Freesurfer

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30088 discussions

mri_glmfit-sim error
by GREGORY R KIRK 10 Mar '11

10 Mar '11

hi folks, when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg i get an error message ERROR: cannot find /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd there is fsaverage... should i just make a soft link ? also when i run the mri_glmfit-sim with or without --cache i get WARNING: unrecognized mri_glmfit cmd option doss, the glm fit anal was -doss and went without problem or complaints. and using sim without --cache the simulations are running. is this a nuisance error message that i should just ignore ? thanks greg

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DODS and DOSS
by Christopher Bell 10 Mar '11

10 Mar '11

FreeSurfers, I have been analyzing my qdec data in version 5.0 and have some interesting although somewhat confusing results. Basically I have run a very simple analysis with DODS and DOSS. My discrete factor is group and my covariate is age, about as simple as can be. When I look at the results for DODS I get: thickness-age correlation (accounting for group)---result: much of brain significant group difference (I assume controlling for age, but it doesn't say explicitly)--result: one small roi significant thickness-age correlation group difference--result: one small roi spatially adjacent to group difference roi When I run DOSS I get: thickness-age correlation (accounting for group)---result: much of brain significant group difference (I assume controlling for age, but it doesn't say explicitly)--result: much of brain significant thickness-age correlation group difference--result: much of brain significant I am mostly surprised by how much larger the (group difference), and the (thickness-age correlation group difference) increase with the DOSS method. I am also not quite how to interpret the thickness-age correlation group difference in DOSS. I was thinking the DOSS method constrained both groups to have the "same slope" and so I was expecting to get nothing for difference in thickness-age correlation difference by group; isn't this suggesting my two groups have significantly different ageXthickness slopes even though they are constrained to have the same slope by the DOSS method? It would almost make more sense to me if the results were reversed between DOSS and DODS. If I had a large thicknessXage correlation group difference using the DODS method which allows for different slopes. Thanks for any enlightenment. Chris Bell University of Minnesota

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mri_glmfit allocate memory error
by Andrew Mendlowitz 10 Mar '11

10 Mar '11

Hello All, I get the following error while trying to run mri_glmfit. I am running a 2.93 ghz imac with 8gb of ram. I am also running freesurfer version 5.0.0 on Snow Leopard OS version 10.6. /Applications/freesurfer/subjects/qdec$ mri_glmfit --glmdir lh.paired-diff --fsgd paired-diff.fsgd --C mean.mtx --y lh.paired-diff.thickness.mghgdfReadHeader: reading paired-diff.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 1.5 Class Means of each Continuous Variable 1 Main 1.5000 INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /Applications/freesurfer/subjects/qdec cmdline mri_glmfit --glmdir lh.paired-diff --fsgd paired-diff.fsgd --C mean.mtx --y lh.paired-diff.thickness.mgh sysname Darwin hostname larry machine i386 user amend FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh logyflag 0 usedti 0 FSGD paired-diff.fsgd glmdir lh.paired-diff IllCondOK 0 DoFFx 0 Creating output directory lh.paired-diff Loading y from /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIallocIndices: could not allocate 1714511945 elt index array Cannot allocate memory The mri_info for the file is : mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh, -1): could not open file amend@larry /Applications/freesurfer/subjects/qdec$ mri_info /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh Volume information for /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh type: MGH dimensions: 1714510945 x 1853057372 x 1634628457 x 1668310833 voxel sizes: 72950800688805540228332034981888.0000, 0.0000, 70387746064971392794503413760.0000 type: UNKNOWN (842347100) fov: inf dof: 1668244335 xstart: -inf, xend: inf ystart: -39.8, yend: 39.8 zstart: -57528904905339976080461439864148066304.0, zend: 57528904905339976080461439864148066304.0 TR: 71446969504754118412748034408448.00 msec, TE: 17862977898376175754203558313984.00 msec, TI: 4464583905807213894543171649536.00 msec, flip angle: 4128358109894647822155776.00 degrees nframes: 1668310833 PhEncDir: UNKNOWN ras xform present xform info: x_r = 19441367164500690594879212879872.0000, y_r = 282670772483715414097920.0000, z_r = 4630517930517356511053742080.0000, c_r = 18179207505345150839094025125888.0000 : x_a = 72953300747400503281465327353856.0000, y_a = 71756401321839400437789128392704.0000, z_a = 4721224652433019196440490016768.0000, c_a = 0.0000 : x_s = 0.0000, y_s = 208210237828607676252160.0000, z_s = 4286666299869639999488.0000, c_s = 4622889417339745644740714954752.0000 talairach xfm : Orientation : AAA Primary Slice Direction: coronal voxel to ras transform: inf 12133604733747200.0000 inf -inf inf 3080133850722982464323584.0000 inf -inf 36752183205510726549504.0000 8937395835633664.0000 inf -inf 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant nan ras to voxel transform: mat = NULL! Invalid argument MatrixFree: NULL mat POINTER! Invalid argument -Andrew

