[Freesurfer] Begginer!
Hi there, I am totally a begginer in the Neurodebian world so please be patient :( I installed FS but I don't know how to setup freesurfer? I don't know how to locate my FS home Simply, I'm stuck at this step: setenv FREESURFER_HOME freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh any help? ___ 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] R: Re: R: Re: R: Re: R: Re: incomplete tracts
I have this error: writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 11109: 1 negative trianglesmris_resample: Command not found. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 30-apr-2013 21.12 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: incomplete tracts Like I said in my previous email to you, please do not specify the CVS template. This means delete the cvstempdir line from your configuration file, or comment it out. On Tue, 30 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, when I run the configuration file (which I'm attaching) ERROR: Could not find CVS template I apologize but which is the correct directory of CVS template? Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 26-apr-2013 20.08 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts Hi Stefano - Just use the default for that, you don't need to specify the location. a.y On Sun, 21 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, I apologize but I do not find CVS template? Where it should be located? Thank you very much, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: incomplete tracts Hi Stefano - Did you try CVS for the inter-subject registration? It doesn't look like it from the configuration file. a.y On Tue, 9 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I tried.I'm attacking the last configuration file that I used. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 1.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts What registration methods are you using for the intra-subject and inter-subject registration? Have you tried the different options? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.57 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts What you say again you mean with 5.2? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, for some subject the low-b volume is in the end. Some subjects have again incomplete tracts. I'm attacking an example of configuration file that I'm using. I hope that you can check it please. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] incomplete tracts Hi Stefano - In your case we determined that the ones that had the low-b volume in the end didn't run correctly, right? In that case, I didn't need to see anything, you were going to try running 5.2. a.y On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, could I send you the data of a subject that I don't run correctly? I still have some subjects with tracts incomplete and I do not know if it depends from my analysis or whether the images are not good. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 17.37 A: Gerit Pfuhlgerit.pf...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend running 5.2 with bbregister for the registration (which is the default in 5.2 anyway). You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Hope this helps, a.y On Fri, 5 Apr 2013, Gerit Pfuhl wrote: Dear Anastasia, thanks for the help. There is also a line option in freeview. However we still have brains with missing tracks, I rerun them with increasing the ncpts and registering to bbr (since that is default in Tracula 5.2.). We are reasonable
[Freesurfer] Visualize a fixed number of voxels using Tksurfer
Hi all, is there a way to visualize a fixed number of voxesl using TKsurfer. I want to display the 200 most active voxels (i.e. highest beta values) on the inflated surface. Is there a possibility within tksurfer or do I have to determine the corresponding threshold beforehand? Thanks Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to flip L/R image in the freeview?
Freesurfer users, I'm a newbie for FS and have a rudimentary question for you. I have to overlay the group map for right hemisphere onto the lh.inflated (due to using sym space, where left surface map became symmetrical to the right), but I wonder if there is any way of reverting it back to rh.inflated after the overlay using the freeview software. Your help would be appreciated. -Glen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to flip L/R image in the freeview?
Hi Glen have you done the cross-hemisphere registration? If so, you can do this with mri_surf2surf, although the syntax is a bit tricky. Doug would know the details, but he's probably not going to be able to answer questions until tomorrow cheers Bruce On Wed, 1 May 2013, Glen Lee wrote: Freesurfer users, I'm a newbie for FS and have a rudimentary question for you. I have to overlay the group map for right hemisphere onto the lh.inflated (due to using sym space, where left surface map became symmetrical to the right), but I wonder if there is any way of reverting it back to rh.inflated after the overlay using the freeview software. Your help would be appreciated. -Glen ___ 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] Which space is TRACULA statistics in?
Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what space this data is reported in? Thanks! -- Susie Kuo ___ 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] Use our own training subjects?
Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of the corpus callosum. Would it be possible for you to document how your group created your priors? Are we constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be a good learning process for me. Thank you! Susan Kuo On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - If you can label the connection that you want in trackvis consistently in a set of subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk files with the trackvis streamlines and the aparc+aseg's from all the training subjects to either the MNI or the CVS template. Then there's a trainfile variable that you can set in the configuration file that tells trac-all where to find the training data. If you decide to go through with this, I can try to document it in more detail on the wiki. a.y On Mon, 15 Apr 2013, Susan Kuo wrote: Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ 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] Which space is TRACULA statistics in?
Thank you, Anastasia! I will keep this in mind when I analyze the group statistics. On Wed, May 1, 2013 at 11:07 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - All outputs of tracula are in native diffusion space. Tractography is performed in the native space, without any transformationon the DWIs to another space. a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what space this data is reported in? Thanks! -- Susie Kuo 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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Use our own training subjects?
