[Freesurfer] mri_surf2surf to fsaverageX introduces offset
Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white > SURFACE INFO > type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 118611 > num faces : 237218 > num strips : 0 > surface area: 77595.6 > AvgVtxArea 0.654202 > AvgVtxDist 0.885026 > StdVtxDist 0.251941 > ctr : (-33.3535, -11.9536, 42.7693) > vertex locs : surfaceRAS > talairch.xfm: > 1.045 -0.093 -0.014 1.081; > 0.099 1.095 0.070 -4.263; > 0.010 -0.083 1.290 -41.092; > 0.000 0.000 0.000 1.000; > surfaceRAS to talaraiched surfaceRAS: > 1.045 -0.093 -0.014 1.177; > 0.099 1.095 0.070 13.377; > 0.010 -0.083 1.290 -49.756; > 0.000 0.000 0.000 1.000; > talairached surfaceRAS to surfaceRAS: > 0.949 0.081 0.006 -1.900; > -0.085 0.902 -0.050 -14.449; > -0.013 0.058 0.772 37.650; > 0.000 0.000 0.000 1.000; > 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) : ( 0.0989, 0.9660, 0.9027) > ... mris_info lh.white.ico6 > SURFACE INFO > type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 40962 > num faces : 81920 > num strips : 0 > surface area: 75477.4 > AvgVtxArea 1.842620 > AvgVtxDist 1.573724 > StdVtxDist 0.523314 > ctr : (-33.3983, -12.0872, 42.7743) > vertex locs : surfaceRAS > volume geometry info is either not contained or not valid. > ... <>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Contrast and F-test
Hi all, I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous) 0 1 -1 0 0 Would this be the correct way for the F-test: 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 Thanks! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Anastasia,
This Ubuntu-related error is a tricky one.
I changed the first line in those files you told me and reran trac-all. All
three steps of trac-all ran without any errrors. I checked the FA maps and the
MNI registration and everything looks fine.
After running trac-all -bedp, the step stopped with the following line:
"Queuing post processing stage
/usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated
${subjdir}.bedpostX/monitor."
I think it's fine, because line 439 is the last line of the script, so it
worked well.
Maybe I have to change all ".sh" in the files to ".bash" to get all messages.
Thank you so much for your big help.
I hope I didn't cause you much trouble with my problems and questions.
Sincerely,
Florian
>>> Anastasia Yendiki 20.08.13 17.56 Uhr >>>
This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
"/bin/bash" on the first line of those two scripts.
On Tue, 20 Aug 2013, Borsodi Florian wrote:
> Hi Anastasia,
>
> Yes, i am running this on ubuntu 12.04.
>
> Sincerely,
> Florian
>
> >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>>
>
> Hi Florian - Are you running this on an ubuntu system by any chance?
>
> a.y
>
> On Tue, 20 Aug 2013, Borsodi Florian wrote:
>
> > Hi Anastasia,
> >
> > Thank you for your help.
> > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the
> > command "xfmrot" changed the dots back to
> > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8
> > and reran trac-all. After changing the
> > system language everything was genereted correctly and trac-all -prep ran
> > without any errors.
> > I'm so glad.
> >
> > Then, I started the next step "trac-all -bedp" and got a syntax error
> > "/usr/local/freesurfer/bin/bedpostx_mgh: 131:
> > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I
> > also attached the the logfile. I was
> reading
> > about this error in the mail archive. Would I have to run "bedpostx"
> > outside of tracula ?
> >
> > Sincerely,
> > Florian
> >
> > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>>
> >
> > Hi Florian - Can you please change the decimal commas to points and try
> > again?
> >
> > a.y
> >
> > On Mon, 19 Aug 2013, Borsodi Florian wrote:
> >
> > > Hi Anastasia,
> > >
> > > Here are the bvec and bval files you asked me about.
> > >
> > > Sincerely,
> > > Florian
> > >
> > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>>
> > >
> > > Hi Florian - Can you please also attach the bvecs/bvals files from the
> > > dmri directory?
> > >
> > > Thanks,
> > > a.y
> > >
> > > On Sun, 18 Aug 2013, Borsodi Florian wrote:
> > >
> > > > Hi Anastasia,
> > > >
> > > > Thanks for your help. I renamed the directories and reran trac-all. It
> > > > worked for the moment.
> > > > However, then I got another error: "bvecs and bvals don't have the same
> > > > number of entries."
> > > > I don't know why, because they actually have the same number of entries.
> > > >
> > > > I attached the logfile so that you may see what is going on. The error
> > > > occours at line 1463.
> > > >
> > > > Thank you in advance for your help.
> > > >
> > > > Sincerely,
> > > > Florian
> > > >
> > > >
> > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>>
> > > >
> > > > Hi Florian - I see what's going on. Can you please rename the directory
> > > > /data/physics/florian/nii into something that doesn't include "nii", and
> > > > rerun? Because "nii" is a file extension, this confuses some of the
> > > > scripts.
> > > >
> > > > Thanks,
> > > > a.y
> > > >
> > > > On Thu, 15 Aug 2013, Borsodi Florian wrote:
> > > >
> > > > > Hi Anastasia
> > > > >
> > > > > I ran the command you sent me and it runs without any errors.
