Re: [Freesurfer] recon_all exited with errors
Hi Nick,
thanks for your advice - Freesurfer v5.2 has now been installed on our
clusters and I am running the recon_all script again with this version. Is
it necessary to re-run everything from scratch again ('mk subjdirs' and
'mri_convert') using this version or will it be okay to just re-run the
'recon_all' step?
Thanks for your help!
Sinead
On 4 March 2013 16:55, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Sinead,
Much has improved since v4.5, so I would recommend updating to v5.2. I
would have to re-run your prior subject data, as you will not be able to
mix results processed with different versions, but any edits you made will
be retained.
The mris_volmask failure you describe will not invalidate the results that
it had produced for the subject up until the failure point (ie, the
subcortical and cortical segmentations should be valid) but it does mean
that stages downstream of that stage will not have run, and so some
measures will not exist (likely even -segstats will not have run).
Nick
Hi Nick,
Thanks for your help. I'm running v4.5.0 on our cluster. I'm don't think
the latest version has been installed. I might just ask them to install
v5.2. Should I re-run the recon_all steps again with this latest version?
Should I disregard the results that have already been computed with this
error? I am still a Freesurfer beginner unfortunately so apologies for
asking such questions!
Thanks again,
Sinead
On 4 March 2013 14:50, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Sinead
Are you running v5.0.0? This link has some info on fixing the problem,
something your admin will have to do:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012846.html
Or better yet you can them install install v5.2, which doesnt have that
dependency in mris_volmask:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Nick
Dear members,
I am currently conducting cortical thickness analysis and I have ran
the
recon_all step. The appropriate files have been created including
aseg.mgz,
brainmask.mgz, aseg.stats etc. and therefore volumes and cortical
thickness
measures have been calculated, however, when I look at the output of
my
script it states that the job has exited with errors (see below)
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance 001
mris_volmask.bin: error while loading shared libraries: libXss.so.1:
cannot
open shared object file: No such file or directory
Linux tcin-n05.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
EST
2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 1 20:00:42 GMT 2013
I'm not too sure what the error is or how to fix it. However, as the
relevant files have been created, should I be too concerned about
this?
Also, I should mention that I am running my scripts on a high
performance
computing cluster and not locally on my linux.
Thank you for your help!
Sinead
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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properly
dispose of the e-mail.
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
___
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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] entorhinal thickness
Hi Bruce and other users, I have read the article on EC that you have suggested. But, I do not understand how I should obtain the EC thickness outcomes /statistical maps from my analysis. I have some question, please. I have already performed recon-all and cortical thickness analysis. For entorhinal cortex thickness analysis, should I run again mris_prep, surf2surf and glmfit for EC files only? If yes, which are the files that should I use? Which are their names and where these files are locate? An additional question on other matter, please. If I'd like perfomed a ROI based cortical thickness (for example on occipital lobe), can I use a mask that is builded by recon-all? How can I extract it for example from aseg (do you advise it)?About the occipital lobe, I do not understand from tutorial if already exist a particular modality to calculate the cortical thickness specifically in that region. Thank you very much for your patience and kindness, Stefano Hi Stefano look on the wiki and search for entorhinal. In particular, this paper:http://surfer.nmr.mgh.harvard.edu/pub/articles/YNIMG6159.pdf describes how we estimate the location of EC in vivo cheers Bruce On Fri, 1 Mar 2013, std...@virgilio.it wrote: Hi list,Where Can I find basic information about entorhinal cortex analysis?Thank you very much.Stefano ___ 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.
Re: [Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample
it depends on (1) what you want to do with them (e.g. functional analysis vs. thickness) and (2) the quality of the scans On Tue, 5 Mar 2013, Schumman Resonance wrote: This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev ___ 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] recon_all exited with errors
Sinead,
For subjects you have already processed with a prior version, you can just
run:
recon-all -s subjid -all
and it will retain any edits that were made.
Nick
Hi Nick,
thanks for your advice - Freesurfer v5.2 has now been installed on our
clusters and I am running the recon_all script again with this version. Is
it necessary to re-run everything from scratch again ('mk subjdirs' and
'mri_convert') using this version or will it be okay to just re-run the
'recon_all' step?
Thanks for your help!
Sinead
On 4 March 2013 16:55, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Sinead,
Much has improved since v4.5, so I would recommend updating to v5.2. I
would have to re-run your prior subject data, as you will not be able to
mix results processed with different versions, but any edits you made
will
be retained.
