Freesurfer

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30089 discussions

(no subject)
by Ryan 06 Aug '12

06 Aug '12

Hello, I'm conducting a longitudinal analysis and encounter an error when running the "long_mris_slopes" command (this is contained in the online tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) The error that arises within a minute is "ERROR -10 : mris_calc compute sym. pct. change (spc) problem?", any thoughts? Thanks all. -- -Ryan

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file conversion
by Colin Reveley 06 Aug '12

06 Aug '12

also - I'm assisting someone with a dti analysis. the data I have is a martinos centre .hdr .bshort file, acquired at martinos I think, in 2005. I'm having trouble figuring out how to covert this (mainly for use with FSL) I'd like a 4d nifti ultimately (or analyse). I was thinking of writing code (probably matlab) to read in the data with fread, reslice the matrix, write to nifti. I'm no expert in nifti headers, certainly not the format below. by bshort we mean 2 bytes unsigned integer? could I even use mri_convert to make a 4d nifti from the bshort? or else a 3d nifti I can load simply into matlab and re-arrange? the header (people's names blanked out, just to be on safe side) of the bshort is below mainly we simply want line1: 256 128 2816 1 to become line1: 256 128 128 22 right? just getting the data into 3d nifti is fine. 4d a bonus. obviously the dwi scan parameters need not be in the nifti header, included for completeness also: to my unexpert eye this looks like a single shot sequence probably, would that be right? help appreciated Colin --- 256 128 2816 1 MonkBrain_425mic3Ddti fovx=57.599998 fovy=115.199997 fovz=57.599998 name=xxxxxx id=xxxxx dob= sex=female study name: 34667 macaque brain purpose: xxxxx Institution=MGH Biospec 47/40 date=21:17:49_10_Sep_2005 Operator=****** Software=PV 3.0.1 Protocol/descr=A*******C/MonkBrain_425mic3Ddti pulse prog=gdDiffSE.ppg SW=29761.9048 Hz acq_rare_factor=1 acq_inter_echo_time=28.000 acq_echo_time=28.000 acq_repetition_time=250 Method is PVM exam=33 series=5 slices=1 coronal, readout=H_F, thickness=57.60 mm separation=57.60 mm offset=0.00 mm TE=28.00 TR=250.00 TI=0.00 NEX=1, acq time 25h1m52s0ms ExcPulse 1.580ms, 3417.7Hz, flip=90.0, 18.4dB, <hermite.exc> RefPulse 1.001ms, 3416.6Hz, flip=180.0, 8.4dB, <hermite.rfc> $GDDIFF_BigDelta=10.400000$GDDIFF_BigDelta=10.400000 $GDDIFF_LittleDelta=6.925000 $GDDIFF_DiffGrad=0.000 0.000 379.787 379.836 379.879 379.690 379.868 379.823 379.730 379.688 379.729 379.716 379.732 379.905 379.867 379.667 379.702 379.809 380.000 379.984 379.734 379.868 $GDDIFF_DiffGradB=0.000 0.000 4004.836 4005.877 4006.782 4002.793 4006.554 4005.596 4003.634 4002.761 4003.606 4003.338 4003.686 4007.327 4006.534 4002.317 4003.058 4005.309 4009.333 4009.005 4003.722 4006.558 $GDDIFF_PathName=/home/a********c $GDDIFF_DiffGradFileName=Jones20B.txt $GDDIFF_DiffGradRead=0.000 0.000 0.979 0.329 -0.396 0.807 0.006 -0.794 0.834 -0.235 0.817 0.009 -0.062 -0.263 -0.413 -0.588 -0.505 -0.773 0.713 0.259 -0.549 -0.396 $GDDIFF_DiffGradPhase=0.000 0.000 0.000 0.922 0.593 -0.502 -0.355 -0.281 -0.313 0.939 0.266 -0.885 -0.795 -0.382 -0.611 0.762 0.084 -0.594 -0.177 -0.094 -0.686 0.618 $GDDIFF_DiffGradSlice=0.000 0.000 0.000 0.000 0.670 -0.231 0.912 0.499 0.405 0.146 0.468 0.418 -0.568 -0.862 0.644 -0.173 -0.834 0.085 -0.647 -0.940 -0.431 -0.648 ImageType=MAGNITUDE_IMAGE

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contrast matrix
by Meng Li 06 Aug '12

06 Aug '12

Hi Freesurfers, My experimental design includes 3 discrete factors and 1 continuous variables: Discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) Continuous variable: age So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and age. Is the following contrast matrix correct? 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 Any help will be very appreciated. Best wishes, Meng

