Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

Saving subjects
by Garikoitz Lerma-Usabiaga 06 Jun '13

06 Jun '13

Hi list, we have some subjects with acquisition problems. Do you think it is possible to save this two subjects, and if so, how? They have been run with: recon-all -i (file) -s (subject) -qcache -hippo-subfields -all They have been acquired with 3T, MPRAGE (but I didn't add the flags). I've read in the list about -washu-mprage , but I don't know how to use, couldn't find the documentation. Should it be enough adding wm control points? Many thanks in advance! Gari (sorry to post that many images, they belong to only two different subjects) [image: Inline image 5][image: Inline image 4][image: Inline image 3][image: Inline image 2][image: Inline image 1]

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maximum thickness value?
by Colin Reveley 06 Jun '13

06 Jun '13

I'm using data that's 0.35mm isotropic (and lower, but I've just noticed this). to do that I alter the header so that the voxels claim to be 1mm. it's a small brain so this works. Everything in general is fine. the only thing is I'm having touble with the cortical thickness output of mris_make_surfaces. I can't remember if this is a new problem, or has just never mattered to me before. when I run mris_make_surfaces, the ?h.thickness data seems to top out at 5. So that most of the brain has a thickness of 5. I wonder does freesurfer top out the thickness metric data at 5mm, since humans (or monkeys) don't normally have GM that is more than 5mm thick? if that's the case, can I change the behavior? I hope it is my error, and the thickness is topping at 5 for some reason I can control. attahced: pial surface with metric on it and scale bar sagittal slice with little measurements drawn to estimate thickness. if you multiply the meaurements by 0.35 they are roughly what you'd expect. but many are >5mm before scaling. they all report as 5mm. I really need just anyway to calculate the thickness. that would be great. It needs to be quite accurate. maybe I could change the volume back to 0.35 conformed, then scale the surfaces as well, and use mris-refine or something like that? the data would be the same but freesurfer would now know the true dimensions when it ran mris_refine. or anything that generates ?h.thickness. many thanks, Colin

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Group analysis
by Tudor Popescu 06 Jun '13

06 Jun '13

> > Under fsaverage/surf there is both an lh.white and an lh.white_avg file, >> while under average/surf there's only lh.white_avg. I repeated the >> mri_surf2surf command above with "--s fsaverage" instead of "--s average" >> (since I understand in this case it's the same thing), and then it ran to >> completion. >> > It should be close but probably not exact. So if I want to use the study-specific "average" subject surface with mri_surf2surf, rather than the generic "fsaverage" one, how can this be done given that the required ls.white file only exists in the latter but not in the former? Can I just rename (or duplicate) ls.white into ls.white_avg? Also, 1) Doesn't mri_surf2surf also need to be applied to surface of individual study subjects, or only to the (fs)average subject? 2) Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the group tutorial<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalys…>, the former is "lh.gender_age.thickness.*10*.mgh" while the latter is "lh.gender_age.thickness.*10B*.mgh". Or should it just be the unsmoothed output of mris_preproc? 3) Assuming the label files (corresponding to my ROI, and extracted from the Destrieux atlas) are different for each subject, and given mri_glmfit is called just once, for all subjects, which label file (corresponding to what subject) should I point it to? Thanks!

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Re: [Freesurfer] max thickness value
by Colin Reveley 06 Jun '13

06 Jun '13

I just found mris_thickness. which has a setting to override the default 5mm. you just run it. whoops. I'm very tired. apologies. I just assumed it would be hard.

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R: Re: Tracula
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no.Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: Tracula Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example. On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > Hi list and Anastasia, > I'm performing a set of data with tracula version 3.0. I have change my > dmrirc file respect to previous analyses and now I have one problem > > "set: Variable name must begin with a letter. > ERROR: must specify as many DWI dicoms as subjects". > > I do not find the line that is wrong. I think to have approximately used the > same lines of previous and correct analysis. > > I have attached the configuration file. Note that I'm using nii.gz. > > Thanks and best regards. > > > Stefano > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: Re: R: Re: Tracula
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Tracula What do you get when you run "echo $SUBJECTS_DIR"? On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > configuration file start normally and this no. > Do you note some line that might be wrong additionally to setenv > SUBJECTS_DIR line. > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-giu-2013 16.09 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: Tracula > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > SUBJECTS_DIR, see the example configuration file on the wiki and under > $FREESURFER_HOME/bin/dmrirc.example. > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi list and Anastasia, > > I'm performing a set of data with tracula version 3.0. I have change my > > dmrirc file respect to previous analyses and now I have one problem > > > > "set: Variable name must begin with a letter. > > ERROR: must specify as many DWI dicoms as subjects". > > > > I do not find the line that is wrong. I think to have approximately used > the > > same lines of previous and correct analysis. > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > Thanks and best regards. > > > > > > Stefano > > > > > > > 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: Re: R: Re: Tracula
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

