache-dir you fill-in the CacheDir variable, but it is never used 
> and at line 182 you use for csd directory construction variable SimDir 
> which hard-coded points to $SUBJECTS_DIR/fsaverage/mult-comp-cor.
>
> But when I corrected for this, it works in principle.
>
> Could you please check that I understand the usage correctly?
> I simulated my own distribution in subject's native space by using 
> mri_mcsim, for example for right hemisphere by this command
> mri_mcsim --o subject_name/rh/cortex --base mc-z --surf subject_name 
> rh --nreps 1 --fwhm my_fwhm(from fwhm.dat in analysis directory)
> and then run cluster-sess -analysis analysis_name -thresh 2 -a2009s 
> -2spaces -cache-dir dir_of_my_simulation -s session_ID
>
> Regards,
>
> Antonin
>
> --------
> *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> *To:* Antonin Skoch [mailto:a...@medicon.cz]
> *Sent:* Mon, 02 Mar 2015 21:07:36 +0100
> *Subject:* Re: [Freesurfer] multiple comparisons correction for
> individual hemispheres (native space)
>
> Sorry, try it now
>
> On 03/02/2015 02:42 PM, Antonin Skoch wrote:
> > Dear Douglas,
> >
> > I am also interested in multiple comparisons correction in
> first-level
> > analysis for individual hemispheres in fsFast. Unfortunately,
> your file
> >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess
> >
> > which you provided for Christopher in November 2014 is not
> available
> > at that location. Could you please provide this file permanently
> for
> > other users?
> >
> > Regards,
> >
> > Antonin Skoch
> > Institute for Clinical and Experimental Medicine
> > Czech Republic
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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>
>
>
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Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

[Douglas N Greve]

ge within the ROI?
>
> cheers
> Bruce
> On Thu, 26 Feb 2015, Sarah Finnegan wrote:
>
>> I have a question about the equivalent of fslmaths -mas option in
>> freesurfer.
>> I have several manually defined labels in .label form that I want to use to
>> extract specific regions of functional data from a flat patch. Ordinarily in
>> fsl I would just use
>>
>> fslmaths -invol {functional_data} -mas {bin_label} -outvol
>> {masked_functional_data}
>>
>> but I'm a little confused about an equivalent for this in free surfer as I
>> don't want to perform any further stats on these ROI yet, extract them from
>> any surrounding data and overlay onto the flattened surface.
>>
>> I have tried using
>> mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
>> {anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
>> {func_V2_mask_out}
>> but when overlaying the output file there are no data points visible.
>>
>> Any help would be great as several other functions that I have tried seem to
>> be obsolete,
>>
>> Thanks!
>> Sarah
>>
>>
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Re: [Freesurfer] Bad design matrix

[Douglas N Greve]

I think just using DOSS instead of DODS will do it (--fsgd your.fsgd doss)


On 03/03/2015 12:42 AM, Anders Hougaard wrote:
> Thanks Doug.
> Any suggestions for a more appropriate design?
> I guess this is a common situation where two or more parameters only
> apply to one group (in this case patients) and are zero or constant in
> the other.
>
> Best,
> Anders
>
> 2015-03-02 21:21 GMT+01:00 Douglas N Greve :
>> It looks like the 4th column is always -0.9 and the 6th col is always
>> -9.138 which makes them redundant with column 2 and causes the error.
>> doug
>>
>> On 03/02/2015 03:16 PM, Anders Hougaard wrote:
>>> Dear Doug,
>>>
>>> Thanks for the answer. I deliberately chose not to demean.
>>> With demeaning I get the same error (see below). Any suggestions?
>>>
>>> Best,
>>> Anders
>>>
>>> Design matrix --
>>>1.000   0.000  -0.600   0.000   17.137   0.000;
>>>1.000   0.000  -0.800   0.000   11.962   0.000;
>>>1.000   0.000   7.100   0.000   11.190   0.000;
>>>1.000   0.000   0.700   0.000   30.736   0.000;
>>>1.000   0.000   3.100   0.000   23.735   0.000;
>>>1.000   0.000   0.100   0.000   21.121   0.000;
>>>1.000   0.000   1.100   0.000   12.395   0.000;
>>>1.000   0.000   2.100   0.000   24.912   0.000;
>>>1.000   0.000   0.100   0.000  -8.021   0.000;
>>>1.000   0.000  -0.700   0.000   8.877   0.000;
>>>1.000   0.000   0.100   0.000   0.893   0.000;
>>>1.000   0.000   7.100   0.000   29.849   0.000;
>>>1.000   0.000  -0.400   0.000  -1.825   0.000;
>>>1.000   0.000   2.100   0.000   14.361   0.000;
>>>1.000   0.000   2.100   0.000   7.267   0.000;
>>>1.000   0.000   0.100   0.000   34.169   0.000;
>>>1.000   0.000   0.100   0.000   30.500   0.000;
>>>1.000   0.000   1.100   0.000   9.219   0.000;
>>>1.000   0.000   0.100   0.000   26.270   0.000;
>>>1.000   0.000   1.100   0.000   2.320   0.000;
>>>1.000   0.000   0.100   0.000   22.325   0.000;
>>>1.000   0.000   0.100   0.000   13.323   0.000;
>>>1.000   0.000   1.100   0.000  -2.628   0.000;
>>>1.000   0.000   7.100   0.000   12.379   0.000;
>>>1.000   0.000   1.100   0.000  -2.581   0.000;
>>>1.000   0.000   0.100   0.000  -4.492   0.000;
>>>1.000   0.000   1.100   0.000   11.549   0.000;
>>>1.000   0.000   0.100   0.000  -8.413   0.000;
>>>1.000   0.000   1.100   0.000   9.663   0.000;
>>>1.000   0.000   1.100   0.000   8.655   0.000;
>>>1.000   0.000   1.100   0.000   25.778   0.000;
>>>1.000   0.000   3.100   0.000   2.739   0.000;
>>>1.000   0.000   0.100   0.000   21.745   0.000;
>>>1.000   0.000  -0.400   0.000  -5.762   0.000;
>>>1.000   0.000   0.100   0.000   14.969   0.000;
>>>1.000   0.000   0.100   0.000   3.535   0.000;
>>>1.000   0.000   0.100   0.000  -0.287   0.000;
>>>1.000   0.000   1.100   0.000  -2.283   0.000;
>>>1.000   0.000   0.100   0.000  -0.257   0.000;
>>>1.000   0.000   0.100   0.000  -1.207   0.000;
>>>1.000   0.000   0.100   0.000   1.140   0.000;
>>>1.000   0.000   0.600   0.000  -4.829   0.000;
>>>1.000   0.000   1.100   0.000   2.213   0.000;
>>>1.000   0.000   0.100   0.000   2.503   0.000;
>>>1.000   0.000   0.600   0.000   3.193   0.000;
>>>1.000   0.000   0.100   0.000   10.361   0.000;
>>>1.000   0.000   0.100   0.000   3.546   0.000;
>>>1.000   0.000   6.600   0.000   12.532   0.000;
>>>1.000   0.000   0.100   0.000  -1.286   0.000;
>>>1.000   0.000   0.100   0.000  -5.428   0.000;
>>>1.000   0.000  -0.400   0.000  -1.661   0.000;
>>>1.000   0.000  -0.800   0.000   21.444   0.000;
>>>1.000   0.000   0.100   0.000   21.517   0.000;
>>>1.000   0.000  -0.600   0.000   8.515   0.000;
>>>1.000   0.000   0.100   0.000   19.530   0.000;
>>>1.000   0.000   1.100   0.000   1.824   0.000;
>>>1.000   0.000   0.100   0.000   15.795   0.000;
>>>1.000   0.000   0.600   0.000  -6.140   0.000;
>>>1.000   0.000   2.600   0.000   0.803   0.000;
>>>1.000   0.000   0.100   0.000   16.904   0.000;
>>>0.000   1.000   0.000  -0.900   0.000  -9.138;
>>>0.000   1.000   0.000  -0.900   0.000  -9.138;
>>>0.000   1.000   0.000  -0.900   0.000  -9.138;
>>>0.000 

