Freesurfer

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30132 discussions

mprage flag in recon-all
by Caspar M. Schwiedrzik 14 Jun '13

14 Jun '13

Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar

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Re: [Freesurfer] Hippocampal subfields intensity
by Juan Eugenio Iglesias 13 Jun '13

13 Jun '13

Hi Marcos, 1. your fix of MRIread.m is great. I forgot of this bug; we should totally take care of it. 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in difference voxel space. So, you need to resample norm.mgz to the space of the subfields. To do so, you can use mri_convert with the option -rl ("reslice like"): mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 3. Now you can do: A=MRIread('norm.mgz'); data=A.vol(:); B=MRIread('posterior_subiculum.mgz'); post=double(B.vol(:)); mean=sum(data.*post)/sum(post); variance=sum((data-mean).^2.*post)/sum(post); Cheers, /Eugenio On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote: > Hi, Eugenio > TY for your fast help. I understood you were suggesting to compute > that on MatLab and I tried this: > > NU=MRIread('nu.mgz') ### that runs ok > Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the > following message > WARNING: error reading MR params > Attempted to access mr_parms(1); index out of bounds because > numel(mr_parms)=0. > > Error in MRIread (line 100) > tr = mr_parms(1); > > I solved creating a little customized nMRIread.m with the following > changes: > > if numel(mr_parms) > 0 > tr = mr_parms(1); > flip_angle = mr_parms(2); > te = mr_parms(3); > ti = mr_parms(4); > else > mr_parms(1) = 0; > mr_parms(2) = 0; > mr_parms(3) = 0; > mr_parms(4) = 0; > tr = mr_parms(1); > flip_angle = mr_parms(2); > te = mr_parms(3); > ti = mr_parms(4); > end > > With those changes I assigned 0 to mr-parms elements so it runs > without errors > But whe I tried the following line I copy and pasted from your > message: > mean=sum(Ps.*NU)/sum(Ps); ### I got the following error > Undefined function 'times' for input arguments of type 'struct'. > > Any help? > Cheers, Marcos > > PS: I promised I will post the final solution to list. But I guess it > is more didactic if these little problems are solved before. > TY, again. > Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: > > Hi Marcos, > > the right way of doing this is using the soft posteriors to compute the > > mean and variance, rather than thresholding at p=0.5. For instance, if > > you wanted to compute the mean and variance of the intensitites of the > > subiculum, you would do something like this: > > mean=sum(Ps.*NU)/sum(Ps); > > variance=sum(Ps.*(NU-mean).^2)/sum(Ps); > > (where Ps is the posterior of the subiculum) > > Cheers, > > /Eugenio > > > > > > > > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote: > > > Hi, Freesurfer Experts > > > > > > After usual processing with recon-all -all we get the aseg.stats file > > > with several data including intensity values like: > > > normMean normStdDev > > > normMin normMax normRange > > > Left-Hippocampus 77.8939 7.5748 46.0000 > > > 105.0000 59.0000 > > > > > > How could I get similar results for each hippocampal subfield, > > > assuming I also generated all posterior*.mgz files corresponding to > > > each subfield? > > > I guess I should first binarize each of the subfields file with a > > > threshold=127 to map all the pertinent voxels, and then use these > > > files as masks over nu.mgz and calculate the intensities values. But I > > > do not know the best way to accomplish this after the binarize step. > > > > > > Thank you in advance for any help. > > > > > > Marcos > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias(a)nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.

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Installing optseq2!!
by fMRI 13 Jun '13

13 Jun '13

Hi all, I am trying to install optseq2 in my own laptop. I have linux installed as a virtual window. I am sorry but I really do not have any idea how I should install it after downloading the file. I am new to linux! Any guide please, Thanks AS

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versus baseline in mkcontrast-sess
by Reza Rajimehr 13 Jun '13

13 Jun '13

... and one more question: In the latest version of FS-FAST (v5.3), is there a difference between the following two: mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 -c 0 mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 I have blocks with no stimulus that I have specified them as 0 in the paradigm files. Thanks, Reza ***************** Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University *****************

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Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess
by Douglas Greve 13 Jun '13