2 1

Mac Pro with 12cores
by 汪贵宏 10 Mar '11

10 Mar '11

Hi,all: As we have too many controls and patients to run the "recon-all",and it is really time-suming,so,how can I reduce the time of recon-all in a group of patients? After read the statistic info on the website https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllRunTimes It seems the mac pro will take much more time than others,so ,can anybody give me a suggestion?Is itMac Pro with 12 cores works? http://www.apple.com/macpro/ Thanks a lot! Wang

4 5

about recon-all command
by Kenichiro Tanaka 10 Mar '11

10 Mar '11

Hello All, I have a question about recon-all command with "-cw256" option. What is the difference between "recon-all" and "recon-all with -cw256"? What is "-cw256 option"? When I tried executing recon-all command, I had an error message: /**************************************** // ERROR! FOV=320.000 > 256 // Include the flag -cw256 with recon-all! //**************************************** / I did the following using another 001.mgz file: I compared aseg.stats file after "recon-all" execution with aseg.stats file after "recon-all -cw256" execution using "diff" command. aseg.stats file after "recon-all " execution was much different from aseg.stats file after "recon-all -cw256" execution. What's wrong with it? I tried to search information about "-cw256"on internet, but I could not find out. Please tell me -cw256. Thanks. Kenichiro Tanaka

2 1

Re: [Freesurfer] 2 questions on folding index, local gyrification index
by Chris Hyatt 09 Mar '11

09 Mar '11

Hi Marie, Thank you for the information. The routine fspecial() is used in four M-files, 'make_outer_surface.m' where it is used to setup a 2-D Gaussian filter; 'read_eccen_patch.m', 'read_freq_patch.m' and 'read_patch.m', where in all 3 cases it's used to setup a simple averaging filter. Other than fspecial and imclose, I'm not aware of any other image processing toolbox routines used in the lGI calculation, but I will let you know if I find additional routines. Thanks again, Chris >>> Marie Schaer 03/09/11 5:00 PM >>> Hi Chris, Regarding your question on lGI, I am sure that imclose is one of the required function belonging to the Image Processing Toolbox. I may be wrong but I think that it is the only one. More specifically I don't remember that I used fspecial, where did you see it? (Apart from imclose, if you identify other functions from the Image Processing Toolbox called by lGI , could you please inform me? Thanks!) Then for you first question, maybe you can have a look at this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15683.html and adapt it for the Folding Index (?). Hope it helps, Marie On Mar 9, 2011, at 3:56 PM, Chris Hyatt wrote: > I had asked the Listserv a week or so ago if there was a way to get the Folding Index measurement for each subject and ROI using aparcstats2table, similar to area, thickness, gray volume etc.. The data are in the ?h.aparc.stats files for each subject, along with thickness, thickness std, surface area, gray volume, mean curv, gauss curv and curv index. Can this be done, or the feature added to aparcstats2table? If not, I'll write my own code to do this. > > Also, I'm calculating the local Gyrification Index (lGI) for my subjects. It works well, but our group currently has only one Image Processing Toolbox license. It appears Freesurfer calls the toolbox only briefly. Does anyone know which toolbox functions are called? I know that fspecial() is one of the functions called, and if that is the only function, it probably can be replaced with a custom function to eliminate the need for the toolbox. > > Thanks! > Chris > > > > > > > > _______________________________________________ > 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. >

1 0

mri_mask problem
by Gabriel Go.Es. 09 Mar '11

09 Mar '11

Hello, I'm making some manual segmentation changes in the brainmask.mgz and using mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the output from the mri_vol2vol looks perfectly normal,and retains all changed made by me, but when I use the mri_mask command over the rawavg.mgz no segmentation seems to be donne in the final output file. Does any one has an idea of what could be wrong? the commands after manual corrections are: mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheadermri_mask rawavg.mgz brain2raw.mgz outbrain.mgz Thanks in advanced,Gabriel