The mris_volmask failure you describe will not invalidate the results
that
it had produced for the subject up until the failure point (ie, the
subcortical and cortical segmentations should be valid) but it does mean
that stages downstream of that stage will not have run, and so some
measures will not exist (likely even -segstats will not have run).
Nick
Hi Nick,
Thanks for your help. I'm running v4.5.0 on our cluster. I'm don't
think
the latest version has been installed. I might just ask them to
install
v5.2. Should I re-run the recon_all steps again with this latest
version?
Should I disregard the results that have already been computed with
this
error? I am still a Freesurfer beginner unfortunately so apologies for
asking such questions!
Thanks again,
Sinead
On 4 March 2013 14:50, Nick Schmansky ni...@nmr.mgh.harvard.edu
wrote:
Sinead
Are you running v5.0.0? This link has some info on fixing the
problem,
something your admin will have to do:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012846.html
Or better yet you can them install install v5.2, which doesnt have
that
dependency in mris_volmask:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Nick
Dear members,
I am currently conducting cortical thickness analysis and I have
ran
the
recon_all step. The appropriate files have been created including
aseg.mgz,
brainmask.mgz, aseg.stats etc. and therefore volumes and cortical
thickness
measures have been calculated, however, when I look at the output
of
my
script it states that the job has exited with errors (see below)
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance 001
mris_volmask.bin: error while loading shared libraries:
libXss.so.1:
cannot
open shared object file: No such file or directory
Linux tcin-n05.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9
12:20:03
EST
2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 1 20:00:42 GMT 2013
I'm not too sure what the error is or how to fix it. However, as
the
relevant files have been created, should I be too concerned about
this?
Also, I should mention that I am running my scripts on a high
performance
computing cluster and not locally on my linux.
Thank you for your help!
Sinead
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
___
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.
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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[Freesurfer] Error
All, Any idea how can I sort this error, Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 1 ERROR: QdecDataTable::Load: problem parsing file /Users/chikkuvarghese/subject/qdec/qdec.table.dat This line did not appear to end with a newline: truetest2.long.eFemale70 Righthippocampus 4006 Error loading the data table. Many Thanks chikku ___ 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] FDR questions
Dear Freesurfer experts, I am interested in a specific brain region that is based on the 2009 atlas. I used Qdec to 'Generate Stats Data Tables' to get the cortical thickness info for this region and saved them in a file. Then I used SPSS and did an ANOVA test. The ANOVA test reveals that the patient group (versus the neurotypical group) has significantly cortical thinning in this region (p .05). I am also able to see this significant effect in this region using 'Display' in Qdec. However, once I hit 'FDR' button (q = .05), the minimum t-value associated with significant data increased from around 2 to more than 4. And the significant effect in this region does not survive FDR, as seen in the Display. My questions: 1. Is what I did the usual procedure to do FDR correction? How do I see the significance value of this region under FDR (q=.05)? 2. Is the normal that the minimum t-value increased so much when doing FDR? 3. Do I have to do FDR since I'm only interested in a very specific region? Thank you! Daniel ___ 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] Extract cortex surface with Freesurfer
Hi, I'm a new user of Freesurfer. 1) I would like to extract only the cortex cerebrum . So I think I don't need the complete subcortical segmentation ( 20-40 hours). Do you know a way to segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already try the complete subcortical segmentation ( about 12 hours, with the recon-all command). Do you know a way to extract only the cortex surface from the software? I would like to get the 3D surface mesh for analysis on Matlab. Could you help me, Thanks. VP. ___ 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] Extract cortex surface with Freesurfer
Hi VP sorry, the subcortical stuff is needed to automate the cortical surface modeling, so you need teh whole thing. We do distribute matlab scripts for reading the surfaces in (read_surf.m). cheers Bruce On Wed, 6 Mar 2013, Valtina Pouegue wrote: Hi, I'm a new user of Freesurfer. 1) I would like to extract only the cortex cerebrum . So I think I don't need the complete subcortical segmentation ( 20-40 hours). Do you know a way to segment only cortex or only ( cortex+ pial ( left/rigt hemispher)? 2) I already try the complete subcortical segmentation ( about 12 hours, with the recon-all command). Do you know a way to extract only the cortex surface from the software? I would like to get the 3D surface mesh for analysis on Matlab. Could you help me, Thanks. VP. ___ 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] FreeSurfer 5.2 TRACULA and FSL 5
Hi Sean - Thanks for trying out the new version! From what I've seen, the file $FSLDIR/etc/fslversion exists in FSL 5 as well. Does it exist in your distribution? a.y On Wed, 6 Mar 2013, Sean Hatton wrote: Hi all, I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA. When I run trac-all -bedp I get an error: .../freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Looking at the programming it is faulting on line 131 where it is checking the FSL version. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`) Is this syntax correct? Is TRACULA compatible with FSL 5+? Sean Hatton Brain and Mind Research Institute University of Sydney ___ 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] Can I skip some folders to install freesurfer