13 Jun '13

In that case, you could break it up in to several shorter runs. It won't affect the stats much (probably help it), but it does make it a little more difficult to set up the data. If you want to do this, you would need to do something like this: cd session/bold mv 001 001.big --> move the original data mkdir 001 002 003 004 --> create 4 folders mri_convert 001.big/f.nii.gz 001/f.nii.gz --fsubsample 0 1 99 --> first 200 time points mri_convert 001.big/f.nii.gz 002/f.nii.gz --fsubsample 200 1 299 ... You will also need a paradigm file in each subdir. For 001, you can just cp 001.big/paradigmfile 001 For 002 003 004, it will need to be changed to reflect the new timing with something like cat 001.big/paradigmfile | awk '{print $1-200*2" "$2" "$3" "$4} > 002/paradigmfile cat 001.big/paradigmfile | awk '{print $1-400*2" "$2" "$3" "$4} > 003/paradigmfile cat 001.big/paradigmfile | awk '{print $1-600*2" "$2" "$3" "$4} > 004/paradigmfile The "2" in the "200*2" is the TR, change it if it is something different. It does not matter if the paradigm files have events that are before the start of the "run" or after its end. doug ps. Adding more memory would fix it, but I don't know how much you would need to add On 6/13/13 4:29 PM, Marcel Falkiewicz wrote: > Hello Doug, > I've got only one run with approximately 800 timepoints. I'm doing > the analysis in 2mm space. > > Marcel > > > 2013/6/13 Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > It is not a matlab problem per se, though their memory management > is not great. This sometimes happens for the mni305 when you have > a lot of time points in one run or many runs. How many runs and > how many time points per run? And you are doing 2mm (the default) > or 1mm? > doug > > > > > > > > On 6/13/13 2:19 PM, Marcel Falkiewicz wrote: >> >> Hello, >> I know this problem has been discussed earlier, but I think in >> my case the source of the problem might be quite different. I'm >> running FS 5.3.0 and MATLAB R2011a on Ubuntu machine with 12 GB >> RAM. selxavg3-sess runs perfectly for both hemis, but I get the >> following error when trying to run it on subcortical volume: >> >> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ >> /home/marcel/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /home/marcel/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /home/marcel/freesurfer/matlab/MRIread.m >> ------------------------- >> outtop = /media/2TB/SDT_MRI/FS >> Extension format = nii.gz >> 1 DC_vs_HC.mat >> 2 HI_vs_DC.mat >> 3 HI_vs_HC.mat >> 4 NAT_vs_PAL.mat >> 5 NAT_vs_PAT.mat >> 6 PAL_vs_NAT.mat >> 7 PAL_vs_PAT.mat >> nruns = 1 >> autostimdur = >> >> >> outanadir = /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni >> Found 52644/537168 ( 9.8) voxels in mask >> Creating Design Matrix >> ... creation time = 0.007 sec >> DoMCFit = 1 >> ntptot = 851, nX = 19, DOF = 832 >> Saving X matrix to >> /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni/Xtmp.mat >> XCond = 31.0456 (normalized) >> Computing compensation for resdual AR1 bias >> 1 -0.5 -0.500489 (t=0.097569) >> 2 -0.25 -0.255326 (t=0.427178) >> 3 0 -0.011955 (t=0.516085) >> 4 0.25 0.229273 (t=0.839369) >> 5 0.5 0.466983 (t=0.928175) >> AR1 Correction M: 0.0147777 1.03322 >> Computing contrast matrices >> OLS Beta Pass >> run 1 t= 0.0 >> Global Mean 1120.98 >> Global In-Mask Mean = 1120.98 (983.432) >> Rescale Target = 100 >> RescaleFactor = 0.0892077 >> OLS Residual Pass >> run 1 t= 0.0 >> ??? Out of memory. Type HELP MEMORY for your options. >> >> Error in ==> fast_selxavg3 at 489 >> rsserun = sum(rrun.^2); >> >> >> ------------------------------------------ >> >> >> I observed memory consuption with top(8) and noticed that around >> 11 GBs are eaten after about 30 second of running OLS residual >> pass. Do you think adding more memory to the PC would solve the >> problem, or is it some MATLAB/FS-related bug? >> >> Best regards, >> Marcel >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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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Fwd: Out of memory problem during selxavg3-sess
by Marcel Falkiewicz 13 Jun '13

13 Jun '13

Hello, I know this problem has been discussed earlier, but I think in my case the source of the problem might be quite different. I'm running FS 5.3.0 and MATLAB R2011a on Ubuntu machine with 12 GB RAM. selxavg3-sess runs perfectly for both hemis, but I get the following error when trying to run it on subcortical volume: $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/marcel/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/marcel/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/marcel/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/2TB/SDT_MRI/FS Extension format = nii.gz 1 DC_vs_HC.mat 2 HI_vs_DC.mat 3 HI_vs_HC.mat 4 NAT_vs_PAL.mat 5 NAT_vs_PAT.mat 6 PAL_vs_NAT.mat 7 PAL_vs_PAT.mat nruns = 1 autostimdur = outanadir = /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni Found 52644/537168 ( 9.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 851, nX = 19, DOF = 832 Saving X matrix to /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni/Xtmp.mat XCond = 31.0456 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500489 (t=0.097569) 2 -0.25 -0.255326 (t=0.427178) 3 0 -0.011955 (t=0.516085) 4 0.25 0.229273 (t=0.839369) 5 0.5 0.466983 (t=0.928175) AR1 Correction M: 0.0147777 1.03322 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 1120.98 Global In-Mask Mean = 1120.98 (983.432) Rescale Target = 100 RescaleFactor = 0.0892077 OLS Residual Pass run 1 t= 0.0 ??? Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 489 rsserun = sum(rrun.^2); >> ------------------------------------------ I observed memory consuption with top(8) and noticed that around 11 GBs are eaten after about 30 second of running OLS residual pass. Do you think adding more memory to the PC would solve the problem, or is it some MATLAB/FS-related bug? Best regards, Marcel