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

I don't know, esp since it is an approximation to begin with. An 
alternative is to take the offsets from your multi-time-point subjects 
and the single maps from your subjects with one time point and run that 
through the one-sample-group-mean (--osgm in mri_glmfit). If you go this 
route, then you should subtract the mean age of the one time-point 
subjects from the age of the multi-time point subjects before the 1st 
stage of analysis.

doug


On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
> Hi Doug,
>
> thank you very much for your answer!
>
> Am 02.03.2015 um 11:30 schrieb Douglas N Greve :
>
>> You would do the long analysis using a random effects analysis.
> OK, so basically do 2-stage modeling 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?
>
>> For each subject you can get a slope (this won't work if the subject only 
>> has 1 time point), then concatenate the slopes into a file and run 
>> mri_glmfit, then follow the procedures from the archive email you reference.
> One quarter of my subjects only has one measurement time point. Can I still 
> use this method (which would only consider the 3/4 of the subjects) to 
> correct clusters found in the whole group? Or would it only be valid for 
> correcting clusters from an LME model for the reduced group?
>
> Thanks,
>
> Janosch
>
>> doug
>>
>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
>>> Hi Doug and others,
>>>
>>> I would like apply (Monte Carlo simulation) cluster correction (as opposed 
>>> to the implemented vertex-wise FDR correction) on the results from a 
>>> longitudinal study I analyzed using the LME toolbox. The design is 
>>> unbalanced (different number of time points, from 1 to 4, per subject).
>>>
>>> In this thread 
>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
>>>  you, Doug, suggested, if I understand correctly:
>>>
>>> - concatenating the images using `mris_preproc --paired-diff`
>>> - smooth with the same kernel size as used in the lme analysis
>>> - running `mri_glmfit` on them with an fsgd file that uses the same 
>>> covariates and the same contrast (excluding the interaction term with time) 
>>> as used in the lme analysis
>>> - overwriting sig.mgh with the one from the lme analysis
>>> - running `mri_glmfit-sim --cache`
>>>
>>> How would I extend this to my case where I don't have pairwise images, but 
>>> 1 image for some participants, for others up to 4?
>>>
>>> Thanks a lot,
>>>
>>> Janosch
>>>
>>>
>>>
>>>
>> -- 
>> 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
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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
>> 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.
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>
>

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Phone Number: 617-724-2358
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Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface

[Douglas N Greve]

That is the right way (or one of them). Did you look at the result in 
tksurfer?