Thanks for the info, Nick. That is very helpful. Our install partition has limited size. So the idea is not to get rid of anything, but rather move these big data files somewhere else with much larger disk quota. I guess I could move the whole subject away. As long as SUBJECTS_DIR is set correctly, it should look at the right place when needed. However, can the same method applied to other big directories, e.g. average, lib? I don't see any corresponding environment variables. Please advice. On Tue, Mar 5, 2013 at 4:54 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: DJ, Agreed that the distribution has gotten bloated. In future releases I'd like to change it to not include most of the data and to have recon-all or other utilities print a 'wget' command to use to download the data when needed. I've updated the ReleaseNotes section with a list of some directories of stuff that is not used in the default stream. So deletion depends on whether you or your local user-base will ever need these, which can be tough to predict: * freesurfer/average/mult-comp-cor - Correction for Multiple Comparisons pre-calc - 1.3G * freesurfer/subjects/fsaverage? - fsaverage at other iso-levels - 310M * freesurfer/subjects/fsaverage_sym - symmetric fsaverage for contra-lateral surface mapping - 197M * freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface registration target - 531M * freesurfer/trctrain - Tracula training set - 886M These files in total are about 3GB. https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Nick On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote: Hi, I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance. DJ ___ 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.
Re: [Freesurfer] Error
Hi Chikku-- can you try with a /newline at the end of your .dat file? shantanu On Wed, March 6, 2013 10:40 am, Varghese Chikku wrote: All, Any idea how can I sort this error, Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 1 ERROR: QdecDataTable::Load: problem parsing file /Users/chikkuvarghese/subject/qdec/qdec.table.dat This line did not appear to end with a newline: truetest2.long.eFemale70 Righthippocampus 4006 Error loading the data table. Many Thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ 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] Can I skip some folders to install freesurfer
DJ, symbolic links would work. for instance: cd freesurfer mv average path_to_larg_disk_space/freesurfer_data ln -s path_to_larg_disk_space/freesurfer_data/average then you should have a link to average remaining in the freesurfer dir but the space is consumed elsewhere. Nick On Wed, 2013-03-06 at 10:33 -0600, Dian Jiao wrote: Thanks for the info, Nick. That is very helpful. Our install partition has limited size. So the idea is not to get rid of anything, but rather move these big data files somewhere else with much larger disk quota. I guess I could move the whole subject away. As long as SUBJECTS_DIR is set correctly, it should look at the right place when needed. However, can the same method applied to other big directories, e.g. average, lib? I don't see any corresponding environment variables. Please advice. On Tue, Mar 5, 2013 at 4:54 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: DJ, Agreed that the distribution has gotten bloated. In future releases I'd like to change it to not include most of the data and to have recon-all or other utilities print a 'wget' command to use to download the data when needed. I've updated the ReleaseNotes section with a list of some directories of stuff that is not used in the default stream. So deletion depends on whether you or your local user-base will ever need these, which can be tough to predict: * freesurfer/average/mult-comp-cor - Correction for Multiple Comparisons pre-calc - 1.3G * freesurfer/subjects/fsaverage? - fsaverage at other iso-levels - 310M * freesurfer/subjects/fsaverage_sym - symmetric fsaverage for contra-lateral surface mapping - 197M * freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface registration target - 531M * freesurfer/trctrain - Tracula training set - 886M These files in total are about 3GB. https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Nick On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote: Hi, I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance. DJ ___ 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] Longitudinal analysis of one timepoint
Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. __ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. ___ Freesurfer mailing list Freesurfer at 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 -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
Re: [Freesurfer] Longitudinal analysis of one timepoint
Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. __ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. ___ Freesurfer mailing list Freesurfer at 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 ___ 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] corRead() error with Tracula / FS 5.2
Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil Soman ___ 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] corRead() error with Tracula / FS 5.2
Hi Salil - Can you send your trac-all.log and dmrirc files? Thanks! a.y On Wed, 6 Mar 2013, Salil Soman wrote: Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil Soman ___ 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] Fwd: Tracula 5.2 debugging
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping. a.y On Wed, 6 Mar 2013, Salil Soman wrote: Thank you. Please see attached. -S On Wed, Mar 6, 2013 at 12:40 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Salil - Can you send your trac-all.log and dmrirc files? Thanks! a.y On Wed, 6 Mar 2013, Salil Soman wrote: Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil Soman 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] T2pial's use of bbregister failing
