Freesurfer

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Re: [Freesurfer] mri_vol2surf visualization problem
by Bruce Fischl 16 Feb '12

16 Feb '12

try using label2patch and loading the resulting patch in tksurfer from the interface after loading another surface on the command line On Thu, 16 Feb 2012, Klein, Holger wrote: > Dear Bruce, > Thanks for your help. I did what you advised me to do in freeview. It works, > but the problem is that an overlay does not ameliorate my view on the Heschl > Gyrus. Thus I am looking for a solution to only view the pial surface of > this certain label without the rest of the brain, i.e. just the surface of > the volume that I created with mri_label2vol. > > Do you have a clue to do that? > > Thanks, Holger > > 2012/2/16 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Holger > > the file you are outputing isn't a surface, it's a surface > overlay. Try loading the inflated surface then load the .w file > with tksurfer load overlay > > cheers > Bruce > > > On Thu, 16 Feb 2012, Klein, Holger wrote: > > > Dear FreeSurfers, > > To get a better view on the pial surface of the > Heschl' Gyri I used the > command mri_vol2surf after having created the > suitable volume with > label2vol. My goal is to get the pial surface of > this single label. > > My Command is: *mri_vol2surf --src pf_lh_vol.mgz > --hemi lh --surf pial --sr > creg > register.dat --out_type paint --o A1surf-lh.w* > > The output file was created without any error, but > loading the file in > freeview or tksurfer an error occured: > > *command: tksurfer WH lh A1surf-lh.w > > *subject is WH* > *hemi is lh* > *surface is A1surf-lh.w* > *surfer: current subjects dir: > /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide* > *surfer: not in "scripts" dir ==> using cwd for > session root* > *surfer: session root data dir ($session) set to:* > *surfer: /freesurfer/Kontrollen/A1_Wilts_Heide* > *checking for nofix files in 'A1surf-lh.w'* > *Reading image info > (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)* > *Reading > /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* > *surfer: Reading header info from > /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* > *ERROR: MRISread: file > '/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf- > l > h.w' > has 0 vertices!* > *Probably trying to use a scalar data file as a > surface!* > > What am I doing wrong? > > Any help would be greatly appreciated. Thanks in > advance > > Holger > > > > > > 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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mri_vol2surf visualization problem
by Klein, Holger 16 Feb '12

16 Feb '12

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable volume with label2vol. My goal is to get the pial surface of this single label. My Command is: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --surf pial --srcreg register.dat --out_type paint --o A1surf-lh.w* The output file was created without any error, but loading the file in freeview or tksurfer an error occured: *command: tksurfer WH lh A1surf-lh.w *subject is WH* *hemi is lh* *surface is A1surf-lh.w* *surfer: current subjects dir: /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide* *surfer: not in "scripts" dir ==> using cwd for session root* *surfer: session root data dir ($session) set to:* *surfer: /freesurfer/Kontrollen/A1_Wilts_Heide* *checking for nofix files in 'A1surf-lh.w'* *Reading image info (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)* *Reading /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *surfer: Reading header info from /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *ERROR: MRISread: file '/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf-lh.w' has 0 vertices!* *Probably trying to use a scalar data file as a surface!* What am I doing wrong? Any help would be greatly appreciated. Thanks in advance Holger

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talairach.xfm
by cloud.ctrl＠me.com 15 Feb '12

15 Feb '12

I am having trouble with 2 scans that exit with errors. Both have the same error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** This is actually preceded by a message stating that talairach.xfm already exists and will not be copied. If I use the --clean-tal option, my recon-all finishes without error. I haven't checked to see if any manual intervention is needed yet, but even if recon-all processed just fine this way, why is it happening? Regards, Vincent

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Exclude cortical region for one subject during qdec analysis
by Jeff Sadino 15 Feb '12

15 Feb '12

Hello, I have 200 subjects and I am analyzing their cortex in qdec. I have several subjects that have poor cortical surfaces on a local basis. Is there a way for exclude just one area for just one subject during qdec analysis? For example, on some images, the patient nose is in their occipital lobe...no pathologies, just image wraparound during acquisition :). This makes the cortical surfaces unreliable in this area. Is there a way to tell qdec to ignore the occipital regions in this one subject in its analysis? Thank you very much, Jeff Sadino

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A question about mri_convert
by Jie Shi 15 Feb '12

15 Feb '12

Hi, experts. I have recently used mri_convert to convert some dicom files into both .nii and .img. But when observing in BrainSuite, I found the image orientation of the .nii and .img was not consistent. Any idea about the problem and how to make them same? Thanks a lot. Jie

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A question about mri_convert
by Jie Shi 15 Feb '12

15 Feb '12

Hi, experts. I have recently used mri_convert to convert some dicom files into both .nii and .img. But when observing, I found the image orientation of the .nii and .img was not consistent. Any idea about the problem and how to make them same? Thanks a lot. Jie

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trac-all -prep error
by Chris Watson 15 Feb '12

15 Feb '12

Hello, in running trac-all -prep, I get an error saying that it can't open "lowb.nii.gz.hdr": fslroi /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz 0 1 fslmaths /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz -Tmean /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz bet /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this problem with other subjects that I am processing. Any thoughts? Thanks, Chris

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Interactions between categorical and continuous variables
by Katherine Reiter 15 Feb '12

15 Feb '12

Hey freesurfers, I'm interested in running an interaction between a continuous and categorical variable, covarying for another categorical variable. I understand that this analysis is not possible through the QDEC GUI so I am working through the command line group analysis and setting up the contrast matrix. Discrete Factors: Group with 2 levels: Patient and Control Gender with 2 levels: Male and Female Continuous variables: Age Meaning, I have 8 Regressors: 1: PatientMale intercept 2: PatientFemale intercept 3. ControlMale intercept 4. ControlFemale intercept 5: PatientMale age 6: PatientFemale age 7. ControlMale age 8. ControlFemale age In order to look at the interaction of group and age, covarying for gender, would the matrix be: 0 0 0 0 -.5 .5 -.5 .5 However, this matrix seems looks more like a difference in slopes comparison and less like an interaction. Any help would be much appreciated! Thanks, Katie

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monte carlo simulation question
by Govindarajan, Koushik Athreya 15 Feb '12

15 Feb '12

Hello group, I am running the multiple comparisons simulation after my mri_glmfit finished. I see that it went through all the iterations and then quit with the following error message it could not find the talairach.xfm file in my average brain. I did not use the fsaverage and instead created my own template based on average normal brains. I went back and checked my average subject folder and indeed, there is no talairach.xfm file in there. I also see that the 'tmp' directory in there has a lot of the intermediate files. I do not recollect seeing an error message when I created my average brain. So, was not sure what was going on. My 2 questions are: 1. How can I finish the rest of the make_average_subject processing to create my talairach.xfm file? Do I have to start from scratch or can I continue from where it left off? 2. The same question with the mri_glmfit-sim analysis also. Is there a way for me to continue from where it left off using the new talairach.xfm file or do I have to start from scratch and go through so many hours of simulation again? Thanks a lot for all the help Koushik Govindarajan

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make average subject error
by Adam David Felton 15 Feb '12

15 Feb '12

Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. *The version of Freesurfer I am using:* v 1.313.2.6 2010/08/04 15:50:56 nicks *My memory:* 8 GB 1333 MHz DDR3 *Hard-drive:* 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote "sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface)." But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam

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