On 03/03/2015 11:34 AM, Jin, Tony wrote:
> Hi all,
>
> I’d like to map my own stats (one value per Desikan-Killiany region) 
> onto a subject's surface file, to create a figure similar to the 
> following:
> http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001&req=4
>
> To do this, I tried to create a "scalar overlay file" using 
> mris_convert’s --parcstats option, per the following mris_convert example:
>
> “”"
> Create a scalar overlay file where each parcellation region
> contains a single value:
>   mris_convert \
> --annot lh.aparc.annot \
> --parcstats lh.parcstats.txt \
> lh.white \
> lh.parcstats
>
> (...)
>
> --parcstats  is the name of text file containing label/val 
> pairs, where label is an annot name and val is a value associated with 
> that label.
> “”"
>
> However, looking at the output file, stats didn’t seem to map to any 
> vertices; instead, I observed zeroes across all in both Freeview and 
> after conversion to ASCII (see first few lines below). I tried a few 
> other ways to delimit the “label/val” pairs of the "--parcstats" file, 
> including using tab, space, and forward-slash, but each way seemed to 
> produce the same results:
>
> 000 -10.67346 -71.19921 6.09064 0.0
> 001 -11.29567 -71.20504 6.32133 0.0
> 002 -12.26970 -71.62605 6.00416 0.0
> 003 -13.11823 -71.40913 6.45834 0.0
> 004 -14.22002 -71.39742 6.28750 0.0
>
> So, I wonder: is using mris_convert with the --parcstats flag a 
> correct way to create such a map? If so, what could have gone wrong? 
> If not, what’s the easiest way to map my own regional stats onto a 
> surface?
>
> Your expertise is greatly appreciated;
>
> Thanks and all the best,
>
> Tony Jin
> Data Technician
> Dept. of Psychiatry
> Stony Brook Medicine
>
>
> This e-mail message, including any attachments, is for the sole use of 
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

Some of this Martin will have to comment on, but my comments below

On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
> Hey Doug,
>
> thanks again! That means, I would do something like:
>
> 1.) construct longitudinal qdec table
> - only use fsid, fsid-base, and years/age columns
> - substract the average age of the one-time point subjects from years/age 
> value for every subject at every time point
>
> 2.) run long_mris_slopes
> - use the --do-avg flag?
Yes, I think so
>
> 3.) concatenate the output files from 2) and the maps from the one-time point 
> subjects with mris_preproc
> - use --is flag to select maps by specifying full path
What command are you talking about to do the concatenation? Otherwise 
sounds right. Make sure you use the average of the time points from 
long_mris_slopes and not the slope.
>
> 4.) run mri_glmfit
> - use --osgm flag for one-sample group mean
Yes
>
> 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim
Yes
>
> Is that correct? (especially, is using --do-avg what you meant by taking the 
> offset)
>
> Thanks,
>
> Janosch
>
>
> Am 03.03.2015 um 08:32 schrieb Douglas N Greve :
>
>> I don't know, esp since it is an approximation to begin with. An alternative 
>> is to take the offsets from your multi-time-point subjects and the single 
>> maps from your subjects with one time point and run that through the 
>> one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you 
>> should subtract the mean age of the one time-point subjects from the age of 
>> the multi-time point subjects before the 1st stage of analysis.
>>
>> doug
>>
>>
>> On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
>>> Hi Doug,
>>>
>>> thank you very much for your answer!
>>>
>>> Am 02.03.2015 um 11:30 schrieb Douglas N Greve :
>>>
>>>> You would do the long analysis using a random effects analysis.
>>> OK, so basically do 2-stage modeling 
>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), 
>>> right?
>>>
>>>> For each subject you can get a slope (this won't work if the subject only 
>>>> has 1 time point), then concatenate the slopes into a file and run 
>>>> mri_glmfit, then follow the procedures from the archive email you 
>>>> reference.
>>> One quarter of my subjects only has one measurement time point. Can I still 
>>> use this method (which would only consider the 3/4 of the subjects) to 
>>> correct clusters found in the whole group? Or would it only be valid for 
>>> correcting clusters from an LME model for the reduced group?
>>>
>>> Thanks,
>>>
>>> Janosch
>>>
>>>> doug
>>>>
>>>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
>>>>> Hi Doug and others,
>>>>>
>>>>> I would like apply (Monte Carlo simulation) cluster correction (as 
>>>>> opposed to the implemented vertex-wise FDR correction) on the results 
>>>>> from a longitudinal study I analyzed using the LME toolbox. The design is 
>>>>> unbalanced (different number of time points, from 1 to 4, per subject).
>>>>>
>>>>> In this thread 
>>>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
>>>>>  you, Doug, suggested, if I understand correctly:
>>>>>
>>>>> - concatenating the images using `mris_preproc --paired-diff`
>>>>> - smooth with the same kernel size as used in the lme analysis
>>>>> - running `mri_glmfit` on them with an fsgd file that uses the same 
>>>>> covariates and the same contrast (excluding the interaction term with 
>>>>> time) as used in the lme analysis
>>>>> - overwriting sig.mgh with the one from the lme analysis
>>>>> - running `mri_glmfit-sim --cache`
>>>>>
>>>>> How would I extend this to my case where I don't have pairwise images, 
>>>>> but 1 image for some participants, for others up to 4?
>>>>>
>>>>> Thanks a lot,
>>>>>
>>>>> Janosch
>>>>>
>>>>>
>>>>>
>>>>>
>>>> -- 
>>>> 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.harv

Re: [Freesurfer] from vol timecourse to surf timecourse

[Douglas N Greve]

You can use something like
rawfunc2surf-sess -i fstcmc -hemi lh -fwhm 5 -o 
fstcmc.sm05.fsaverage.lh.nii.gz

Then in mkanalysis-sess, use -funcstem fstcmc.sm05.fsaverage.lh (and do 
not include preprocessing options)

doug


On 03/03/2015 02:12 PM, Jan Willem Koten wrote:
>
> Dear Surfer experts,
>
> (Most likely Dough)
>
> It is common practice to perform the slice time correction first and 
> than the motion correction. However free surfer seems to work in the 
> opposite way.
>
> I have tried to write a mini matlab freesurfer script for the common way.
>
> system(['stc-sess -s 'funcdir(i).name ' -i f -o fstc -so siemens'])
>
> system(['mc-sess -s 'funcdir(i).name ' -fstem fstc -fmcstem fstcmc 
> -per-run'])
>
> This seems to work.
>
> My problem is how do I get the resulting fstcmc.ni.gz on to the 
> fsaverage surface using spherical alignment?
>
> Jan
>
>
>
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Re: [Freesurfer] tksurfer overlay threshold