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pvr help
by Gautam, Prapti 13 Jun '13

13 Jun '13

Dear FreeSurfers I am trying to control for thickness in another surface using the pvr option in mri_glmfit. However, I'm confused as to how I can include the pvr option correctly in the contrast files. I have two groups, and would like to utilize DODS for this analyses as I think that my groups both have different intercepts and slopes. This is my fsgd set up : GroupDescriptorFile 1 Title MyTitle Class Controls CLASS FA Variables Age Input PMS1 Controls 14.442163 Input PMS2 Controls 14.354552 .. Input PMS7 FA 15.726215 Input PMS28 FA 14.45859 This is the command I run: mri_glmfit --y lh.surface.mgh --fsgd SA_age.fsgd --C con.mtx --surf fsaverage lh --cortex --glmdir test.glmdir --pvr lh.thickness.psc.mgh --pvr lh.thickness2.psc.mgh The contrast I would like to run is: 0 0 0 0 1 -1 so as to look at group interactions within thickness after controlling for another cortical surface. However, I can't get this to run as there is a "Matrix ill-conditioned" error. The contrast that does run is 0 0 0 0 1 (after passing only one pvr file). But this option seems to be neither dods nor doss. Is there a correct way to do a DODS analyses looking for interactions using the pvr option? Thank you, Prapti --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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Fwd: Talairach Positioning in Horizontal View
by Peter Boulos 13 Jun '13

13 Jun '13

Hi Doug, I am using a GE 3T scanner with a slice thickness of 1.7 mm. I tried using the new script you provided (thanks for the help!) and it did not seem to make any difference with the couple of subjects that I tried. I have attached a screenshot. The right image in the screenshot is the original Talairaching and the left is after I ran the script you provided. Does this mean I will be forced into manually editing the Talairach for all of my subjects and re-running recon-all for all of them after I do that or is there another solution? Peter ----------------------------------------------------------------------------------------------------------- Message: 4 Date: Tue, 11 Jun 2013 13:41:47 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: Talairach Positioning in Horizontal View To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51B7615B.7000606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Peter, what scanner are you using? You might be better off with using a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that cleans it up. You can run just the talairaching with recon-all -s subject -schwartzya3t-atlas -talairach doug On 06/11/2013 01:03 PM, Peter Boulos wrote: > I am very new to the software and have just begun assessing Talairach > outputs for my subjects. I am confused in that I cannot seem to find a > balance I am happy with between positioning of the green lines in both > the horizontal and sagittal views for multiple subjects. I opened the > talairach output with the following command (tkregister2 --mgz --s > SUBJID --fstal --surf orig) and everything looked perfectly aligned > for all the subjects I have tried in both the coronal and sagittal > views but in the horizontal view the green lines went well off the > back of the brain. I have attached a screenshot. I tried to translate > the brain but that did not seem to solve my issue and I realized I > needed to scale the length of the brain. When I did that I was more > pleased with the outcome but the corpus callosum did not match up > nearly as well after I did that (second attached screenshot) and that > was the primary landmark I was using to pass my images in terms of > talairach output assessment. Do you have any advice for me? > > Peter > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Visualizing functional maps in tksurfer
by Reza Rajimehr 13 Jun '13

13 Jun '13

Hi, Using anatomical parcellation, I have labels for the occipital and temporal lobes in my subject. I have a functional map in the same subject that I want to show the activity only in the occipital and temporal cortex, and I want to mask the activity in the other parts of the cortical surface. How can I do this with FS-FAST/Freesurfer? Thanks, Reza ***************** Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University *****************

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Local GI - longitudinal analysis
by Pedro Rosa 13 Jun '13

13 Jun '13

Dear all, I have two issues: 1) I would like to run localGI in a longitudinal analysis. I runned the recon-all, the -base and the -long in all subjects. Then, I tried to run the -localGI command on .long. directories (I believe this it the directory I should run the command), the error below returned. How can I solve this issue? 2) I tried to download the 5.2 version, but the link does not seem to be working (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/) I tried both Chrome and Firefox. Regards, Pedro Rosa. ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.

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