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Re: [Freesurfer] glm question
by Douglas N Greve 09 Mar '11

09 Mar '11

Gabriel Go.Es. wrote: > > Thank you so much, Doug > > I've check at your update and saw that this contrast has to be /2, > wich I guess means 0.5 instead of one to keep the scale right? Yes. > > and the contrast for me, would be something like: > Let's suppose > group1_males > group1_females > group2_males > group2_females > group3_males > group3_females > for differences between males and females (males > females) > regreessing the efects of group would be: > [0.333 -0.333 0.333 -0.333 0.333 -0.333] Correct > differences between group1 & group 3 regressing the effects of gender: > [0.5 0.5 0 0 -0.5 -0.5] Correct > and the differences between males and females for a single group can be: > [1 -1 0 0 0 0] > am I right??? Yes > but I don't yet figure out how to set a difference from 0 in any of > the group means (to meassure the effect of group), nor the interaction > between group and gender, and that's because my model is not like the > one from the example, Try using [1 -1 -1 1 0 0] [1 0 0 0 -1 1] This is a single matrix with two rows. The first row tests for an interaction between G1/2 and M/F. The second row tests for G1/3 and M/F. Note that you don't need a third row. > > > > > > > Date: Wed, 9 Mar 2011 14:52:37 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: gabriellbk(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] glm question > > > > That contrast is wrong. I've updated this page with the correct contrast > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V > > which is: > > > > |+1 -1 0 -1 +1 0| > > |+1 0 -1 -1 0 +1| > > > > This is an F-contrast (two rows). The first row looks for a difference > > between L and R for M and F (ie, a simple interaction between LR and > > MF). The second row looks for a difference between L and A for M and F. > > If either of these subcontrasts shows an effect, then there is an > > interaction. > > > > doug > > > > > > Gabriel Go.Es. wrote: > > > > > > Dear FreeSurfer experts, > > > > > > > > > > > > I'm doing some group analyses and I'm a little stocked with this: > > > > > > I have Six Groups (2 Factors, one with three levels and the other one > > > with two levels), and one covariate. I don't know the rule for > setting > > > the contrasts for an ANOVA and for the interaction between the two > > > factors regressing out the covariate. I've checked at the FS wiki and > > > found the following contrast for six groups (two factors) and zero > > > covariates. > > > > > > > > > > > > Contrast 6 gender-x-handedness.mtx (interaction between gender and > > > handedness) > > > > > > [0.333 -0.333 -0.333 0.333 0.000 0.000 0.000 0.000 0.000] > > > > > > [0.000 0.000 0.000 0.000 0.000 0.333 -0.333 -0.333 0.333] > > > > > > > > > > > > I don’t understand the rule that has been followed. > > > > > > Can any one help me with this? > > > > > > > > > > > > Bests, > > > > > > Gabriel > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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 > > 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 > > > > > > > > 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

1 0

2 questions on folding index, local gyrification index
by Chris Hyatt 09 Mar '11

09 Mar '11

I had asked the Listserv a week or so ago if there was a way to get the Folding Index measurement for each subject and ROI using aparcstats2table, similar to area, thickness, gray volume etc.. The data are in the ?h.aparc.stats files for each subject, along with thickness, thickness std, surface area, gray volume, mean curv, gauss curv and curv index. Can this be done, or the feature added to aparcstats2table? If not, I'll write my own code to do this. Also, I'm calculating the local Gyrification Index (lGI) for my subjects. It works well, but our group currently has only one Image Processing Toolbox license. It appears Freesurfer calls the toolbox only briefly. Does anyone know which toolbox functions are called? I know that fspecial() is one of the functions called, and if that is the only function, it probably can be replaced with a custom function to eliminate the need for the toolbox. Thanks! Chris

2 1

Original Brain Surface Transparent
by Allie Rosen 09 Mar '11

09 Mar '11

Hi Everyone Again, I thought I'd re-state my question more clearly: I managed to make an annotation with 2 parts: one, of interest, and the other, not. On the color table file, the "not of interest" part has 0 0 0 0 for Red, Green, Blue, and Opacity. However, when I load the annotation in TkSurfer, the "not of interest" part of the brain is the original grey. So, here is my question: is there a way to make the original brain surface transparent? If not, then it is pointless for me to have the "not of interest" part in my annotation at all. Thanks very much, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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