[Douglas N Greve]

I'm not sure what you mean. optimal in what sense?
doug

On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote:
> Hi Fs experts,
>
> I had a quick question about settings thresholds of surface overlays 
> in Tksurfer. I am currently generating images of the thickness, volume 
> and surface area of individual subjects, and would like to know if 
> there are optimal minimum and maximum threshold values to be set for 
> different surfaces. For example, when overlaying thickness (from 
> /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see 
> attached); however I'm not sure this same threshold holds up in the 
> other surfaces (e.g. surface area).
>
> In summary, is there an optimal way to determine what this min. and 
> max. threshold should be in function of the distribution displayed in 
> the threshold window (see attached, on the left)?
>
> Thank you!
>
> Gabriella
>
>
> ___
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface

[Douglas N Greve]

It looks like you made your txt file under windows which creates an 
obscure situation where there are carriage returns instead of line feeds 
and that causes the error. If you run 'more my_parcstats.txt' you see a 
bunch of ^M strings. So, you'll need to recreate it under a linux system.

doug

On 03/03/2015 05:50 PM, Jin, Tony wrote:
> Hi Dr. Greve (and co.),
>
> Good to hear that I’m using a proper command, but alas, visualizing 
> the surface overlay file using tksurfer confirmed that my stats didn’t 
> transfer. I believe I’m calling tksurfer correctly, since I replaced 
> the lh.parcstats file with lh.thickness, and a cortical thickness heat 
> map overlaid just fine.
>
> Would you please confirm that my parcstats.txt file is arranged 
> correctly? It is an ascii file with 36 lines. Here are the first few:
>
> ctx-lh-bankssts 0.905
> ctx-lh-caudalanteriorcingulate 0.838
> ctx-lh-caudalmiddlefrontal 0.922
> ctx-lh-cuneus 0.892
>
> And here are my calls:
>
> > To generate overlay file:
> mris_convert --annot lh.aparc.annot --parcstats parcstats.txt lh.pial 
> *lh.parcstats* <— new desired annotation file
>
> > To visualize overlay file mapped onto lh.pial surface using Tksurfer:
> tksurfer  lh pial -overlay *lh.parcstats*
>
> > To convert overlay file to ASCII for validation:
> mris_convert -c *lh.parcstats* lh.pial lh.parcstats.asc
>
> I tried doing this with version 5.3.0 on both Mac and Linux platforms 
> and got the same results (zeroes across all vertices). If it helps, 
> I’ve attached both my —parcstats text file and the resulting overlay 
> file.  Any ideas as to how I can successfully transfer my stats onto a 
> surface overlay file?
>
> Thank you for your assistance,
> Tony
>
> Tony Jin
> Data Technician
> Dept. of Psychiatry
> Stony Brook Medicine
>
> From: Douglas N Greve  <mailto:gr...@nmr.mgh.harvard.edu>>
> Reply-To: "freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Tuesday, March 3, 2015 at 11:43 AM
> To: "freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface
>
>
> That is the right way (or one of them). Did you look at the result in
> tksurfer?
>
> On 03/03/2015 11:34 AM, Jin, Tony wrote:
>
> Hi all,
>
> I’d like to map my own stats (one value per Desikan-Killiany region)
> onto a subject's surface file, to create a figure similar to the
> following:
> 
> http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001&req=4
>
> To do this, I tried to create a "scalar overlay file" using
> mris_convert’s --parcstats option, per the following mris_convert
> example:
>
> “”"
> Create a scalar overlay file where each parcellation region
> contains a single value:
>mris_convert \
> --annot lh.aparc.annot \
> --parcstats lh.parcstats.txt \
> lh.white \
> lh.parcstats
>
> (...)
>
> --parcstats  is the name of text file containing label/val
> pairs, where label is an annot name and val is a value associated
> with
> that label.
> “”"
>
> However, looking at the output file, stats didn’t seem to map to any
> vertices; instead, I observed zeroes across all in both Freeview and
> after conversion to ASCII (see first few lines below). I tried a few
> other ways to delimit the “label/val” pairs of the "--parcstats"
> file,
> including using tab, space, and forward-slash, but each way seemed to
> produce the same results:
>
> 000 -10.67346 -71.19921 6.09064 0.0
> 001 -11.29567 -71.20504 6.32133 0.0
> 002 -12.26970 -71.62605 6.00416 0.0
> 003 -13.11823 -71.40913 6.45834 0.0
> 004 -14.22002 -71.39742 6.28750 0.0
>
> So, I wonder: is using mris_convert with the --parcstats flag a
> correct way to create such a map? If so, what could have gone wrong?
> If not, what’s the easiest way to map my own regional stats onto a
> surface?
>
> Your expertise is greatly appreciated;
>
> Thanks and all the best,
>
> Tony Jin
> Data Technician
> Dept. of Psychiatry
> Stony Brook Medicine
>
>
> This e-mail message, including any attachments, is for the sole
> use of
> the intended recipient(s) and may contain confidential and privileged
> information. Any unauthorized review, use, disclosure or distribution
> 

Re: [Freesurfer] order of fMRI prepro

[Douglas N Greve]