Thank you, Anastasia. I think we can recruit some hard-working neuroanatomists here to help us with the labeling. I believe I will give this a shot for the IFO. Again, thanks for your support on this - I really appreciate it! Susie Kuo On Wed, May 1, 2013 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of the corpus callosum. Would it be possible for you to document how your group created your priors? Are we constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be a good learning process for me. Thank you! Susan Kuo On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - If you can label the connection that you want in trackvis consistently in a set of subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk files with the trackvis streamlines and the aparc+aseg's from all the training subjects to either the MNI or the CVS template. Then there's a trainfile variable that you can set in the configuration file that tells trac-all where to find the training data. If you decide to go through with this, I can try to document it in more detail on the wiki. a.y On Mon, 15 Apr 2013, Susan Kuo wrote: Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear 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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] incomplete tracts
Hi Stefano - You'll have to include the log file, so that we can see the exact command line that was being run when the error happened. Thanks, a.y On Wed, 1 May 2013, std...@virgilio.it wrote: Hi Bruce, trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also attaching dmrirc files. Thank you very much. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 1-mag-2013 15.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu, ayend...@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts Hi Stefano you need to tell us what command you were running. cheers Bruce On Wed, 1 May 2013, std...@virgilio.it wrote: I have this error: writing registered surface to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av g35.sphere.reg... expanding nbhd size to 1 1109: 1 negative triangles mris_resample: Command not found. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 30-apr-2013 21.12 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: incomplete tracts Like I said in my previous email to you, please do not specify the CVS template. This means delete the cvstempdir line from your configuration file, or comment it out. On Tue, 30 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, when I run the configuration file (which I'm attaching) ERROR: Could not find CVS template I apologize but which is the correct directory of CVS template? Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 26-apr-2013 20.08 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts Hi Stefano - Just use the default for that, you don't need to specify the location. a.y On Sun, 21 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, I apologize but I do not find CVS template? Where it should be located? Thank you very much, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: incomplete tracts Hi Stefano - Did you try CVS for the inter-subject registration? It doesn't look like it from the configuration file. a.y On Tue, 9 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I tried.I'm attacking the last configuration file that I used. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 1.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts What registration methods are you using for the intra-subject and inter-subject registration? Have you tried the different options? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.57 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts What you say again you mean with 5.2? On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, yes, for some subject the low-b volume is in the end. Some subjects have again incomplete tracts. I'm attacking an example of configuration file that I'm using. I hope that you can check it please. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 18.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] incomplete tracts Hi Stefano - In your case we determined that the ones that had the low-b volume in the end didn't run correctly, right? In that case, I didn't need to see anything, you were going to try running 5.2. a.y On Fri, 5 Apr 2013, std...@virgilio.it wrote: Hi Anastasia, could I send you the data of a subject that I don't run correctly? I still have some subjects with tracts incomplete and I do not know if it depends from my analysis or whether the images are not good. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-apr-2013 17.37 A: Gerit Pfuhlgerit.pf...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] incomplete tracts
Re: [Freesurfer] error in longitudinal processing dimension mismatch
Keith
On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Keith
can you cc the list so that others can answer? Like Martin!
thanks
Bruce
On Wed, 1 May 2013, Qi Wu wrote:
Hi Bruce,
Thank you so much for your quick reply.
I used the following script to do the first step
cross-sectional
preprossessing
#!/bin/tcsh -ef
# add 'x' to '-ef' to trace code as it is executed
# GO_FS1 - The Easy button #
# Usage: GO_FS-123 subjects directory name
# Feeds multiple subjects into autorecon1, autorecon2,
and autorecon3
# Requires that original scan data be placed in
$SUBJECTS_DIR/_orig_
# (Place each subject's anat series in separate
folders)
echo \n GO FreeSurfer!
\n
### Check if subjects directory specified ###
if ( $1 != ) then
set subjdir = $1
else
echo \n ERROR: No subjects directory specified \n
exit 1
endif
### Set FREESURFER_HOME and SUBJECTS_DIR ###
setenv FREESURFER_HOME /usr/local/freesurfer5.1
if ( -e
/data/keith/freesurferdata/subjects_longitudinal/$subjdir)
then
setenv SUBJECTS_DIR
/data/keith/freesurferdata/subjects_longitudinal/$subjdir
else
echo \n ERROR: Specified subjects directory does not
exist \n
exit 1
endif
### Check if original scan data exists ###
if ( ! -e /$SUBJECTS_DIR/_orig_ ) then
echo \n ERROR: Original scan data not found. \n
exit 1
endif
### disable functional tools ###
setenv NO_FSFAST
# (To enable functional tools, disable the above line,
enable the
following:)
# (HAVE NOT TESTED THIS YET) (MAYBE BETTER IF
NO_FSFAST ANYWAYS)
#setenv FUNCTIONALS_DIR $FREESURFER_HOME/sessions
# echo FUNCTIONALS_DIR = $FUNCTIONALS_DIR
# (and add the following to ~/matlab/startup.m)
#fsfasthome = getenv('FSFAST_HOME');
#fsfasttoolbox = sprintf('%s/toolbox',fsfasthome');
#path(path,fsfasttoolbox);
### Set up FreeSurfer ###
setenv prompt
source $FREESURFER_HOME/FreeSurferEnv.csh
echo
### List out directories in _orig_ , set subj array,
prompt to continue ###
echo Found the following subjects: \n
set i = 0
set subjID
foreach d ($SUBJECTS_DIR/_orig_/*)
@ i++
set subjID = ($subjID $d:t)
echo Subject $i: $subjID[$i]
end
set subjCount = $i
set response
while ($response != n $response != y)
echo -n \n Process these $subjCount subjects? [y/n]
set response = $
end
if ($response == n) then
echo \n Program ended by user \n
exit 1
endif
### Prompt user for First Anat Filename's ###
set firstAnatSame
while ($firstAnatSame != y $firstAnatSame != n)
echo -n \n Are all the anat series named identically?