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Re: [Freesurfer] no CSF
by Colin Reveley 05 Aug '12

05 Aug '12

Thanks Ritobrato yes, I'm aware of this. the trouble is I can't get it right to my satisfaction. I tried a lot! my problem is finding the right parameters that you show below. My experience (since you have not tired yet) is that you will have to use these parameters, absolutely. you have to mess with them till the surfaces seem right. your results may look pretty nice. Mine have, in 250um monkey. but they don't do justice to the resolution. the GM/WM boundary is a single voxel in this data pretty much, but the surfaces don't reflect that. I really want it super, insanely perfect for this bit of the project (150um marmoset). GM/WM and GM/CSF. so part of what I'm asking is how to "fake CSF". another is to ensure that gaps between gyri look like CSF, not like low GM. and for e.g. extreme capule to look like WM, not high GM. it seems to do with nu-correct in the end. you can't just use the WM segmentation and set all WM to 110 unfortunately. it seems that there needs to be variation even though the nean should be 110 also that there needs to be a gradient between WM and GM and GM and CSF. It's basically to complex for me to understand. I don't quite get the results I need, and I just bash away with the parameters trial and error. it seems to me that I need to adjust the relative intensities differently in different parts of the volume. I don't know how. by faking coil locations and distances maybe? but where? and how?. At one point a year ago I tried with about 16,000 control points that I placed manually. getting something that is good is entiely doable bear inn mind. getting something that exactly follows a GM/WM boundary (and GM/CSF) that you know is in the data is really super tough. And I need to unfortunately. I really do. I need it exact. if you are mostly guessing ... but not really understanding (that means me, not you), it is hard. Hence I ask. best, Colin On 5 August 2012 17:44, Ritobrato Datta <ridatta(a)mail.med.upenn.edu> wrote: > Hi Colin, > > This is Rito. I am stuck at a similar step. I have acquired high-res > ex-vivo T1 images at 7T from canine brains. > > I got the following (P.S. below) from Nick Schmansky. Havent tried it > though. > > Please let me know how it goes for the images u r working with. > > Best > > Rito > > P.S. The flags to mris_make_surfaces are: > > -wlo <val> minimum for wm at border with gm > -ghi <val> maximum for gm at border with wm > -max_gray_at_csf_border <val> maximum for gm at border with csf > -min_gray_at_csf_border <val> minimum for gm at border with csf > > so its that latter two that you would try (the first two are what people > normally use to mess with the gm/wm junction). > > use tkmedit's brightness and contrast adjustments to find where you think > gm actually ends. the danger is that you select a min-gray-at-csf-border > value that is too low and it starts putting the surface out into open > space. > > n. > > Ritobrato Datta, Ph.D. > Post Doctoral Researcher > Department of Neurology > University of Pennsylvania School of Medicine > 3rd Floor, Room 312 > 3710 Hamilton Walk (Goddard Laboratories) > Philadelphia, PA 19104-6241 > > ----- Original Message ----- > From: Colin Reveley <cmr25(a)sussex.ac.uk> > To: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Sun, 05 Aug 2012 12:10:31 -0400 (EDT) > Subject: [Freesurfer] no CSF > > when running mris_make_surfaces it's possible to manually set CSF,GM,WM and > related thresholds. > > now, what of the case where one simply doesn't have any CSF? > > i.e. an ex-vivo scan. > > I find it really hard to get a good pial surface despite much > experimentation. It wants to contract the GM and make the outer edges CSF, > no matter what I do. > > I should say also that the T1 is really an MTR scan (nearly, but not > exactly the same intensity profile) and the brains are macaque and > marmoset. > > I also find it hard to get the intensities such that frontal WM and e.g. > the extreme capsule have WM range intensity. I'm happy to do manually, but > I canot get the gradient from WM to GM right manually in these areas to > satisfy mris_make_surfaces. > > the data is really high resolution. it would be really great to capture the > whole GM ribbon. > > putting in noise at a sensible average intensity for CSF doesn't seem to > help. > > many thanks, > > Colin >

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no CSF
by Colin Reveley 05 Aug '12

05 Aug '12

when running mris_make_surfaces it's possible to manually set CSF,GM,WM and related thresholds. now, what of the case where one simply doesn't have any CSF? i.e. an ex-vivo scan. I find it really hard to get a good pial surface despite much experimentation. It wants to contract the GM and make the outer edges CSF, no matter what I do. I should say also that the T1 is really an MTR scan (nearly, but not exactly the same intensity profile) and the brains are macaque and marmoset. I also find it hard to get the intensities such that frontal WM and e.g. the extreme capsule have WM range intensity. I'm happy to do manually, but I canot get the gradient from WM to GM right manually in these areas to satisfy mris_make_surfaces. the data is really high resolution. it would be really great to capture the whole GM ribbon. putting in noise at a sensible average intensity for CSF doesn't seem to help. many thanks, Colin

