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30132 discussions

mri_binarize VS mri_extract_label
by Palzes, Vanessa 28 Feb '12

28 Feb '12

Could someone please explain to me the difference between mri_binarize and mri_extract_label? I had been using mri_extract_label to create ROI masks of cerebral white matter (2 and 41). I recently became aware that this would give me a label with 0 and 128. I tried mri_binarize (with the same matchvals 2 and 41) and it gave me a label of 0 and 1. However, when comparing the two in tkmedit, it appears as though the mask I created using mri_binarize includes more of the corpus callosum region in mid-sagittal slices. I've tried this on a couple different subjects, so I do not think it is limited to one person. Is this a typical difference between the two commands? And if so, which one is recommended for extracting white matter masks? Also to note that before running either of these commands, I also convert the aseg.mgz to the subject's native space (using rawavg.mgz as a template). The commands I ran are the following: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz mri_extract_label aseg-in-rawavg.mgz 2 41 cerebral_wm.nii mri_binarize --i aseg-in-rawavg.mgz --match 2 41 --wm --o cerebral_wm_binarize.nii On another note, I was wondering if there is a way to create a probability map for the white matter. That is, instead of getting a binary (0s and 1s) mask, I would get the probability of each voxel being part of the white matter ROI with values ranging from 0 to 1. Thanks for your help, Vanessa Palzes Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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qdec and Intracranial volume correction - error message
by Mahinda Yogarajah 28 Feb '12

28 Feb '12

Dear Experts, I am trying to carry out a simple 2 group (conrol and patient) analysis with ICV as nuisance factor, and thickness as the dependent variable. However whenever I include ICV (inputed by following the qdec tutorial and the generate stats table) I get the following output and error message: ------------------------------------------------------------------ lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-thickness-IntraCranialVol-Cor ----------------------- Does the correlation between thickness and IntraCranialVol, accounting for diagnosis, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-Patients-Control-Intercept-thickness ----------------------- Does the average thickness differ between Patients and Control? 1.000 -1.000 0.000 0.000; lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol ----------------------- Does the thickness--IntraCranialVol correlation differ between Patients and Control? 0.000 0.000 1.000 -1.000; ninputs = 40 Checking inputs nframestot = 40 Allocing output Done allocing nframes = 40 Writing to /home/myogaraj/freesurfer/qdec/Untitled/y.mgh gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 IntraCranialVol 1.42401e+06 259214 Class Means of each Continuous Variable 1 diagnosisPatients 1343236.0559 2 diagnosisControl 1497089.0952 INFO: gd2mtx_method is dods Reading source surface /home/myogaraj/freesurfer/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/myogaraj/freesurfer/qdec cmdline mri_glmfit --y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh --fsgd /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/myogaraj/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-thickness-IntraCranialVol-Cor.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol.mat sysname Linux hostname localhost.localdomain machine x86_64 user myogaraj FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd labelmask /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/myogaraj/freesurfer/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/myogaraj/freesurfer/qdec/Untitled Loading y from /home/myogaraj/freesurfer/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/myogaraj/freesurfer/qdec/Untitled/Xg.dat Normalized matrix condition is 175.031 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /home/myogaraj/freesurfer/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 36 Starting fit and test Fit completed in 0.0710833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995672, ar1std=0.001628, gstd=6.144582, fwhm=14.469384 Writing results lh-Avg-Intercept-thickness maxvox sig=19.391 F=349.349 at index 102911 0 0 seed=1330322022 lh-Avg-thickness-IntraCranialVol-Cor maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022 lh-Diff-Patients-Control-Intercept-thickness maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022 lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=1330322022 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /home/myogaraj/freesurfer/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 IntraCranialVol 1.42401e+06 259213 Class Means of each Continuous Variable 1 diagnosisPatients 1343236.3158 2 diagnosisControl 1497089.0476 MatrixMultiply: m1 is null! No such file or directory --------------------------------------------------------- Can anyone advise ? Thanks. Mahinda

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Re: [Freesurfer] ?h.dpial.ribbon.mgz not found
by Douglas N Greve 28 Feb '12

28 Feb '12

It will do it's best, how well depends on the size of the resection. FS it assuming that the input is an intact (though perhaps diseased) brain. Away from the resection, it will probably do ok. Near the resection, it will probably fail, but you can probably fix it manually. doug octavian lie wrote: > > Thank you, Doug, > > One unrelated question: can I run freesurfer on postoperative T1 > MPRAGE sequences, where the relationship of the gray to white matter > (out-in) is disrupted at the site of resection? If so, can you share > any good advice on parameters to adjust? > Thank you, > > Octavian. > > > > > On Mon, Feb 27, 2012 at 10:14 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Octavian, recon-all does not use --save_distance by default. You > can have it add --save_distance to the mris_volmask command line > using the "expert options". Run recon-all with -help to get more info. > doug > > octavian lie wrote: > > Dear all, > to follow up on my prior message below, I must say that I > called the recon-all -autorecon-all command remotely through a > automatic matlab routine in which freesurfer is one leg, with > the command nohup. For some reason, when doing this, the step > mris_volmask was run without the option --save_distance hence > no ?h.dpial.ribbon.mgz fille was created. To fix this, I > manually entered the following command in the linux terminal: > mris_volmask--label_left_white 2 --label_left_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > --save_distance SUB002, which created the output files needed. > Now, do you know why running recon-all -all remotely would > exclude the option --save_distance for mris_volmask. Is there > any way to fix this in the freesurfer itself, so that I do not > have to change the matlab code? > Thank you, also see my message below. > Octavian. > On Sat, Feb 25, 2012 at 6:46 PM, octavian lie > <octavian.lie(a)gmail.com <mailto:octavian.lie@gmail.com> > <mailto:octavian.lie@gmail.com > <mailto:octavian.lie@gmail.com>>> wrote: > > 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 output.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. > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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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question TRACULA
by j janssen 28 Feb '12

28 Feb '12

Hi, TRACULA gives pathstats.txt which includes *weighted* averages, mentioned on the wiki as: "weighted average over the entire support of the path distribution". question: weighted for what (is it the probability)? thanks, -joost

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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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