/Applications/freesurfer/subjects/subject_prova Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: Tracula What do you get when you run "echo $SUBJECTS_DIR"? On Thu, 6 Jun 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > yes, I have check the SUBJECTS_DIR. I do not understand why all previous > configuration file start normally and this no. > Do you note some line that might be wrong additionally to setenv > SUBJECTS_DIR line. > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-giu-2013 16.09 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: Tracula > > > Is the "setenv SUBJECTS_DIR" line really commented out? You must set > SUBJECTS_DIR, see the example configuration file on the wiki and under > $FREESURFER_HOME/bin/dmrirc.example. > > On Wed, 5 Jun 2013, stdp82(a)virgilio.it wrote: > > > Hi list and Anastasia, > > I'm performing a set of data with tracula version 3.0. I have change my > > dmrirc file respect to previous analyses and now I have one problem > > > > "set: Variable name must begin with a letter. > > ERROR: must specify as many DWI dicoms as subjects". > > > > I do not find the line that is wrong. I think to have approximately used > the > > same lines of previous and correct analysis. > > > > I have attached the configuration file. Note that I'm using nii.gz. > > > > Thanks and best regards. > > > > > > Stefano > > > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >

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dimensions of sig.nii.gz
by dgw 05 Jun '13

05 Jun '13

Hi, I am examining the difference in significance between different scan parameters in a retinotopy experiment and analysis. I have loaded the sig.nii.gz file in matlab using MRIread, and I am confused by the dimensions of the "volume". I understand that this is a surface based file, but the dimensions of my sig file from the eccen subfolder are: 1 148498 1 2 Obviously the ones are not a problem and the 148498 refers to the number of vertices in that hemisphere. What does the 2 mean? What is that second component? (note this is using 5.1.0). Thanks, Dan

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first level glm analysis on surface space
by Subhabrata Chaudhury 05 Jun '13

05 Jun '13

Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take each functional volume corresponding to each TR and move each volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). Then I want to run first level glm on the data like its done for volume data in spm, fsl, afni etc. My question is are there tools in freesurfer to do this on surfaces ? If not, can the mgh file be converted to a gifti file and maybe it can be used to make first level glms in afni, spm or fsl ? I will really appreciate your opinion about this. Thank you very much, Subha

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Processing High Res. Data (0.375mm)
by Daniel LaFreniere 05 Jun '13

05 Jun '13

Dear Freesurfer Experts, I'm currently in the middle of processing high resolution MRI through the standard FS pipeline. I've recently read a very interesting article and wanted to attempt a high resolution protocol for a bit of a side project - we initially obtained an iso resolution of 0.375mm so I might as well try and make use of it and learn something along the way! However, I'm starting to run into issues straight from the get-go during -autorecon1. The flag I use is as follows: recon-all -autorecon1 -mprage -hires -nuiterations 10 -subjid fom04_hires2 Often I use -washu_mprage (dark GM) and -nuiterations closer to 50 since it doesn't seem to hurt anything (the hires protocol takes much longer so I've reduced to 10-20). After -nuiterations finishes running, I suddenly get the following error: Writing to ./tmp.mri_nu_correct.mni.902/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.902/nu20.mnc ./tmp.mri_nu_correct.mni.902/nu20.mnc mul 1.33669825436408977556 mris_calc(5163) malloc: *** mmap(size=864002048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug mris_calc: virtual memory exhausted. Cannot allocate memory Darwin dhcp-10-23-184-237.capitalhealth.ca 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s fom04_hires2 exited with ERRORS at Wed Jun 5 10:42:36 MDT 2013 For reference, I've added the more detailed recon-all log as well. I'm running a Macbook Pro, OS X 10.8 with 8GB of RAM/2.9 GHz with FS version 5.1.0. I've also been keeping my eye on the Activity Monitor and continuously purge inactive memory as freesurfer runs. I've even had the program crash when I'm sitting at 5 GB of unused memory with a VM size readout of about 420 GB. I can't seem to figure out what's happening but have a feeling that I just need a much more powerful computer to process the 0.375mm voxels. Any help, suggestions, or insight would be greatly appreciated. Thank you very much for your time, Dan

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