Hi all, Congrats on the new version! I've been excited to see how the use of data from T2 images could help pial surface estimation, but I'm encountering a problem with getting that to work. It seems to be failing to properly execute the bbregister command built into this part of the new recon-all script. My command was 'recon-all -s subjid -i path/to/T1dcm -T2 path/to/T2dcm -all -T2pial', from an x86_64 Linux platform, and using the stable release of FreeSurfer 5.2. Appended below my signature is the full log of errors that I get (which I've replicated with another subject). Any advice or insights would be much appreciated. Thanks! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 # #@# Refine Pial Surfs w/ T2/FLAIR Wed Mar 6 02:52:25 EST 2013 bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.log Wed Mar 6 02:52:25 EST 2013 setenv SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer cd /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/bin/bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz... TR=2800.00, TE=327.00, TI=-1.00, flip angle=120.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) writing to /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii... fslregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fslregister.log Wed Mar 6 02:52:25 EST 2013 --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ rc-twice Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts mri_convert ERROR: could not determine file for /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/ERROR: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for
[Freesurfer] Question re: paradigm files for event-related design
Hi freesurfers, I have an event-related design experiment which outputs a file with a line corresponding to every TR. i.e. for TR = 1 the first 3 columns of the file look like: 0 0 1 1 0 1 2 0 1 3 0 1 4 0 1 5 1 1 6 1 1 7 1 1 8 1 1 9 1 1 Assuming I have 5 seconds of fixation followed by seconds of condition 1. Is this the correct way to format this file? or should it have aline for every condition onset such as: 0 0 5 5 1 5 Perhaps, it makes no difference. Please let me know if you have insight into this Thanks, Cesar ___ 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] Advice on integrating FSL's BET with recon-all
Hi again, We have had some suboptimal results from FreeSurfer's skullstripping algorithm, even after iteratively trying different watershed thresholds and after checking the quality of Talairach registration. The results are pretty good, but often leave some dura matter and bits of neck behind whose higher intensity values, I believe, may end up skewing recon-all's later estimation of the range of intensity values within grey matter, and consequently compromising the accuracy of pial surface estimation. FSL's BET, however, seems to do a better job of extracting the brain, at least for our dataset. So, I was wondering if I might be able to skip over mri_watershed and feed autorecon2 and autorecon3 a brainmask.mgz file created using BET. I tried this procedure: 1) mri_convert path/to/T1dcm T1.nii.gz 2) bet T1.nii.gz BET_brainmask.nii.gz -A 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz 4) recon-all -s subjid -autorecon1 -noskullstrip 5) mv BET_brainmask.nii.gz ./subjid/mri/brainmask.mgz 6) recon-all -s subjid -autorecon2 -autorecon3 And I got this error message, right after normalization2: #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_bet/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match those of brainmask.mgz, resulting during normalization2 in a mismatch between brain.mgz and brainmask.mgz. Does that seem right, and is there a possible workaround? Thank you! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] Advice on integrating FSL's BET with recon-all
you can use mri_convert -rl ... to reslice the output of bet so that it has the same geometry as the rest of our stream cheers Bruce On Wed, 6 Mar 2013, Winter, Warren wrote: Hi again, We have had some suboptimal results from FreeSurfer's skullstripping algorithm, even after iteratively trying different watershed thresholds and after checking the quality of Talairach registration. The results are pretty good, but often leave some dura matter and bits of neck behind whose higher intensity values, I believe, may end up skewing recon-all's later estimation of the range of intensity values within grey matter, and consequently compromising the accuracy of pial surface estimation. FSL's BET, however, seems to do a better job of extracting the brain, at least for our dataset. So, I was wondering if I might be able to skip over mri_watershed and feed autorecon2 and autorecon3 a brainmask.mgz file created using BET. I tried this procedure: 1) mri_convert path/to/T1dcm T1.nii.gz 2) bet T1.nii.gz BET_brainmask.nii.gz -A 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz 4) recon-all -s subjid -autorecon1 -noskullstrip 5) mv BET_brainmask.nii.gz ./subjid/mri/brainmask.mgz 6) recon-all -s subjid -autorecon2 -autorecon3 And I got this error message, right after normalization2: #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_bet/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match those of brainmask.mgz, resulting during normalization2 in a mismatch between brain.mgz and brainmask.mgz. Does that seem right, and is there a possible workaround? Thank you! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] Longitudinal analysis of one timepoint
Thanks Martin and Nick, We have a number of subjects with single time points too, so I think 5.2 is the best way to go. Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)? Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline? Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go? Thanks, Sarah From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. __ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.