My conclusion at the time that I put the stream together (15 or so years 
ago!) was that there was not a clear case to be made for doing it in 
either order when using an interleaved acquisition. When using a 
sequential acq, then it is clear that you do mc first then stc. Given 
that a strong case could not be made for stc then mc for interleaved and 
that stc then mc is definitely wrong for sequential, I opted to go with 
mc then stc. I don't remember testing for differences when the order is 
changed.

doug

On 03/04/2015 08:52 AM, Jan Willem Koten wrote:
> Dear Doug,
> I have a small question.
> What is the reason that FsFast does motion correction first and then 
> slice time correction?
> Does it really make a lot of difference if you change the order of the 
> preprocessing or is this just some ideological stuff?
> P.S.
> Excuse me for writing your name wrongly in my previous email.
> Thank you for quick response.
> I am very pleased that one can run FsFast so flexibel.
>
>
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-- 
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
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Re: [Freesurfer] fsFast by Octave - minor problems

[Douglas N Greve]

Thanks Antonin, I've incorporated the rho1 change into fast_selxavg3.m. 
Was there a change that would fix the parfile problem?

On 03/04/2015 08:00 AM, Antonin Skoch wrote:
> Dear Freesurfer experts,
>
> I run fsFast by Octave and I came across minor problems, which are 
> specific to Octave, to get it to work:
>
> I needed to update Octave from my default version 3.2.4 to version 
> 3.8.1. (version 3.2.4. did not have required textread function).
>
> Paradigm file cannot have trailing newline in the end (this is not 
> problem in MATLAB). fast_ldpar4.m then fails in the reading paradigm 
> file in the while loop starting at line 62.
>
> When there is only one run in FSD directory, the fast_selxavg3.m fails 
> at line 574, since Octave does not allow to mean across non-existent 
> (4th) dimension.
>
> Simple modification of the code like
>
> if (size(rho1.vol,4)==1)
>   rho1mn.vol= rho1.vol
> else
>   rho1mn.vol = mean(rho1.vol,4);
> end
>
> solved the problem in my case.
>
> Regards,
>
> Antonin Skoch
> Institute for Clinical and Experimental Medicine
> National Institute for Mental Health
> Czech Republic
>
>
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-- 
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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
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Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

[Douglas N Greve]

mris_preproc might work. You could also use mri_concat (mris_preproc is 
a front end for mri_concat)

On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote:
>
> Am 03.03.2015 um 14:42 schrieb Douglas N Greve :
>
>> Some of this Martin will have to comment on, but my comments below
>>
>> On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
>>> Hey Doug,
>>>
>>> thanks again! That means, I would do something like:
>>>
>>> 1.) construct longitudinal qdec table
>>> - only use fsid, fsid-base, and years/age columns
>>> - substract the average age of the one-time point subjects from years/age 
>>> value for every subject at every time point
>>>
>>> 2.) run long_mris_slopes
>>> - use the --do-avg flag?
>> Yes, I think so
>>> 3.) concatenate the output files from 2) and the maps from the one-time 
>>> point subjects with mris_preproc
>>> - use --is flag to select maps by specifying full path
>> What command are you talking about to do the concatenation?
> mris_preproc, I thought.
>
> Thanks for your help,
>
> Janosch
>
>> Otherwise sounds right. Make sure you use the average of the time points 
>> from long_mris_slopes and not the slope.
>>> 4.) run mri_glmfit
>>> - use --osgm flag for one-sample group mean
>> Yes
>>> 5.) replace sig.mgz file with the one from LME analysis and run 
>>> mri_glmfit-sim
>> Yes
>>> Is that correct? (especially, is using --do-avg what you meant by taking 
>>> the offset)
>>>
>>> Thanks,
>>>
>>> Janosch
>>>
>>>
>>> Am 03.03.2015 um 08:32 schrieb Douglas N Greve :
>>>
>>>> I don't know, esp since it is an approximation to begin with. An 
>>>> alternative is to take the offsets from your multi-time-point subjects and 
>>>> the single maps from your subjects with one time point and run that 
>>>> through the one-sample-group-mean (--osgm in mri_glmfit). If you go this 
>>>> route, then you should subtract the mean age of the one time-point 
>>>> subjects from the age of the multi-time point subjects before the 1st 
>>>> stage of analysis.
>>>>
>>>> doug
>>>>
>>>>
>>>> On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote:
>>>>> Hi Doug,
>>>>>
>>>>> thank you very much for your answer!
>>>>>
>>>>> Am 02.03.2015 um 11:30 schrieb Douglas N Greve 
>>>>> :
>>>>>
>>>>>> You would do the long analysis using a random effects analysis.
>>>>> OK, so basically do 2-stage modeling 
>>>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), 
>>>>> right?
>>>>>
>>>>>> For each subject you can get a slope (this won't work if the subject 
>>>>>> only has 1 time point), then concatenate the slopes into a file and run 
>>>>>> mri_glmfit, then follow the procedures from the archive email you 
>>>>>> reference.
>>>>> One quarter of my subjects only has one measurement time point. Can I 
>>>>> still use this method (which would only consider the 3/4 of the subjects) 
>>>>> to correct clusters found in the whole group? Or would it only be valid 
>>>>> for correcting clusters from an LME model for the reduced group?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Janosch
>>>>>
>>>>>> doug
>>>>>>
>>>>>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote:
>>>>>>> Hi Doug and others,
>>>>>>>
>>>>>>> I would like apply (Monte Carlo simulation) cluster correction (as 
>>>>>>> opposed to the implemented vertex-wise FDR correction) on the results 
>>>>>>> from a longitudinal study I analyzed using the LME toolbox. The design 
>>>>>>> is unbalanced (different number of time points, from 1 to 4, per 
>>>>>>> subject).
>>>>>>>
>>>>>>> In this thread 
>>>>>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html)
>>>>>>>  you, Doug, suggested, if I understand correctly:
>>>>>>>
>>>>>>> - concatenating the images using `mris_preproc --paired-diff`
>>>>>>> - smooth with the same kernel size as used in

