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30088 discussions

In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab
by ZhiLiangLong 28 Feb '12

28 Feb '12

Hi freesurfer experts: i'm using qdec to perform statistical analysis in Freesurfer 5.0.0, within 'Measure' menu in 'Design' tab, the default is 'thickness', however, there are other measurements such as 'area' and 'area.pial'. the latter seems meaning area in pial surface. what does the former mean? does it mean area in white matter surface?

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Problem with whit matter inclusion
by Amanda Rodrigue 27 Feb '12

27 Feb '12

HI, I am doing cortical thickness analysis and I am on my 18th round of edits for this particular subject. In 2 places It seems to be including a large chunk of gray matter as white and when viewing the auxiliary volume, there is no white matter there (please see attached images). This continues for several slices. Is there any way to fix this? Thanks. Amanda Rodrigue -- Amanda Rodrigue Doctoral Student Psychology: Brain and Behavior Sciences University of Georgia

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treatment of missing values in mri_glmfit
by Kristine Beate Walhovd 27 Feb '12

27 Feb '12

Hi, we´re running FS 5.1 and have a data set with a lot of missing values. There are different subsets of persons missing different values of interest, and we´re running analyses on concat files. mri_glmfit not qdec). Is there anyway we can run analyses w/ missings in the fsgd file? Best, Kristine

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Problem with covariates in design for surface based analysis
by Charlotte Bernard 27 Feb '12

27 Feb '12

Dear Freesurfur users, I have a question about the design for a surface based analysis! I want to compare controls and patients. I have 5 covariates. One is a continous variable. The others are categorial variables (4 with 2 levels and 1 with 5 levels). I want to ajust my result with all of thoses variables. I am interested in the difference in thickness between patients and controls. Is it possible to construct such design? Can I put some of my variables in the "nuisance factors" ? I don't really understand the difference between "nuisance factor" and covariabes. I really hope somebody can help me. Thanks for all! All the best, Charlotte

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mri_convert
by Jimmy Ghaziri 27 Feb '12

27 Feb '12

Dear FreeSurfer community, I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz. When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test). Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes. Here are the commands I'm launching : mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview. I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image). Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ? Thank you very much ! Jimmy

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Bus error in mri_ca_normalize
by Jürgen Hänggi 27 Feb '12

27 Feb '12

Dear FS experts I am trying to produce surface models with a higher resolution than 1x1x1mm from T1-w. images acquired on a 7T scanner (0.75x0.75x0.75 mm). I have run the following commands so far: recon-all -autorecon1 -cm -noskullstrip -s <subject> cd subject/mri mri_convert -cs 1 nu.mgz nu.conformed.mgz mri_em_register -skull nu.conformed.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta recon-all -skullstrip -s <subject> recon-all -autorecon2 -s <subject> But here in the mri_ca_normalize stage the following error occurred: #@# CA Normalize Mon Feb 27 15:59:02 CET 2012 /Applications/freesurfer/subjects/juergen_div20_mul10/mri \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz \n writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (74, 88, 45) --> (255, 241, 263) using (134, 139, 154) as brain centroid... mean wm in atlas = 107, using box (112,120,127) --> (156, 157,180) to find MRI wm before smoothing, mri peak at 60 after smoothing, mri peak at 59, scaling input intensities by 1.814 scaling channel 0 by 1.81356 using 244171 sample points... INFO: compute sample coordinates transform 0.711 0.342 -0.142 -31.880; -0.390 1.046 0.458 -32.152; 0.229 -0.154 0.686 -1.771; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (136, 101, 33) --> (257, 215, 241) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 255.0 0 of 612 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (92, 84, 39) --> (208, 187, 247) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 125.0 1 of 340 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (147, 176, 65) --> (203, 229, 135) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 255.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 171, 73) --> (158, 204, 145) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 255.0 1 of 4 (25.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (134, 158, 114) --> (185, 219, 154) Bus error Darwin Juergen-Haenggis-Mac-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s juergen_div20_mul10 exited with ERRORS at Mon Feb 27 16:02:08 CET 2012 Any idea what is the problem? I used the Mac OSX version, but the error also occurred in the Linux 32bit version. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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last index missing when using mri_label2vol
by David Grayson 27 Feb '12

27 Feb '12

Hi, I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the final label from the color table file. I tried using the --thresh 1 option, but that didn't work either. i.e... mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o custom_lh.nii.gz --subject FREESURFER --hemi lh --identity The last index is no where to be found in the custom_lh.nii.gz. But the other indices look OK. Has anyone encountered this before, and know what to do? Thanks very much! David

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?h.dpial.ribbon.mgz not found
by octavian lie 27 Feb '12

27 Feb '12

Dear Bruce & FreeSurfers, I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using recon-all -all; it went on for 8 hours, I got the message (Recon complete without errors) in the log.txt file in my subject directory. However, when trying to use mri_convert or tkmedit to see the lh.dpial.ribbon.mgz, there was an error (could not open file). I searched for the file in all the /mri folder and the whole file system on my box, could not find it. I found lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the dpial.ribbon.mgz file or any other ?.ribbon.mgz variety. I appreciate your suggestions. Octavian.

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FSL_niftii
by Gabor Perlaki 27 Feb '12

27 Feb '12

Dear all, I've some fsl niftii MPRAGE images converted by MRIConverter. They look fine in fslview and I can open them by freesurfer as well (tkmedit -f *.nii.gz) , but when I compare the images between fslview and tkmedit they look slightly different. It seems that the orientation is the same in both viewer, but the rotation is slightly different. Why are the images slightly rotated (reoriented) viewing by tkmedit? Is it affect any statistics by freesurfer? Thanks, Gabor

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Re: [Freesurfer] Choosing a Contrast
by Douglas N Greve 27 Feb '12

27 Feb '12

what do you want to test? doug Allie Rosen wrote: > Hi Doug, > > I have. I think that I have two groups (patients/controls) with one > covariate (age), so the following is my situation: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V > > Thank you again, > Allison > > > > On Mon, Feb 27, 2012 at 10:31 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Allison, have you looked at > http://www.freesurfer.net/fswiki/PairedAnalysis ? > doug > > Allie Rosen wrote: > > Hi All, > > I am trying to figure out the contrasts to use for a study. I > am comparing age matched patients and controls (all female). > The FSGD file has 4 columns, but I'm not sure how to make an > appropriate contrast matrix. I can't seem to find an > applicable example on the wiki. > > Any guidance would be appreciated. > Thank you, > Allison > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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