> > > > > I also attached the command line for you.
> > > > >
> > > > > Furthermore i ran data with 12 diffusion directions and i keep
> > > > > getting the
> > > > > same kind of problems.
> > > > >
> > > > > sincerely
> > > > > Florian
> > > > >
> > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr
> > > > >>>
> > > > >
> > > > > Hi Florian - Can you please run this command directly on the command
> > > > > line
> > > > > and see if there are any errors?
> > > > >
> > > > > flip4fsl
> > > > > /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz
> > > > > /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz
> > > > >
> > > > > Thanks,
> > > > > a.y
> > > > >
> > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote:
> > > > >
> > > > > > Hi Anastasia
> > > > > >
> > > > > > Thank you for your answer.
> > > > > >
> > > > > > Yes, those files exist.
> > > > > > I also extracted the bvec an bval files with anotther software then
> > > > > dcm2nii
> > > > > > and i keep getting the same kind of erro
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Florian - My guess is that everything ran fine and you don't need to
change anything else. Check that all the output files were created in the
dmri.bedpostX directory:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
a.y
On Thu, 22 Aug 2013, Borsodi Florian wrote:
Hi Anastasia,
This Ubuntu-related error is a tricky one.
I changed the first line in those files you told me and reran trac-all. All
three steps of trac-all ran without any errrors. I checked the FA maps and
the MNI registration and everything looks fine.
After running trac-all -bedp, the step stopped with the following line:
"Queuing post processing stage
/usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated
${subjdir}.bedpostX/monitor."
I think it's fine, because line 439 is the last line of the script, so it
worked well.
Maybe I have to change all ".sh" in the files to ".bash" to get all
messages.
Thank you so much for your big help.
I hope I didn't cause you much trouble with my problems and questions.
Sincerely,
Florian
>>> Anastasia Yendiki 20.08.13 17.56 Uhr >>>
This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
"/bin/bash" on the first line of those two scripts.
On Tue, 20 Aug 2013, Borsodi Florian wrote:
> Hi Anastasia,
>
> Yes, i am running this on ubuntu 12.04.
>
> Sincerely,
> Florian
>
> >>> Anastasia Yendiki 20.08.13 17.38 Uhr
>>>
>
> Hi Florian - Are you running this on an ubuntu system by any chance?
>
> a.y
>
> On Tue, 20 Aug 2013, Borsodi Florian wrote:
>
> > Hi Anastasia,
> >
> > Thank you for your help.
> > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But
the command "xfmrot" changed the dots back to
> > commas. So, I changed our system language from de_AUT.UTF-8 to
en_US.UTF-8 and reran trac-all. After changing the
> > system language everything was genereted correctly and trac-all -prep
ran without any errors.
> > I'm so glad.
> >
> > Then, I started the next step "trac-all -bedp" and got a syntax error
"/usr/local/freesurfer/bin/bedpostx_mgh: 131:
> > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. "
I also attached the the logfile. I was
> reading
> > about this error in the mail archive. Would I have to run "bedpostx"
outside of tracula ?
> >
> > Sincerely,
> > Florian
> >
> > >>> Anastasia Yendiki 19.08.13 17.54 Uhr
>>>
> >
> > Hi Florian - Can you please change the decimal commas to points and try
> > again?
> >
> > a.y
> >
> > On Mon, 19 Aug 2013, Borsodi Florian wrote:
> >
> > > Hi Anastasia,
> > >
> > > Here are the bvec and bval files you asked me about.
> > >
> > > Sincerely,
> > > Florian
> > >
> > > >>> Anastasia Yendiki 18.08.13 22.52
Uhr >>>
> > >
> > > Hi Florian - Can you please also attach the bvecs/bvals files from the
> > > dmri directory?
> > >
> > > Thanks,
> > > a.y
> > >
> > > On Sun, 18 Aug 2013, Borsodi Florian wrote:
> > >
> > > > Hi Anastasia,
> > > >
> > > > Thanks for your help. I renamed the directories and reran trac-all.
It
> > > > worked for the moment.
> > > > However, then I got another error: "bvecs and bvals don't have the
same
> > > > number of entries."
> > > > I don't know why, because they actually have the same number of
entries.
> > > >
> > > > I attached the logfile so that you may see what is going on. The
error
> > > > occours at line 1463.
> > > >
> > > > Thank you in advance for your help.
> > > >
> > > > Sincerely,
> > > > Florian
> > > >
> > > >
> > > > >>> Anastasia Yendiki 15.08.13 18.01
Uhr >>>
> > > >
> > > > Hi Florian - I see what's going on. Can you please rename the
directory
> > > > /data/physics/florian/nii into something that doesn't include "nii",
and
> > > > rerun? Because "nii" is a file extension, this confuses some of the
> > > > scripts.
> > > >
> > > > Thanks,
> > > > a.y
> > > >
> > > > On Thu, 15 Aug 2013, Borsodi Florian wrote:
> > > >
> > > > > Hi Anastasia
> > > > >
> > > > > I ran the command you sent me and it runs without any errors.