[Freesurfer] Fwd: OHBM Glass Brain Award Reminder: Nomination Deadline March 13th

[Douglas N Greve]

fyi


 Forwarded Message 
Subject:OHBM Glass Brain Award Reminder: Nomination Deadline March 13th
Date:   Wed, 04 Mar 2015 11:20:59 -0600
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu





*ORGANIZATION FOR HUMAN BRAIN MAPPING
GLASS BRAIN AWARD*
/A lifetime achievement award in the field of human brain mapping/

Dear OHBM Member,

As a reminder, the deadline to submit nominations for the Organization 
for Human Brain Mapping Glass Brain Award is *next week, Friday, March 
13th*.

This award has been established to recognize lifetime achievement by 
leading researchers using or facilitating neuroimaging to discover 
original and influential findings regarding the organization and 
function of the human brain. today.

The complete nomination process and information can be found on our 
website. 

We look forward to your involvement in the nomination process.  Please 
contact the OHBM Executive Office at i...@humanbrainmapping.org 
 with any questions.

Sincerely,

JoAnn Taie
Executive Director
Organization for Human Brain Mapping (OHBM)



Organization for Human Brain Mapping (OHBM)
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
i...@humanbrainmapping.org 
www.humanbrainmapping.org 

To opt out of OHBM emails, contact the OHBM Executive Office at 
i...@humanbrainmapping.org .



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Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas N Greve]

#1 is probably better. BTW, why are you changing format from w to curv? 
Why use curv at all? I'd use mgz or nifti.



On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> Thank you Doug for precisely helping me on smooth detailed command.
>
> Concerning projection on fsaverage, is it better, worse or equivalent 
> to do (1) or (2) ?
>
> (1)
>
> */# Project and smooth onto anatomical surface/* (--surf mid : mean 
> surface between pial and white)
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o 
> lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
>
> mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
>
> mv ${DIR}/surf/lh.fwhm${FWHM}.intensity 
> ${DIR}/ictus/lh.fwhm${FWHM}.intensity
>
> rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
>
> *# Resample cbf to fsaverage*
>
> mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg 
> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg 
> --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval 
> lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
>
>
> (2)
>
> */# Project and smooth onto fsaverage/*
> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject 
> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o 
> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> /
> */# Smooth/*
> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i 
> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask 
> brain.fsaverage.lh.mgh//
> /
>
> Many thanks in advance !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-02 21:13 GMT+01:00 Douglas N Greve  <mailto:gr...@nmr.mgh.harvard.edu>>:
>
>
> On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Doug,
> >
> > Thank you for helping !
> >
> > Yes I directly used the regheader option because in the steps
> before I
> > already registered ASL maps on anatomical T1.
> >
> > The brain.fsaverage.lh.mgh come from the projection of the T1 brain
> > mask (dilated by 1) on the fsaverage.
> >
> > 1) So isn't it better to project first on the anatomical subject
> then
> > on fsaverage than what I've done ?
> This is what is done internally when you spec a target subject that is
> not the same as the source subject.
> >
> > 2) Smoothing with mris_fwhm is a good way with --mask option ?
> Yes, though I don't think that masking will have an effect the way you
> created the mask (everything will be in the mask). I would use
> --cortex
> to smooth only within cortex (and so exclude the medial wall).
> doug
>
> >
> > Thank you for your precious advices !
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-01 19:45 GMT+01:00 Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>:
> >
> >
> > Basically looks ok. The only things that jump out at me are that
> > you are using regheader (I would create a registration file with
> > bbregister rather than assuming that there was no motion between
> > the anatomical and the ASL). Where did
> brain.fsaverage.lh.mgh come
> > from?
> > doug
> >
> >
> >
> > On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:
> >> Dear Freesurfer's experts,
> >>
> >> I computed some perfusion maps from ASL data. These perfusion
> >> maps were registered on anatomical T1 and I would like to
> make a
> >> group analysis on surfaces. Please find below my actual
> commands
> >> in order to project these volumic maps on fsaverage then smooth
> >> the data projected on fsaverage :
> >>
> >> *Project CBF maps on fsaverage* :
> >> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> >> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> >> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg
> sp

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas N Greve]

