Freesurfer

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30132 discussions

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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Small voxel size
by Tricia Merkley 10 Mar '11

10 Mar '11

Hello, One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although all other acquisition parameters were the same as the other subjects. I'm wondering to what extent this might affect the results of the subcortical segmentation, cortical thickness measurements, etc., as compared to 1mm cubic voxels. When would it be appropriate to use the '-cm' flag for mri_convert? Thanks, Tricia Merkley

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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

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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

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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

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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. >

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