> > > > > I also attached the command line for you.
> > > > >
> > > > > Furthermore i ran data with 12 diffusion directions and i keep
getting the
> > > > > same kind of problems.
> > > > >
> > > > > sincerely
> > > > > Florian
> > > > >
> > > > > >>> Anastasia Yendiki 02.08.13
19.59 Uhr
> > > > >>>
> > > > >
> > > > > Hi Florian - Can you please run this command directly on the
command line
> > > > > and see if there are any errors?
> > > > >
> > > > > flip4fsl
> > > > >
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz
> > > > >
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz
> > > > >
> > > > > Thanks,
> > > > > a.y
> > > > >
> > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote:
> > > > >
> > > > > > Hi Anastasia
> > > > > >
> > > > > >
Re: [Freesurfer] [tracula] error running trac-all -prep
Hi Anastasia,
I checked the dmri.bedpostx directory.
Unless "nodif_brain", all files are there.
Sincerely,
Florian
>>> Anastasia Yendiki 22.08.13 15.06 Uhr >>>
Hi Florian - My guess is that everything ran fine and you don't need to
change anything else. Check that all the output files were created in the
dmri.bedpostX directory:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
a.y
On Thu, 22 Aug 2013, Borsodi Florian wrote:
> Hi Anastasia,
>
> This Ubuntu-related error is a tricky one.
> I changed the first line in those files you told me and reran trac-all. All
> three steps of trac-all ran without any errrors. I checked the FA maps and
> the MNI registration and everything looks fine.
>
> After running trac-all -bedp, the step stopped with the following line:
> "Queuing post processing stage
> /usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated
> ${subjdir}.bedpostX/monitor."
> I think it's fine, because line 439 is the last line of the script, so it
> worked well.
> Maybe I have to change all ".sh" in the files to ".bash" to get all
> messages.
>
> Thank you so much for your big help.
> I hope I didn't cause you much trouble with my problems and questions.
>
> Sincerely,
> Florian
>
> >>> Anastasia Yendiki 20.08.13 17.56 Uhr >>>
>
> This is an Ubuntu-related error that has surfaced recently because in
> Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
> edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
> $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
> "/bin/bash" on the first line of those two scripts.
>
> On Tue, 20 Aug 2013, Borsodi Florian wrote:
>
> > Hi Anastasia,
> >
> > Yes, i am running this on ubuntu 12.04.
> >
> > Sincerely,
> > Florian
> >
> > >>> Anastasia Yendiki 20.08.13 17.38 Uhr
> >>>
> >
> > Hi Florian - Are you running this on an ubuntu system by any chance?
> >
> > a.y
> >
> > On Tue, 20 Aug 2013, Borsodi Florian wrote:
> >
> > > Hi Anastasia,
> > >
> > > Thank you for your help.
> > > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But
> the command "xfmrot" changed the dots back to
> > > commas. So, I changed our system language from de_AUT.UTF-8 to
> en_US.UTF-8 and reran trac-all. After changing the
> > > system language everything was genereted correctly and trac-all -prep
> ran without any errors.
> > > I'm so glad.
> > >
> > > Then, I started the next step "trac-all -bedp" and got a syntax error
> "/usr/local/freesurfer/bin/bedpostx_mgh: 131:
> > > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. "
> I also attached the the logfile. I was
> > reading
> > > about this error in the mail archive. Would I have to run "bedpostx"
> outside of tracula ?
> > >
> > > Sincerely,
> > > Florian
> > >
> > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr
> >>>
> > >
> > > Hi Florian - Can you please change the decimal commas to points and try
> > > again?
> > >
> > > a.y
> > >
> > > On Mon, 19 Aug 2013, Borsodi Florian wrote:
> > >
> > > > Hi Anastasia,
> > > >
> > > > Here are the bvec and bval files you asked me about.
> > > >
> > > > Sincerely,
> > > > Florian
> > > >
> > > > >>> Anastasia Yendiki 18.08.13 22.52
> Uhr >>>
> > > >
> > > > Hi Florian - Can you please also attach the bvecs/bvals files from the
> > > > dmri directory?
> > > >
> > > > Thanks,
> > > > a.y
> > > >
> > > > On Sun, 18 Aug 2013, Borsodi Florian wrote:
> > > >
> > > > > Hi Anastasia,
> > > > >
> > > > > Thanks for your help. I renamed the directories and reran trac-all.
> It
> > > > > worked for the moment.
> > > > > However, then I got another error: "bvecs and bvals don't have the
> same
> > > > > number of entries."
> > > > > I don't know why, because they actually have the same number of
> entries.
> > > > >
> > > > > I attached the logfile so that you may see what is going on. The
> error
> > > > > occours at line 1463.
> > > > >
> > > > > Thank you in advance for your help.
> > > > >
> > > > > Sincerely,
> > > > > Florian
> > > > >
> > > > >
> > > > > >>> Anastasia Yendiki 15.08.13 18.01
> Uhr >>>
> > > > >
> > > > > Hi Florian - I see what's going on. Can you please rename the
> directory
> > > > > /data/physics/florian/nii into something that doesn't include "nii",
> and
> > > > > rerun? Because "nii" is a file extension, this confuses some of the
> > > > > scripts.