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contrast matrix
by Meng Li 04 Aug '12

04 Aug '12

Hi Freesurfers, My experimental design includes 3 discrete factors and 1 continuous variables: Discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) Continuous variable: age So I can get 8 classes. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and age. Is the following contrast matrix correct? 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 Any help will be very appreciated. Best wishes, Meng

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Re: [Freesurfer] expert option error in recon-all
by james pardon 04 Aug '12

04 Aug '12

Nick or Doug could you help us here? On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi James > can you post to the list so others can answer? I'm not sure what's going > on, but Nick or Doug might > > > Bruce > > On Fri, 3 Aug 2012, james pardon wrote: > > Hi Bruce, >> subject's folder is empty, there is no scripts folder, or anything else. >> Again if I omit -expert everything works fine. >> >> Thanks >> >> On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi James >> >> what happens if you run: >> >> ls -l /home/dir/subject/subname/**scripts/expert-options >> touch /home/dir/subject/subname/**scripts/expert-options >> >> Bruce >> >> On Fri, 3 Aug 2012, james pardon wrote: >> >> Dear all, >> I'm trying to pass the following flags for >> mri_normalize through -expert >> flag in recon-all, with a file, named expert.opts >> with the following single >> line: >> mri_normalize -b 20 -n 5 >> >> my command line is: >> >> recon-all -i inputfile -subject subname -all -expert >> <pathname>/expert.opts >> >> I receive the following error: >> >> cp: cannot create regular file: >> '/home/dir/subject/subname/**scripts/expert-options' >> >> The directory of the subject has been created, but >> it is completely empty. >> At first glance I thought it might be some sort of >> permission problems, >> however I have rwx permission for all the paths >> (even running under the root >> username the same error comes up). Secondly, I >> checked my disk quota, it is >> completely fine. Please note that, if I do not pass >> -expert flag recon-all >> works completely fine. >> >> Any input is much appreciated. >> >> Regards, >> James >> >> >> >> >> 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<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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eccentricity and polar maps?
by dgw 03 Aug '12

03 Aug '12

Hi, I am trying to process a small amount of retinotopy data. I have one run of positive polar stimuli with 64 second cycle and another of positive eccentricity data with a 64 second cycle (I realize that I could use better parameters). I have followed the tutorial on http://www.freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis I was able to get through all of the steps on that page, but now I want to look at the polar and eccentricity maps. I couldn't find anything on the wiki about them. I did find this post on the list: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022464… ; however, the rtview script is not located there on the ftp server (I assume it got deleted at some point). Can anyone point me to the next step(s)? Thanks, Dan

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Thresholding using FDR
by Ian Carroll 03 Aug '12

03 Aug '12

Hello, When thresholding significance using FDR for one of my overlays, I noticed that a rate of .1 and .05 give me the same minimum and maximum threshold values. At both levels, there were no voxels of significance. Does this mean that freesurfer will not continue to update max and min values when nothing is significant? Thanks, Ian

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Re: [Freesurfer] Longitudinal cortical thickness analysis
by Martin Reuter 03 Aug '12