Re: [Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5
Hi Sean - This works on our redhat centos 4 and centos 6. I can dig around some more, but it'll have to wait for Monday b/c I'll be out of the office the next couple of days. As for your other question, the symlink part has been moved to the -prep step, specifically to make it easier to then run bedpostx outside of trac-all if needed. a.y On Wed, 6 Mar 2013, Sean Hatton wrote: Hi Anastasia, FSLVersion is there and does create the variable. I believe it is a syntax error, is the bracket suppose to be there? I have also noticed in the bedp section of trac-all that the Create links named as expected by bedposts section is removed - is this correct? Is it called elsewhere? I am running CentrOS 4 (64bit) on Ubuntu 12.04. Cheers, Sean On 7/03/13 3:29 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Thanks for trying out the new version! From what I've seen, the file $FSLDIR/etc/fslversion exists in FSL 5 as well. Does it exist in your distribution? a.y On Wed, 6 Mar 2013, Sean Hatton wrote: Hi all, I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA. When I run trac-all -bedp I get an error: .../freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Looking at the programming it is faulting on line 131 where it is checking the FSL version. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`) Is this syntax correct? Is TRACULA compatible with FSL 5+? Sean Hatton Brain and Mind Research Institute University of Sydney ___ 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] preproc-sess
Can you send the terminal output? doug On 03/06/2013 04:33 PM, Meryem Ayse Yucel wrote: Hi all, I am running: preproc-sess -s sess01 -fsd bold -fwhm 5 -stc up -per-run However at the end it did not create an output like fmcsm. I only have fmc.nii, fmc.up.nii and fmcpr.up.nii. Am I doing something wrong, or these outputs are smoothed too? Thanks, Meryem ___ 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: 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] Longitudinal analysis of one timepoint
Hi Sarah The linear mixed effects (LME) estimation procedure deals with missing data and variable timing across subjects by specifying the time interval since baseline for each scan. You will have a different number of rows for each subject in your design matrix depending on how many time points they have. If your data exhibit significant between-subject variability in between-scan time intervals and number of time points, and several subjects with a single time point then you should use our LME matlab toolbox for the statistics. Best -Jorge De: Sarah Whittle swhit...@unimelb.edu.au Para: Martin Reuter mreu...@nmr.mgh.harvard.edu; Nick Schmansky ni...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 6 de marzo de 2013 17:17 Asunto: Re: [Freesurfer] Longitudinal analysis of one timepoint Thanks Martin and Nick, We have a number of subjects with single time points too, so I think 5.2 is the best way to go. Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)? Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline? Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go? Thanks, Sarah From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te
Re: [Freesurfer] Longitudinal analysis of one timepoint
Hi Sarah, you deal with the time during post-processing (statistical analysis). Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan. Mixed effects model is the way to go. Best, Martin On 03/06/2013 05:17 PM, Sarah Whittle wrote: Thanks Martin and Nick, We have a number of subjects with single time points too, so I think 5.2 is the best way to go. Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)? Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline? Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go? Thanks, Sarah From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
[Freesurfer] Cannot see control points in tkmedit and freeview when connecting through X11
Dear Freesurfer Team, when I am trying to set control points in tkmedit (FS 5.1 or 4.5) or to see control points in Freeview (FS 5.1), I run into a strange problem when I connect to our server through X11. Namely, I cannot see the control points, although they are being set when I place them (they are saved in the respective .dat file). When I switch to a mosaic view, I can sometimes briefly see them, but as soon as I try to place new ones, the old ones disappear again. Any known workaround (apart from using VNC)? Thank you very much, Caspar ___ 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] Advice on integrating FSL's BET with recon-all