> > > > >
> > > > > Thanks,
> > > > > a.y
> > > > >
> > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote:
> > > > >
> > > > > > Hi Anastasia
> > > > > >
> > > > > > I ran the command you sent me and it runs without any errors.
> > > > > > I also attached the command line for you.
> > > > > >
> > > > > > Furthermore i ran data with 12 diffusion directions and i keep
> getting the
> > > > > > same kind of problems.
> > > > > >
> > > > > > sincerely
> > > > > > Florian
> > > > > >
> > > > > > >>> Anastasia Yendiki 02.08.13
> 19.59 Uhr
> > > > > >>>
> > > > > >
> > > > > > Hi Florian -
Re: [Freesurfer] Contrast and F-test
If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: > Hi all, > > I my manuscript, I examined the association between cognition and cortical > thickness. I first did this in three groups separately and then ran a F-test. > One of the reviewers, now wants me to examine the interaction between > cognition and education (all continuous). > > Would this be the correct contrast for each group separately (last two zeros > are for covariates, also continuous) > > 0 1 -1 0 0 > > Would this be the correct way for the F-test: > > 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 > 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 > > Thanks! > > Heidi > > > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jac...@maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FW: Contrast and F-test
Dear Doug, Thank you for the information. Sorry for not sending this to the list. Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? If I need to include all three of them, can you advise me on the contrasts? If it is only the product, I think I can use the same contrasts as before, right? Thanks Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:34 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast and F-test If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: > Hi all, > > I my manuscript, I examined the association between cognition and cortical > thickness. I first did this in three groups separately and then ran a F-test. > One of the reviewers, now wants me to examine the interaction between > cognition and education (all continuous). > > Would this be the correct contrast for each group separately (last two zeros > are for covariates, also continuous) > > 0 1 -1 0 0 > > Would this be the correct way for the F-test: > > 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 > 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 > > Thanks! > > Heidi > > > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jac...@maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: Contrast and F-test
you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: > Dear Doug, > Thank you for the information. Sorry for not sending this to the list. > Do you mean that I then have to include the three variables (covariate 1, > covariate 2, product of these two) or only the product in the fsgd file? > If I need to include all three of them, can you advise me on the contrasts? > If it is only the product, I think I can use the same contrasts as before, > right? > > Thanks > Heidi > > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jac...@maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Verzonden: donderdag 22 augustus 2013 16:34 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] Contrast and F-test > > If you want to test for an interaction between continuous variables, > then you should create a new regressor by multiplying them together then > test that regressor > doug > > > On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >> Hi all, >> >> I my manuscript, I examined the association between cognition and cortical >> thickness. I first did this in three groups separately and then ran a F-test. >> One of the reviewers, now wants me to examine the interaction between >> cognition and education (all continuous). >> >> Would this be the correct contrast for each group separately (last two zeros >> are for covariates, also continuous) >> >> 0 1 -1 0 0 >> >> Would this be the correct way for the F-test: >> >> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >> >> Thanks! >> >> Heidi >> >> >> Dr. Heidi Jacobs >> Postdoc researcher >> Faculty of Health, Medicine and Life Sciences >> School for Mental Health and Neurosciences >> Division Cognitive Neuropsychiatry and Clinical Neurosciences >> Alzheimer Center Limburg >> h.jac...@maastrichtuniversity.nl >> www.maastrichtuniversity.nl >> www.heidijacobs.nl >> >> Dr. Tanslaan 12, 6229 ET Maastricht >> P.O. Box 616, 6200 MD Maastricht, The Netherlands >> T +31 43 38 84 090 F +31 43 38 84 092 >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FW: FW: Contrast and F-test
Arrghh, again wrong email, sorry Thanks. I think I understand the rational behind it. Just to be sure, would this be correct: For each group separately 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - ICV) For the F-test (same order) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:46 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Contrast and F-test you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: > Dear Doug, > Thank you for the information. Sorry for not sending this to the list. > Do you mean that I then have to include the three variables (covariate 1, > covariate 2, product of these two) or only the product in the fsgd file? > If I need to include all three of them, can you advise me on the contrasts? > If it is only the product, I think I can use the same contrasts as before, > right? > > Thanks > Heidi > > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jac...@maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Verzonden: donderdag 22 augustus 2013 16:34 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] Contrast and F-test > > If you want to test for an interaction between continuous variables, > then you should create a new regressor by multiplying them together then > test that regressor > doug > > > On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >> Hi all, >> >> I my manuscript, I examined the association between cognition and cortical >> thickness. I first did this in three groups separately and then ran a F-test. >> One of the reviewers, now wants me to examine the interaction between >> cognition and education (all continuous). >> >> Would this be the correct contrast for each group separately (last two zeros >> are for covariates, also continuous) >> >> 0 1 -1 0 0 >> >> Would this be the correct way for the F-test: >> >> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >> >> Thanks! >> >> Heidi >> >> >> Dr. Heidi Jacobs >> Postdoc researcher >> Faculty of Health, Medicine and Life Sciences >> School for Mental Health and Neurosciences >> Division Cognitive Neuropsychiatry and Clinical Neurosciences >> Alzheimer Center Limburg >> h.jac...@maastrichtuniversity.nl >> www.maastrichtuniversity.nl >> www.heidijacobs.nl >> >> Dr. Tanslaan 12, 6229 ET Maastricht >> P.O. Box 616, 6200 MD Maastricht, The Netherlands >> T +31 43 38 84 090 F +31 43 38 84 092 >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ___ > Freesurfer 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-
Re: [Freesurfer] FW: FW: Contrast and F-test
both of those contrasts are correct doug On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: > Arrghh, again wrong email, sorry > > Thanks. I think I understand the rational behind it. > Just to be sure, would this be correct: > > For each group separately > 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - > ICV) > > For the F-test (same order) > 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 > > Heidi > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Verzonden: donderdag 22 augustus 2013 16:46 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] FW: Contrast and F-test > > you need to have all 3. If you want to examine the interaction, then you > need a new contrast to test the interaction. Set all to 0 except for the > interaction term > doug > > > On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: >> Dear Doug, >> Thank you for the information. Sorry for not sending this to the list. >> Do you mean that I then have to include the three variables (covariate 1, >> covariate 2, product of these two) or only the product in the fsgd file? >> If I need to include all three of them, can you advise me on the contrasts? >> If it is only the product, I think I can use the same contrasts as before, >> right? >> >> Thanks >> Heidi >> >> Dr. Heidi Jacobs >> Postdoc researcher >> Faculty of Health, Medicine and Life Sciences >> School for Mental Health and Neurosciences >> Division Cognitive Neuropsychiatry and Clinical Neurosciences >> Alzheimer Center Limburg >> h.jac...@maastrichtuniversity.nl >> www.maastrichtuniversity.nl >> www.heidijacobs.nl >> >> Dr. Tanslaan 12, 6229 ET Maastricht >> P.O. Box 616, 6200 MD Maastricht, The Netherlands >> T +31 43 38 84 090 F +31 43 38 84 092 >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Verzonden: donderdag 22 augustus 2013 16:34 >> Aan: freesurfer@nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] Contrast and F-test >> >> If you want to test for an interaction between continuous variables, >> then you should create a new regressor by multiplying them together then >> test that regressor >> doug >> >> >> On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >>> Hi all, >>> >>> I my manuscript, I examined the association between cognition and cortical >>> thickness. I first did this in three groups separately and then ran a >>> F-test. >>> One of the reviewers, now wants me to examine the interaction between >>> cognition and education (all continuous). >>> >>> Would this be the correct contrast for each group separately (last two >>> zeros are for covariates, also continuous) >>> >>> 0 1 -1 0 0 >>> >>> Would this be the correct way for the F-test: >>> >>> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >>> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >>> >>> Thanks! >>> >>> Heidi >>> >>> >>> Dr. Heidi Jacobs >>> Postdoc researcher >>> Faculty of Health, Medicine and Life Sciences >>> School for Mental Health and Neurosciences >>> Division Cognitive Neuropsychiatry and Clinical Neurosciences >>> Alzheimer Center Limburg >>> h.jac...@maastrichtuniversity.nl >>> www.maastrichtuniversity.nl >>> www.heidijacobs.nl >>> >>> Dr. Tanslaan 12, 6229 ET Maastricht >>> P.O. Box 616, 6200 MD Maastricht, The Netherlands >>> T +31 43 38 84 090 F +31 43 38 84 092 >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> _
Re: [Freesurfer] FW: FW: Contrast and F-test
Great!! Thank you so much! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 17:52 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test both of those contrasts are correct doug On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: > Arrghh, again wrong email, sorry > > Thanks. I think I understand the rational behind it. > Just to be sure, would this be correct: > > For each group separately > 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - > ICV) > > For the F-test (same order) > 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 > > Heidi > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Verzonden: donderdag 22 augustus 2013 16:46 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] FW: Contrast and F-test > > you need to have all 3. If you want to examine the interaction, then you > need a new contrast to test the interaction. Set all to 0 except for the > interaction term > doug > > > On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: >> Dear Doug, >> Thank you for the information. Sorry for not sending this to the list. >> Do you mean that I then have to include the three variables (covariate 1, >> covariate 2, product of these two) or only the product in the fsgd file? >> If I need to include all three of them, can you advise me on the contrasts? >> If it is only the product, I think I can use the same contrasts as before, >> right? >> >> Thanks >> Heidi >> >> Dr. Heidi Jacobs >> Postdoc researcher >> Faculty of Health, Medicine and Life Sciences >> School for Mental Health and Neurosciences >> Division Cognitive Neuropsychiatry and Clinical Neurosciences >> Alzheimer Center Limburg >> h.jac...