Also, you can do everything in one vol2surf command with --trgsubject 
fsaverage. It is identical to doing it in two steps
On 03/05/2015 08:12 AM, Matthieu Vanhoutte wrote:
> *Update from precedent mail*
>
> Concerning projection on fsaverage, is it better, worse or equivalent 
> to do (1) or (2) ?
>
> (1)
>
> */# Project and smooth onto anatomical surface/* (--surf mid : mean 
> surface between pial and white)
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o 
> lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
>
> mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
>
> *# Resample cbf to fsaverage*
>
> mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg 
> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg 
> --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval 
> lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
>
>
> (2)
>
> */# Project and smooth onto fsaverage/*
> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject 
> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o 
> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> /
> */# Smooth/*
> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i 
> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask 
> brain.fsaverage.lh.mgh//
> /
>
> Many thanks in advance !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-05 14:10 GMT+01:00 Matthieu Vanhoutte 
> mailto:matthieuvanhou...@gmail.com>>:
>
> Thank you Doug for precisely helping me on smooth detailed command.
>
> Concerning projection on fsaverage, is it better, worse or
> equivalent to do (1) or (2) ?
>
> (1)
>
> */# Project and smooth onto anatomical surface/* (--surf mid :
> mean surface between pial and white)
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
>
> mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
>
> mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> ${DIR}/ictus/lh.fwhm${FWHM}.intensity
>
> rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
>
> *# Resample cbf to fsaverage*
>
> mri_surf2surf --srcsubject /subj_id/// --srchemi lh
> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh
> --trgsurfreg sphere.reg --sval /lh.fwhm3.cbf/// --sfmt curv
> --noreshape --no-cortex --tval lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
>
>
> (2)
>
> */# Project and smooth onto fsaverage/*
> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> /
> */# Smooth/*
> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh
> --mask brain.fsaverage.lh.mgh//
> /
>
>     Many thanks in advance !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-02 21:13 GMT+01:00 Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>>:
>
>
> On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Doug,
> >
> > Thank you for helping !
> >
> > Yes I directly used the regheader option because in the
> steps before I
> > already registered ASL maps on anatomical T1.
> >
> > The brain.fsaverage.lh.mgh come from the projection of the
> T1 brain
> > mask (dilated by 1) on the fsaverage.
> >
> > 1) So isn't it better to project first on the anatomical
> subject then
> > on fsaverage than what I've done ?
> This is what is done internally when you spec a target subject
> that is
> not the same as the source subject.
> >
> > 2) Smoothing with mris_fwhm is a good way with --mask option ?
> Yes, though I don't think that masking will have an effect the
> way you
> created the mask (everything will be in the mask). I would use
> --cortex
> to smooth only within cortex (and so exclude the medial wall).
> doug
>
>  

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

[Douglas N Greve]

You can also get the cras from

mri_info --cras orig.mgz





On 03/04/2015 07:35 PM, Bruce Fischl wrote:
> hmmm, not sure why. If this is a problem we can certainly change it, 
> just let us know
> On Thu, 5 Mar 2015, Krieger, Donald N. wrote:
>
>>
>> Hi Zack,
>>
>>
>>
>> It looks like mris_info send that matrix out on the error output 
>> rather than
>> the standard output.
>>
>> I just tried it and you can get it by redirecting both to your file like
>> this:
>>
>> Try  mris_info lh.pial >& lh_info.txt
>>
>>
>>
>> Regards,
>>
>>
>>
>> Don
>>
>>
>>
>> Signature0001
>>
>> Don Krieger, Ph.D.
>>
>> Department of Neurological Surgery
>>
>> University of Pittsburgh
>>
>>
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary
>> Greenberg
>> Sent: Wednesday, March 04, 2015 7:05 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate
>> shift
>>
>>
>>
>> Thanks bruce. It will work out fine if I can just pull out that c_(ras)
>> array in a pipelined way to apply it to the ascii data.
>>
>>
>>
>> I'm struggling a bit to achieve that though. I think because mris_info
>> outputs the tables of *_(ras) info in a strange way. For example, if 
>> I try
>> to cat the output of mris_info to a txt file: 'mris_info lh.pial >
>> lh_info.txt', the text file will contain everything except the 
>> *_(ras) info
>> table that you see if you just call the command by itself:
>>
>>
>>
>> volume geometry:
>>
>> extent  : (256, 256, 256)
>>
>> voxel   : ( 1.,  1.,  1.)
>>
>> x_(ras) : (-1.,  0.,  0.)
>>
>> y_(ras) : ( 0.,  0., -1.)
>>
>> z_(ras) : ( 0.,  1.,  0.)
>>
>> c_(ras) : (-1.6000, -5.1750, -15.3313)
>>
>> file: ../mri/filled-pretess255.mgz
>>
>>
>>
>> Are there any mris_info experts on the team who might know how to 
>> circumvent
>> this?
>>
>>
>>
>> thanks again for your help!
>>
>> -zack
>>
>>
>>
>> On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl 
>> 
>> wrote:
>>
>> Hi Zack
>>
>> the ascii format I don't think supports the c_ras info, which is why 
>> you see
>> a shift
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 4 Mar 2015, Zachary Greenberg wrote:
>>
>> Ok I figured out that this shift corresponds to the c_(RAS) value in the
>> header of lh.pial, which you can get with 'mris_info lh.pial'
>> Alternatively you can get the first coordinate and subtract it from the
>> first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'
>>
>> Is there a way I'm not thinking of to output c_(RAS) directly using
>> mris_info or a bash command (cat grep)?
>>
>> Thanks again,
>>
>> -zack
>>
>> On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
>>  wrote:
>>   Hi all,
>> I discovered that converting the mesh data from freesurfer lh.pial
>> format to ascii (.asc) causes a shift in the coordinates of the mesh.
>> You can see this by overlaying the two surfaces in freeview, and
>> looking at the difference between the [0 0 0] surface RAS coordinate
>> in lh.pial vs lh.pial.asc.
>>
>> The shift is not consistent across different subjects. I'm wondering
>> if there is a way to fix this, or if there is some regularity in the
>> coordinate shift that can be used to correct (that I'm not seeing).
>>
>> For example the difference coordinates between lh.pial and lh.pial.asc
>> in two different subjects are:
>> [  1.6 ,   5.18,  15.33]
>> [2.02, -15.80, 0.18]
>>
>>
>> Thanks for any help you can offer!
>>
>> -zack
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> 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
&g

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas N Greve]

Just add --trgsubject fsaverage to the mri_vol2surf command line. Run 
mri_vol2surf with --help to get more info

