Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

Surface region masking
by Mustafa, Nazahah 12 Mar '11

12 Mar '11

Hi all I used mri_annot2label and then mri_mergelabels to get frontal lobe region. Now I am going to get structures which lie under that frontal lobe. I was thinking to overlay between the lobe mask and the structures. I tried mri_label2vol but it was not completely masking the lobe areas. Is there any other way I can do? Thank you Regards; Naza The University of Aberdeen is a charity registered in Scotland, No SC013683.

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Mac intel - OSX tiger installation
by Seán Froudist Walsh 12 Mar '11

12 Mar '11

Hi Freesurfer group, I would like to know if it is possible for me to download FreeSurfer on my Intel based Mac with OSX Tiger (10.4.11)? I have been unable to update to Leopard/Snow Leopard due to a problem with the super-drive so that is not currently an option for me. Many thanks in advance All the best, Seán

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Pial surface error
by Allie Rosen 11 Mar '11

11 Mar '11

Hi, Can someone please tell me how I would fix an error such as the one illustrated in the attached pictures? Thanks, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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Re: [Freesurfer] mri_glmfit allocate memory error
by Douglas N Greve 11 Mar '11

11 Mar '11

If you re-run mris_preproc does the same thing happen? Are you running out of disk space? doug Andrew Mendlowitz wrote: > The code for the lh.paired-diff.thickness.mgh file is > mris_preproc --target fsaverage --hemi lh \ > > --meas thickness --out lh.paired-diff.thickness.mgh \ > > --fsgd pairss.fsgd --paired-diff > > > On Thu, Mar 10, 2011 at 10:13 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > There appears to be something wrong with the > lh.paired-diff.thickness.mgh file. How was it created? > doug > > Andrew Mendlowitz wrote: > > 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 > ------------------------------------------------------------------------ > > _______________________________________________ > 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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multimodality registration problem
by Jing Ming 11 Mar '11

11 Mar '11

Hi surfers: I would like to project some fMRI data into fsaverage surface. And the fMRI result is registered into AFNI template, which is talariach template. I wonder how can I register this fMRI result into fsaverage template. The mri_vol2surf need a register.dat, between moving data and anatomical data, and requires this anatomaical data processed by freesurfer. So, that means, I need to run recon-all to AFNI talariach template? Thanks much for your help! Jing

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

11 Mar '11

two row contrast matrix [1 1 -1 -1 0 0] [1 1 0 0 -1 -1]/2 1st row test for a difference bet G1 and G2 2nd row tests for a difference bet G1 and G3 Note that you don't need to test G2 vs G3 (that is implied by the other two tests). doug On 3/9/11 7:33 PM, Gabriel Go.Es. wrote: > > Thanks a lot, > just one another question Doug, > how to set an ANOVA for group differences??' > > Gabriel > > > > > > > Date: Wed, 9 Mar 2011 17:52:03 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: gabriellbk(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] glm question > > > > > > > > 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 > >

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CUDA error in file 'devicemanagement.cu'
by Rojas, Don 11 Mar '11

11 Mar '11

Hi, I'm having a problem similar to those that some others have posted previously on the list, but I did not see a clear resolution posted and I have tried the suggestions as far as I could follow them. The error message is: Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : invalid argument. Linux meggpu 2.6.32-29-generic #58-Ubuntu SMP Fri Feb 11 20:52:10 UTC 2011 x86_64 GNU/Linux The output of cudadetect is as follows: Detecting CUDA... There is 1 device supporting CUDA: Device 0: "Quadro 4000" CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 2 CUDA Capability Minor revision number: 0 Total amount of global memory: 2146631680 bytes Number of multiprocessors: 8 Number of cores: 256 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 0.95 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) I have updated my nvidia driver to the latest available since the previous one gave me a different error (segmentation fault on cudadetect). I also downloaded what I think are the latest freesurfer cuda binaries, but there was no difference in behavior between those and the distribution. Anyone have additional ideas for me to try? Thanks in advance, Don Rojas

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extracting thickness values from group level map
by Beth Mormino 10 Mar '11

10 Mar '11

Hi Surfers! I have done a group level analysis relating a variable to thickness values. I have a sig.mgh file that shows the relationship between the variable and thickness at each vertex. Now I would like to threshold the sig.mgh file (at values of 3 and above), and then extract an average thickness value across this entire mask for all my subjects. I have been able to convert the sig.mgh to an annotation using mri_surfcluster, but this file contains multiple clusters when all I'd like is 1 mask. Once I get to this step, I assume there is a way to then extract thickness values using the thickness.mgh file originally fed into mri_glmfit, but can't seem to get this to work with mri_segstats. My solution has been moving the annotation back into each subject's space with mri_surf2surf, but this seems like a very round-about way of completing this analysis. Thanks in advance! Beth

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Newbie - Group analysis on a single session with multiple runs.
by Shay Ohayon 10 Mar '11

10 Mar '11

Hi All, We are trying to speed things up in our functional analysis pipeline, and I wanted to consult with the experts here about the following suggestion... At the moment, we typically collect multiple runs per subject (say, 10-20). We usually then run pre-processing on each run, and then do first-order analysis on all available runs. This step is obviously a bottleneck because all runs need to be loaded to memory and the analysis takes a long time. As an alternative, we were thinking about doing 1st order analysis on each individual run, and then combine them somehow using 2nd order group analysis. My silly questions are: 1. Does this workflow make sense? 2. How should we go about and do this? My initial thought was to use mri_glmfit, and to build a 4D volume that will contain the beta's of interest from each individual 1st order analysis. Thanks, -- Shay

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Reconchecker error
by Shashwath Meda 10 Mar '11

10 Mar '11

Hi all - I am trying to run the reconchecker program to get some QA done on my data and I get the below error. Any help on this would be greatly appreciated! Also are there any other QA programs that would enable me to easily visualize the outputs at various stages of Freesurfer recon-all? ****************************** Running recon_checker on: Thu Mar 10 17:17:23 EST 2011 Checking Last Version Used: /usr/analysis/bin/freesurfer/bin/recon-all Checking ALL Versions Used: /home/virtualuser/apps/freesurfer/bin/recon-all, /usr/analysis/bin/freesurfer/bin/recon-all, --- checking output files ... Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker -subjid Dykens_2250_3_1_freesurfer --- /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker: Command not found. /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker: Command not found. --- checking step order ... Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker -subjid Dykens_2250_3_1_freesurfer --- /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker: Command not found. /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker: Command not found. --- *making snapshots ...* *Running command: /autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh -subjid Dykens_2250_3_1_freesurfer -o QA.html* *---* */autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh: Command not found.*

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Freesurfer March 2011