[y/n]:
set firstAnatSame = $
end
switch ($firstAnatSame)
case [y]:
echo -n \n Please enter the first filename (e.g.
p1_000.dcm) for all
anat series:
set firstAnat = $
breaksw
case [n]:
echo \n Please enter the first filename (e.g.
p1_000.dcm) in the anat
series for:
set i = 0
set firstAnat
while ($i $subjCount)
@ i++
echo -n $subjID[$i]:
set firstAnat = ($firstAnat $)
end
breaksw
endsw
### Run autorecon1 for each subject ###
cd $SUBJECTS_DIR
switch ($firstAnatSame)
case [y]:
set i = 0
while ($i $subjCount)
@ i++
echo \n| NOW PROCESSING
$subjID[$i]
|\n
recon-all -i
$SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat -all -s
$subjID[$i]
end
breaksw
case [n]:
set i = 0
while ($i $subjCount)
@ i++
echo \n| NOW PROCESSING
$subjID[$i]
|\n
recon-all -i
$SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat[$i] -all -s
$subjID[$i]
end
breaksw
endsw
echo
date +Finished $0 without error at %T on %a %b %d %Y
echo
exit 0
###
### Simple working loop
#set i = 0
#while ($i 10)
# echo $i
# @ i++
#end
###
#
### TO DO ###
#
# why don't env's remain 'set' after running this? (they
do after running
SetUpFreeSurfer.csh or FreeSurferEnv.csh)
# why can't FS_FAST be set up?
Then I did the base step and the long step with the
following
recon-all -base kp5_base -tp kp5 -tp
Re: [Freesurfer] convert labels to volumetric masks
Hi Meng, On 04/30/2013 09:53 PM, limengsecret wrote: Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions. what do you mean you downloaded them? where did they come from exactly? Are they your own data? And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi. How was your functional data normalized? Specifically what atlas was used? Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517ee666.8050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng -- 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] (no subject)
Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- * * ___ 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] (no subject)
Hi Ashley yes, a bunch of times. The dura can cause some problems, but mostly they run ok Bruce On Wed, 1 May 2013, Ashley Hannah wrote: Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- ___ 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] Using the muscle ROI in the FreeSurferColorLUT
Hello Freesurfers,
I would like to use the muscle ROI in the LUT (number 123). Can anyone
tell me which muscles (all cranial? cervical too?) are included? I
tried making a subject-specific label using the following command:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz
--id 123 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/muscle_${identifier}.label
This yielded the error Found 0 label voxels, presumably because aseg.mgz
is skull-stripped. When I used orig.mgz instead of aseg.mgz in the
command line above, the assigned label is a scattering of single voxels
throughout the cortex and subcortical white matter. I am guessing that
this is because orig.mgz is not registered to the same space as aseg.mgz -
is this correct?
Any suggestions for how to use the muscle ROI would be much appreciated.
Thanks,
Jeff
___
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] Using the muscle ROI in the FreeSurferColorLUT
Hi Jeff
our standard segmentation doesn't include muscle. We did have some
prototypes that labeled all cranial muscles but they are not much more than
prototypes
Bruce
On Wed, 1 May 2013,
jwa...@nmr.mgh.harvard.edu wrote:
Hello Freesurfers,
I would like to use the muscle ROI in the LUT (number 123). Can anyone
tell me which muscles (all cranial? cervical too?) are included? I
tried making a subject-specific label using the following command:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz
--id 123 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/muscle_${identifier}.label
This yielded the error Found 0 label voxels, presumably because aseg.mgz
is skull-stripped. When I used orig.mgz instead of aseg.mgz in the
command line above, the assigned label is a scattering of single voxels
throughout the cortex and subcortical white matter. I am guessing that
this is because orig.mgz is not registered to the same space as aseg.mgz -
is this correct?
Any suggestions for how to use the muscle ROI would be much appreciated.
Thanks,
Jeff
___
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] Freesurfer License issue/bug on Opensuse 12.3
Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurferecho $shell /bin/tcsh /usr/freesurfersource SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfertkmedit bert orig.mgz -- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- /usr/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick ___ 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] convert labels to volumetric masks
Hi Doug, The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data. The functional data have been preprocessed with slice-timing, realignment, and normalization. And the masks overlay the functional data created above to define the retinotopic visual areas. Thank you! Meng 发件人： Douglas N Greve 发送时间： 2013-05-02 02:02 收件人： limengsecret 抄送： freesurfer 主题： Re: [Freesurfer] convert labels to volumetric masks Hi Meng, On 04/30/2013 09:53 PM, limengsecret wrote: Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions. what do you mean you downloaded them? where did they come from exactly? Are they your own data? And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi. How was your functional data normalized? Specifically what atlas was used? Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517ee666.8050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ 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.