@maastrichtuniversity.nl >> www.maastrichtuniversity.nl >> www.heidijacobs.nl >> >> Dr. Tanslaan 12, 6229 ET Maastricht >> P.O. Box 616, 6200 MD Maastricht, The Netherlands >> T +31 43 38 84 090 F +31 43 38 84 092 >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Verzonden: donderdag 22 augustus 2013 16:34 >> Aan: freesurfer@nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] Contrast and F-test >> >> If you want to test for an interaction between continuous variables, >> then you should create a new regressor by multiplying them together then >> test that regressor >> doug >> >> >> On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >>> Hi all, >>> >>> I my manuscript, I examined the association between cognition and cortical >>> thickness. I first did this in three groups separately and then ran a >>> F-test. >>> One of the reviewers, now wants me to examine the interaction between >>> cognition and education (all continuous). >>> >>> Would this be the correct contrast for each group separately (last two >>> zeros are for covariates, also continuous) >>> >>> 0 1 -1 0 0 >>> >>> Would this be the correct way for the F-test: >>> >>> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >>> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >>> >>> Thanks! >>> >>> Heidi >>> >>> >>> Dr. Heidi Jacobs >>> Postdoc researcher >>> Faculty of Health, Medicine and Life Sciences >>> School for Mental Health and Neurosciences >>> Division Cognitive Neuropsychiatry and Clinical Neurosciences >>> Alzheimer Center Limburg >>> h.jac...@maastrichtuniversity.nl >>> www.maastrichtuniversity.nl >>> www.heidijacobs.nl >>> >>> Dr. Tanslaan 12, 6229 ET Maastricht >>> P.O. Box 616, 6200 MD Maastricht, The Netherlands >>> T +31 43 38 84 090 F +31 43 38 84 092 >>> >>> ___ >>> 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/B
[Freesurfer] gradient table question for Tracula
Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components." (from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.VisualizationTool ). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6
Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I tried the commands in tutorial and got error message, listed as follows. Nevertheless, FS can read in volume and surface from GUI. Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04? 1. tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl 2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz Couldn't create output file .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, -1): could not open file a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory. Note: In fact, I can load segmentation volume from window. 3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert Thanks for your help, JoJo___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] gradient table question for Tracula
Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to do this on one of the data sets from your sequence just to make sure they're oriented correctly. Also, if the gradient vectors need flipping, the tracts from tracula will come out looking visibly wrong. So you'll know that something went wrong. Hope this helps, a.y On Thu, 22 Aug 2013, Salil Soman wrote: Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components."(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua lizationTool). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] gradient table question for Tracula
I have GE data and never had to make any changes to the gradient table. On 08/22/2013 01:05 PM, Anastasia Yendiki wrote: Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to do this on one of the data sets from your sequence just to make sure they're oriented correctly. Also, if the gradient vectors need flipping, the tracts from tracula will come out looking visibly wrong. So you'll know that something went wrong. Hope this helps, a.y On Thu, 22 Aug 2013, Salil Soman wrote: Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components."(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua lizationTool). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem with mris_ca_label (seg fault)
Dear Support line of free surfer, I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults Environment: FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: Fedora release 18 (Spherical Cow) Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped) Am I doing something wrong? How can I diagnose and fix this? Thanks D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with mris_ca_label (seg fault)
Hi Demian does this happen if you run it through recon-all? Bruce On Thu, 22 Aug 2013, Demian Wassermann wrote: > Dear Support line of free surfer, > > I have a problem when I try to apply a new atlas to the surfaces. Even with > the standard free surfer atlases it segfaults > > Environment: > > FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 > > RedHat release: Fedora release 18 (Spherical Cow) > > Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 > > Command: > $FREESURFER_HOME/bin/mris_ca_label -t > $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh > lh.sphere.reg > $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs > lh.test.annot > > > Output: > $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ > reading atlas from > /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... > reading color table from GCSA file > average std = 1.0 using min determinant for regularization = 0.011 > 0 singular and 384 ill-conditioned covariance matrices regularized > Segmentation fault (core dumped) > > > > > Am I doing something wrong? How can I diagnose and fix this? > > Thanks > D > > > > > -- > Demian Wassermann, PhD > dem...@bwh.harvard.edu > LMI / PNL / SPL Labs > Harvard Medical School > Brigham and Women's Hospital > 1249 Boylston, Boston, MA, USA > http://lmi.bwh.harvard.edu/~wassermann/ > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with mris_ca_label (seg fault)