On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> Thank you Douglas but I don't understand the solution you propose. 
> Could you please show me the command lines ?
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-05 16:45 GMT+01:00 Douglas N Greve  <mailto:gr...@nmr.mgh.harvard.edu>>:
>
>
>
> #1 is probably better. BTW, why are you changing format from w to
> curv?
> Why use curv at all? I'd use mgz or nifti.
>
>
>
> On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> > Thank you Doug for precisely helping me on smooth detailed command.
> >
> > Concerning projection on fsaverage, is it better, worse or
> equivalent
> > to do (1) or (2) ?
> >
> > (1)
> >
> > */# Project and smooth onto anatomical surface/* (--surf mid : mean
> > surface between pial and white)
> >
> > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint
> --surf-fwhm 3
> >
> > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/
> lh.fwhm3.cbf//
> >
> > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> > ${DIR}/ictus/lh.fwhm${FWHM}.intensity
> >
> > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
> >
> > *# Resample cbf to fsaverage*
> >
> > mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg
> > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
> > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex
> --tval
> > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
> >
> >
> > (2)
> >
> > */# Project and smooth onto fsaverage/*
> > /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> > fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> > lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
> > /
> > */# Smooth/*
> > /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> > lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask
> > brain.fsaverage.lh.mgh//
>     > /
> >
> > Many thanks in advance !!
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-02 21:13 GMT+01:00 Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>:
> >
> >
> > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > Dear Doug,
> > >
> > > Thank you for helping !
> > >
> > > Yes I directly used the regheader option because in the steps
> > before I
> > > already registered ASL maps on anatomical T1.
> > >
> > > The brain.fsaverage.lh.mgh come from the projection of the
> T1 brain
> > > mask (dilated by 1) on the fsaverage.
> > >
> > > 1) So isn't it better to project first on the anatomical
> subject
> > then
> > > on fsaverage than what I've done ?
> > This is what is done internally when you spec a target
> subject that is
> > not the same as the source subject.
> > >
> > > 2) Smoothing with mris_fwhm is a good way with --mask option ?
> > Yes, though I don't think that masking will have an effect
> the way you
> > created the mask (everything will be in the mask). I would use
> > --cortex
> > to smooth only within cortex (and so exclude the medial wall).
> > doug
> >
> > >
> > > Thank you for your precious advices !
> > >
> > > Best regards,
> > >
> > > -
> > > Matthieu Vanhoutte, MSc
> > > Research Engineer - Department of Neuroradiology
> > > Regional University Hosp

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas N Greve]

w format is the paint format output from your vol2surf command. We tend 
not to use either w or curv formats anymore
On 03/05/2015 11:19 AM, Matthieu Vanhoutte wrote:
> I don't know if we are talking about the same thing.
>
> In precedent mail you told me solution #1 was better :
>
> */# Project and smooth onto anatomical surface/* (--surf mid : mean 
> surface between pial and white)
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o 
> lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3
>
> mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/ lh.fwhm3.cbf//
>
> *# Resample cbf to fsaverage*
>
> mri_surf2surf --srcsubject /subj_id/// --srchemi lh --srcsurfreg 
> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg 
> --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval 
> lh.fwhm3.fsaverage.cbf.mgh --tfmt curv
>
>
> /
> But you told me :
> /BTW, why are you changing format from w to curv?
> Why use curv at all? I'd use mgz or nifti.
>
> /
> At this point I don't know what this means ?
>
> Thanks,
>
> Matthieu
>
> 2015-03-05 17:12 GMT+01:00 Douglas N Greve  <mailto:gr...@nmr.mgh.harvard.edu>>:
>
>
> Just add --trgsubject fsaverage to the mri_vol2surf command line. Run
> mri_vol2surf with --help to get more info
>
> On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> > Thank you Douglas but I don't understand the solution you propose.
> > Could you please show me the command lines ?
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-05 16:45 GMT+01:00 Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>:
> >
> >
> >
> > #1 is probably better. BTW, why are you changing format from
> w to
> > curv?
> > Why use curv at all? I'd use mgz or nifti.
> >
> >
> >
> > On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> > > Thank you Doug for precisely helping me on smooth detailed
> command.
> > >
> > > Concerning projection on fsaverage, is it better, worse or
> > equivalent
> > > to do (1) or (2) ?
> > >
> > > (1)
> > >
> > > */# Project and smooth onto anatomical surface/* (--surf
> mid : mean
> > > surface between pial and white)
> > >
> > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> > > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint
> > --surf-fwhm 3
> > >
> > > mris_w_to_curv subj_id/ / lh ///lh.fwhm3.cbf.w/
> > lh.fwhm3.cbf//
> > >
> > > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> > > ${DIR}/ictus/lh.fwhm${FWHM}.intensity
> > >
> > > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w
> > >
> > > *# Resample cbf to fsaverage*
> > >
> > > mri_surf2surf --srcsubject /subj_id/// --srchemi lh
> --srcsurfreg
> > > sphere.reg --trgsubject fsaverage --trghemi lh
> --trgsurfreg sphere.reg
> > > --sval /lh.fwhm3.cbf/// --sfmt curv --noreshape
> --no-cortex
> > --tval
> > > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/
> > >
> > >
> > > (2)
> > >
> > > */# Project and smooth onto fsaverage/*
> > > /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject
> > > fsaverage --interp trilin --projfrac 0.5 --hemi lh --o
> > > lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg
> sphere.reg//
> > > /
> > > */# Smooth/*
> > > /mris_fwhm --s fsaverage --hemi lh --smooth-only --i
> > > lh.fsaverage.cbf.mgh --fwhm 3 --o
> lh.fwhm3.fsaverage.cbf.mgh --mask
> > > brain.fsaverage.lh.mgh//
> > > /
> > >
> > > Many thanks in advance !!
> > >
> > > Best regards,
> > >
> > > -
> > > Mat