Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Re: [Freesurfer] mri_vol2surf visualization problem
by Klein, Holger 16 Feb '12

16 Feb '12

Dear Bruce, The patch (only 16 kb ???) was successfully created via label2patch. But loading it in tksurfer after having loaded a surface the following error occured: % surface not flattened - disabling 2d code... What am I doing wrong? Isn't there a way via the command mri_vol2surf? What output format should I use for the surface I create with this command? Thanks, Holger 2012/2/16 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > p.s. could you cc the list on your replies so others can learn (I did on > mine) > > > 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<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. >> >> >> >>

2 5

TRACULA bvecs question
by Tetiana Dadakova 16 Feb '12

16 Feb '12

Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, Tanja.

5 16

Re: [Freesurfer] (no subject)
by Meryem Ayse Yucel 16 Feb '12

16 Feb '12

Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129 (t=0.192235) 2 -0.25 -0.238292 (t=1.09283) 3 0 -0.00411884 (t=1.27811) 4 0.25 0.228971 (t=2.16243) 5 0.5 0.459511 (t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide Matrix dimensions must agree. Error in ==> fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean; > Hi, > > > I am trying to use selxavg3-sess function and getting this error. Below is > the error I get. I actually have this fingertap.par file but freesurfer > somehow does not see it. Any help would be > appreciated. > > Thanks! > > Meryem Yucel > PMI Lab > > > > Extension format = nii.gz > ERROR: opening > /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap > No such file or directory > ??? Output argument "partype" (and maybe others) not assigned during call > to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m > (fast_ldpar4)". > > Error in ==> fast_ldpar4 at 45 > par4 = []; > > Error in ==> flac_customize at 121 > [par partype] = fast_ldpar4(parpath); > > Error in ==> fast_selxavg3 at 65 > flac0 = flac_customize(flac0); > >

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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. > > > >

1 0

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

2 1

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

3 2

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

2 1

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

2 1

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

2 1

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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Freesurfer February 2012