Hi Bruce, No, but I was hoping not to have to run the whole process again (for all the subjects I need to relabel) Thanks for the quick response D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/ On Aug 22, 2013, at 3:39 PM, Bruce Fischl wrote: > Hi Demian > > does this happen if you run it through recon-all? > > Bruce > On Thu, 22 Aug 2013, Demian Wassermann wrote: > >> Dear Support line of free surfer, >> >> I have a problem when I try to apply a new atlas to the surfaces. Even with >> the standard free surfer atlases it segfaults >> >> Environment: >> >> FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 >> >> RedHat release: Fedora release 18 (Spherical Cow) >> >> Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 >> >> Command: >> $FREESURFER_HOME/bin/mris_ca_label -t >> $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh >> lh.sphere.reg >> $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs >> lh.test.annot >> >> >> Output: >> $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ >> $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ >> reading atlas from >> /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... >> reading color table from GCSA file >> average std = 1.0 using min determinant for regularization = 0.011 >> 0 singular and 384 ill-conditioned covariance matrices regularized >> Segmentation fault (core dumped) >> >> >> >> >> Am I doing something wrong? How can I diagnose and fix this? >> >> Thanks >> D >> >> >> >> >> -- >> Demian Wassermann, PhD >> dem...@bwh.harvard.edu >> LMI / PNL / SPL Labs >> Harvard Medical School >> Brigham and Women's Hospital >> 1249 Boylston, Boston, MA, USA >> http://lmi.bwh.harvard.edu/~wassermann/ >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with mris_ca_label (seg fault)
is the command line that recon-all runs exactly the same as what you run? On Thu, 22 Aug 2013, Demian Wassermann wrote: > Hi Bruce, > > No, but I was hoping not to have to run the whole process again (for all the > subjects I need to relabel) > > Thanks for the quick response > > D > -- > Demian Wassermann, PhD > dem...@bwh.harvard.edu > LMI / PNL / SPL Labs > Harvard Medical School > Brigham and Women's Hospital > 1249 Boylston, Boston, MA, USA > http://lmi.bwh.harvard.edu/~wassermann/ > > On Aug 22, 2013, at 3:39 PM, Bruce Fischl wrote: > >> Hi Demian >> >> does this happen if you run it through recon-all? >> >> Bruce >> On Thu, 22 Aug 2013, Demian Wassermann wrote: >> >>> Dear Support line of free surfer, >>> >>> I have a problem when I try to apply a new atlas to the surfaces. Even with >>> the standard free surfer atlases it segfaults >>> >>> Environment: >>> >>> FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer >>> >>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 >>> >>> RedHat release: Fedora release 18 (Spherical Cow) >>> >>> Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 >>> >>> Command: >>> $FREESURFER_HOME/bin/mris_ca_label -t >>> $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh >>> lh.sphere.reg >>> $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs >>> lh.test.annot >>> >>> >>> Output: >>> $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ >>> $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ >>> reading atlas from >>> /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... >>> reading color table from GCSA file >>> average std = 1.0 using min determinant for regularization = 0.011 >>> 0 singular and 384 ill-conditioned covariance matrices regularized >>> Segmentation fault (core dumped) >>> >>> >>> >>> >>> Am I doing something wrong? How can I diagnose and fix this? >>> >>> Thanks >>> D >>> >>> >>> >>> >>> -- >>> Demian Wassermann, PhD >>> dem...@bwh.harvard.edu >>> LMI / PNL / SPL Labs >>> Harvard Medical School >>> Brigham and Women's Hospital >>> 1249 Boylston, Boston, MA, USA >>> http://lmi.bwh.harvard.edu/~wassermann/ >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with mris_ca_label (seg fault)
How would I check this? I thought you meant when I run recon-all -autorecon-all -subjid case01009 -i my_t1.nii.gz D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/ On Aug 22, 2013, at 3:42 PM, Bruce Fischl wrote: > is the command line that recon-all runs exactly the same as what you run? > On Thu, 22 Aug 2013, Demian Wassermann wrote: > >> Hi Bruce, >> >> No, but I was hoping not to have to run the whole process again (for all the >> subjects I need to relabel) >> >> Thanks for the quick response >> >> D >> -- >> Demian Wassermann, PhD >> dem...@bwh.harvard.edu >> LMI / PNL / SPL Labs >> Harvard Medical School >> Brigham and Women's Hospital >> 1249 Boylston, Boston, MA, USA >> http://lmi.bwh.harvard.edu/~wassermann/ >> >> On Aug 22, 2013, at 3:39 PM, Bruce Fischl wrote: >> >>> Hi Demian >>> >>> does this happen if you run it through recon-all? >>> >>> Bruce >>> On Thu, 22 Aug 2013, Demian Wassermann wrote: >>> Dear Support line of free surfer, I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults Environment: FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: Fedora release 18 (Spherical Cow) Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped) Am I doing something wrong? How can I diagnose and fix this? Thanks D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with mris_ca_label (seg fault)