I would check the mri_em_register registrations of the step that immediately precedes mri_watershed (and produces talairach_with_skull.lta). We found that most of the variability and failures occurred in this step, and mri_watershed itself is a very robust brain extraction algorithm when it is given an accurate registration (my experience with BET is that it is probably not the best tool for getting very accurate brainmasks and sometimes takes away too much). I would recommend using the BET extracted image instead of the image with skull for the initial registration step, and then you can use mri_watershed on the original image and get good results every time. This is the type of strategy we use in the HCP Pipelines (except we use something more robust than BET for the initial mask). Note that the talairach registration (done by the -talairach step with the talairach_avi tool) has nothing to do with the registration that precedes brain extraction. Perhaps it should is more robust and should be used, but the affine would have to be converted to the correct format. Peace, Matt. On 3/6/13 3:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you can use mri_convert -rl ... to reslice the output of bet so that it has the same geometry as the rest of our stream cheers Bruce On Wed, 6 Mar 2013, Winter, Warren wrote: Hi again, We have had some suboptimal results from FreeSurfer's skullstripping algorithm, even after iteratively trying different watershed thresholds and after checking the quality of Talairach registration. The results are pretty good, but often leave some dura matter and bits of neck behind whose higher intensity values, I believe, may end up skewing recon-all's later estimation of the range of intensity values within grey matter, and consequently compromising the accuracy of pial surface estimation. FSL's BET, however, seems to do a better job of extracting the brain, at least for our dataset. So, I was wondering if I might be able to skip over mri_watershed and feed autorecon2 and autorecon3 a brainmask.mgz file created using BET. I tried this procedure: 1) mri_convert path/to/T1dcm T1.nii.gz 2) bet T1.nii.gz BET_brainmask.nii.gz -A 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz 4) recon-all -s subjid -autorecon1 -noskullstrip 5) mv BET_brainmask.nii.gz ./subjid/mri/brainmask.mgz 6) recon-all -s subjid -autorecon2 -autorecon3 And I got this error message, right after normalization2: #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20 12_bet/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match those of brainmask.mgz, resulting during normalization2 in a mismatch between brain.mgz and brainmask.mgz. Does that seem right, and is there a possible workaround? Thank you! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] Longitudinal analysis of one timepoint
Thanks very much! From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 10:22 AM To: Sarah Whittle Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sarah, you deal with the time during post-processing (statistical analysis). Yes, you have differently many rows for each subject. Years could be time from baseline, or time from start of study (e.g. start of drug treatment). It may be the same, but if some subjects are missing the baseline scan in a drug study it may be better to use the start of the drug instead of the first scan. Mixed effects model is the way to go. Best, Martin On 03/06/2013 05:17 PM, Sarah Whittle wrote: Thanks Martin and Nick, We have a number of subjects with single time points too, so I think 5.2 is the best way to go. Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post processing by specifying the years between scans (which would be different for these two cases)? Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline? Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go? Thanks, Sarah From: Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Thursday, 7 March 2013 5:41 AM To: Nick Schmansky Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint Hi Sara, yes, should work, just make sure that all cross are 5.1 (and not mixed) to remain consistent. By the way 5.1 can process differently many time points for each subject. Just not subjects with a single time point only. To include those you'd need 5.2 Best, Martin On 03/06/2013 01:32 PM, Nick Schmansky wrote: Sarah, I'm cc'ing martin reuter on this, but yes, you should be able to use your cross-sectionally processed scans from v5.1 in a longitudinal analysis using v5.2. Nick On Wed, 2013-03-06 at 05:46 +, Sarah Whittle wrote: Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote: Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled “Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models”. In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I’m very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan __ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum
[Freesurfer] 3T MPRage flags
The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences. I use 3T MPRages. What is the recommended use in this case? Thanks Josh ___ 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] 3T MPRage flags
Josh, The new -3T flag affects the nu correction stage, and specifies a 3T-based target for the talairach alignment, and the existing -mprage flag affects mri_normalize and mri_segment, so you can use both. Nick The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences. I use 3T MPRages. What is the recommended use in this case? Thanks Josh ___ 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.