03 Aug '12

Hi Venkat, in 5.0 images are not aligned as longitudinal runs are done in their native (cross sectional spaces). since 5.1 we map everything to the base in the initial conform reslicing step to make visualization and debugging easier. this further decreases variability. Although 5.0 does not align the images it should still work. So maybe you have no problem at all. If you rerun, make sure you re-run the base and the longitudinal directories from scratch, not on top of the old ones. About processing stats files, there are several options: 1. grab the measures from the stats files yourself and input them into any statistic package you desire. For this asegstats2table may be helpful (also aparcstats2table). This is recommended as it is most flexible, e.g. you can run linear mixed models, which is better than looking simply at slopes. In your case (only 2 time points) it may not matter much, but linear mixed models can deal with missing data (e.g. if you have subjects with a single time point only). 2. (some quick stuff I implemented for simple analysis, similar to long_mris_slopes) get long_stats_slopes (and all the other files there) from: http://martinos.org/~mreuter/long/ backup yours and replace with these. long_stats_slopes works the same way as long_mris_slopes. You can run the output (e.g. rate/year or percent change) through glm_fit for your group analysis (there is a tutorial about glm_fit). We are working on making available more powerful statistical tools for longitudinal analyses in the future. Then we will also create a better tutorial for it. Best, Martin On Fri, 2012-08-03 at 10:31 -0400, Rajagopalan, Venkateswaran wrote: > Hi Martin, > > Thanks for your immediate response. > > are you using version 5.1 ? > No version 5.0 I am undating it. > After the upgarde I will run the program again and see whether the > same problem persists. > > The most common > reason is that skull strip fails in the cross sectional runs. Large > chunks of skull can throw off the registration in the base. > > I verified my skull strip (I always do) and it is fine in this case. > In your case, you have only 2 time points and an error in the > registration would immediately result in a messed up norm.mgz image in > the base:nonhyper_24_templ/mri/norm.mgz would be very blurry or show > two ghost > images. > > I didn't see base image being messed up in my case though. > > Also I am interested in seeing whether is there any reduction in > cortical thickness between the two time points. In that case how to do > stats. I am unable to find guidelines to do stats after the > longitudinal processing (processing steps for longitudinal is very > good but unfortunately I am unable to find one for stats part). > > Thanks > > Venkat > > > > > > ______________________________________________________________________ > From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > Sent: Thu 8/2/2012 3:37 PM > To: Rajagopalan, Venkateswaran > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Longitudinal cortical thickness analysis > > > Hi Venkat, > > are you using version 5.1 ? In earlier versions, time points were not > aligned to the base, so they don't align. Since 5.1 they should > perfectly align. If not it can have several reasons. The most common > reason is that skull strip fails in the cross sectional runs. Large > chunks of skull can throw off the registration in the base. > > In your case, you have only 2 time points and an error in the > registration would immediately result in a messed up norm.mgz image in > the base: > > nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost > images. > > So take a look at that and also the skull strip in > nonhyper_24_06/mri/brainmask.mgz > nonhyper_24_07/mri/brainmask.mgz > > and fix them if it they are bad. > > Best, Martin > > On Thu, 2012-08-02 at 13:48 -0400, Rajagopalan, Venkateswaran wrote: > > > > Dear All, > > > > I ran the following steps in a patient of mine at two time points > > nonhyper_24_06 and nonhyper_24_07 > > > > recon-all -autorecon1 -subjid nonhyper_24_06 > > recon-all -autorecon1 -subjid nonhyper_24_07 > > recon-all -autorecon2 -subjid nonhyper_24_06 > > recon-all -autorecon3 -subjid nonhyper_24_06 > > recon-all -autorecon2 -subjid nonhyper_24_07 > > recon-all -autorecon3 -subjid nonhyper_24_07 > > > > # template creation > > > > recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp > > nonhyper_24_07 -all > > > > recon-all -long nonhyper_24_06 nonhyper_24_templ -all > > recon-all -long nonhyper_24_07 nonhyper_24_templ -all > > > > When I tried to inspect my longitudinal result using > > freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \ > > nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \ > > -f > > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \ > > > > nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \ > > > > > nonhyper_24_07.long.nonhyper_24_templ/surf/lh.pial:edgecolor=255,128,128 \ > > > > > nonhyper_24_07.long.nonhyper_24_templ/surf/lh.white:edgecolor=lightblue > > > > My norm images from two time points doesn't overlap (so does the > pial > > and white surfaces from two points they appear on two distinct > places > > on the freeview instead of being overlaped as shown in tutorial) > when > > I load then it looks like there is some registration problem. I > don't > > know where I made a mistake and how to correct for this. > > Any help will be greatly appreciated. > > > > Thanks > > Venkat > > > > > > =================================== > > > > > > Please consider the environment before printing this e-mail > > > > Cleveland Clinic is ranked one of the top hospitals in America by > > U.S.News & World Report (2010). Visit us online at > > http://www.clevelandclinic.org for a complete listing of our > services, > > staff and locations. Confidentiality Note: This message is intended > > for use only by the individual or entity to which it is addressed > and > > may contain information that is privileged, confidential, and exempt > > from disclosure under applicable law. If the reader of this message > is > > not the intended recipient or the employee or agent responsible for > > delivering the message to the intended recipient, you are hereby > > notified that any dissemination, distribution or copying of this > > communication is strictly prohibited. If you have received this > > communication in error, please contact the sender immediately and > > destroy the material in its entirety, whether electronic or hard > copy. > > Thank you. > > > > > > _______________________________________________ > > 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. > > > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals in America by > U.S.News & World Report (2010). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, > staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and > may contain information that is privileged, confidential, and exempt > from disclosure under applicable law. If the reader of this message is > not the intended recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are hereby > notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this > communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > Thank you. > >

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