I do. You can look in the recon-all.log (or recon-all.cmd I think) and see if they are identical. If they are, make sure you are using the same binary On Thu, 22 Aug 2013, Demian Wassermann wrote: > How would I check this? > > I thought you meant when I run > > recon-all -autorecon-all -subjid case01009 -i my_t1.nii.gz > > > D > -- > Demian Wassermann, PhD > dem...@bwh.harvard.edu > LMI / PNL / SPL Labs > Harvard Medical School > Brigham and Women's Hospital > 1249 Boylston, Boston, MA, USA > http://lmi.bwh.harvard.edu/~wassermann/ > > On Aug 22, 2013, at 3:42 PM, Bruce Fischl wrote: > >> is the command line that recon-all runs exactly the same as what you run? >> On Thu, 22 Aug 2013, Demian Wassermann wrote: >> >>> Hi Bruce, >>> >>> No, but I was hoping not to have to run the whole process again (for all >>> the subjects I need to relabel) >>> >>> Thanks for the quick response >>> >>> D >>> -- >>> Demian Wassermann, PhD >>> dem...@bwh.harvard.edu >>> LMI / PNL / SPL Labs >>> Harvard Medical School >>> Brigham and Women's Hospital >>> 1249 Boylston, Boston, MA, USA >>> http://lmi.bwh.harvard.edu/~wassermann/ >>> >>> On Aug 22, 2013, at 3:39 PM, Bruce Fischl >>> wrote: >>> Hi Demian does this happen if you run it through recon-all? Bruce On Thu, 22 Aug 2013, Demian Wassermann wrote: > Dear Support line of free surfer, > > I have a problem when I try to apply a new atlas to the surfaces. Even > with the standard free surfer atlases it segfaults > > Environment: > > FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 > > RedHat release: Fedora release 18 (Spherical Cow) > > Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 > > Command: > $FREESURFER_HOME/bin/mris_ca_label -t > $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh > lh.sphere.reg > $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs > lh.test.annot > > > Output: > $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ > reading atlas from > /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... > reading color table from GCSA file > average std = 1.0 using min determinant for regularization = 0.011 > 0 singular and 384 ill-conditioned covariance matrices regularized > Segmentation fault (core dumped) > > > > > Am I doing something wrong? How can I diagnose and fix this? > > Thanks > D > > > > > -- > Demian Wassermann, PhD > dem...@bwh.harvard.edu > LMI / PNL / SPL Labs > Harvard Medical School > Brigham and Women's Hospital > 1249 Boylston, Boston, MA, USA > http://lmi.bwh.harvard.edu/~wassermann/ > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>> >>> >>> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Otto: unsupported slice timing pattern 5
Hi, I am trying to convert a SIEMENS T1-weighted volume to the mgz format (via mri_convert) but I am getting constantly the error message unsupported slice timing pattern 5 in file I saw in the archives that a lot of people had problems with this but could not find any solutions posted - what am I missing? Many thanks Otto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Otto: unsupported slice timing pattern 5
Hi, One option is to open the volume in 3D Slicer and save it in .mgz format. 3D Slicer is free to download. John On 2013-08-22, at 4:30 PM, Otto Muzik wrote: > > Hi, > > I am trying to convert a SIEMENS T1-weighted volume to the mgz > format (via mri_convert) but I am getting constantly the error message > > unsupported slice timing pattern 5 in file > > I saw in the archives that a lot of people had problems with this but > could not find any solutions posted - what am I missing? > > Many thanks > > Otto > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards Pedro Rosa On 21 Aug 2013, at 04:16 PM, Z K wrote: > Getting 'make' on Mac systems requires installing XCode AND Command Line > Tool. You can download these from Apple using the following link: > > https://developer.apple.com/downloads > > FYI: This will require opening a developer account (free) if you do not > already have one. > > -Zeke > > > > On 08/21/2013 12:33 PM, Douglas N Greve wrote: >> >> Yea, I don't think mac os comes with it by default. If you want to use >> this functionality, you'll have to install it. Zeke, can you point him >> in the right direction? >> >> to get back to your original problem, I think I gave you the wrong >> version of mri_segstats. What version of mac os do you have? If I get >> you the right version, then you might not need the make option. >> >> doug >> >> >> On 08/21/2013 12:06 PM, Pedro Rosa wrote: >>> Hi, >>> I could not find the make file. I am using Mac OS (most recent). >>> Thanks >>> >>> Pedro Rosa >>> >>> On 21 Aug 2013, at 10:51 AM, Douglas N Greve >>> wrote: >>> You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug On 08/20/2013 10:12 PM, Pedro Rosa wrote: > Hi, > Sorry for that! > I tried using several targets: all / autorecon1-2-3, and for all I get > 'make: command not found.' > I used recon-all -s subject -make target > Thank you again, > Pedro Rosa > > On 20 Aug 2013, at 12:34 PM, Douglas N Greve > wrote: > >> They should be fine. BTW, you can run >> >> recon-all -s subject -make all >> >> and it will only run the parts that need to be run >> >> doug >> >> >> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>> Hi, >>> I am mainly interested in using the wmparc.mgz files. Are they alright >>> in the subjects with this error in autorecon2? It would be better if I >>> could use this processing, as doing it again in 80 subjects would take >>> a lot of time. Autorecon 1 and 3 ended without errors for all subjects. >>> I inspected the wmparc.mgz files as labels using Slicer 4, and they >>> seem fine. >>> Thanks, >>> Pedro Rosa. >>> >>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>> wrote: >>> Hi Pedro, see the release notes for the issue http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug On 08/19/2013 10:06 PM, Pedro Rosa wrote: > Hi experts, > I am processing several subjects, and they all ended up with the same > error at the autorecon2: ribbon.mgz could not be opened. I ran at > first the autorecon1 to check the skull striping, and then autorecon2 > and 3. Autorecon3 always finished without error. I attached a log > file. > > > Any help is appreciated. > Regards, > Pedro Rosa. > > > ___ > 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. >> -- >> 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
