Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] mri_vol2surf
by Douglas N Greve 02 Dec '13

02 Dec '13

On 12/01/2013 11:40 PM, Arash Nazeri wrote: > Hi all, > > I wanted to make sure how one could assign intensities from the > subjacent white matter voxels to the cortical surfaces using mri_vol2surf. > > Based on the documentation page --projfrac, if used with negative > values, would assign white matter values to the surface. I was > wondering if this holds true for other options such as projfrac-avg, > projfrac-max, projdist-max ... . Further, I wanted to make sure if the > third value, designated as del, means the minimum value that could be > projected to the surface. > For instance: --projdist-max 0 -4 0.1 means to assign the maximum > value in the distance 0-4 mm of the gray/white matter boundary to the > white matter, that is larger than 0.1 . You basically have the right idea (ie, negative values go into the white matter). I'm not sure exactly what you are asking in your example. If you want to go from the gray/white surface into the WM by 4 mm, I would use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1 This will sample along the normal in 40 places spaced 0.1mm apart and return the maximum. Note that this does not assure that all points will be in WM because 4mm may put you into the GM on an adjacent bank (but for a T1 this will be dark so probably does not affect the max). > > In case of the local/global outliers, is there any good way of > finding, discarding, and replacement of these values, through > thresholding+resampling for instance? We don't have anything. > > Finally, I was wondering how it is possible to use these resulting mgh > files for group comparison in an uncached dataset, presumably using > mris_preproc. You can save them in the surf folder and then use "--meas yourfile.mgh" with mris_preproc. I'm not sure what you are aiming for, but David Salat did a similar analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073 This was done using the pctsurfcon program, so you might want to take a look at that doug > > Bests, > Arash > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] viewing slices dynamically by tkmedit
by Louis Nicholas Vinke 02 Dec '13

02 Dec '13

Hi Rujing, You can use a tcl script to take several snapshots in tkmedit, then you could use the convert command (part of ImageMagick distro) or something similar to create an animated gif. With the convert command you would use the -adjoin and -delay flags. You could use one of the tcl scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). You could also get multiple snapshots with freeview using command line flags and a shell script. -Louis On Sat, 30 Nov 2013, Rujing Zha wrote: > Dear all, > I want to see the slices as a shape of movie in tkmedit. Do anyone can tell > me how to do it? > Thanks. > All the best. > > 2013-11-30 > > ____________________________________________________________________________ > Rujing Zha > >

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Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
by Anastasia Yendiki 02 Dec '13

02 Dec '13

Hi Skyler - Are you using freesurfer 5.1 or 5.3? Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg. a.y On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > Hi all, > > I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. > See error below: > > INFO: Distances between consecutive points are 25 24 25 26 > WARN: Could not find satisfactory control point fit - try 1665 > Finding center streamline > INFO: Step is 4 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 4 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 4 voxels > INFO: Length of center streamline is 96 voxels > Selecting 5 points on center streamline > INFO: Step is 4 voxels > WARN: Defaulting to equidistant control points > INFO: Selected control points are > 108 193 84 > 112 173 72 > 98 153 75 > 74 157 75 > 74 184 86 > INFO: Distances between consecutive points are 24 25 24 29 > WARN: Could not find satisfactory control point fit - try 1666 > Finding center streamline > INFO: Step is 4 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 4 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 4 voxels > > > Best, > Skyler > >

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Re: [Freesurfer] Which boost version is used in CVS, mris_resample
by Martin Kavec 02 Dec '13

02 Dec '13

Hi Zeke, Thanks a lot for explanation. I think I will install centOS into a virtual machine for quick solution. I only need it to run CVS. Thanks and best regards, Martin Sent from my iPad > On 2.12.2013, at 22:50, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > > Martin, > > Upx (http://upx.sourceforge.net) is an executable packaging utility we run on all our binaries before shipping to reduce their overall size. One consequence of upx is that it changes the way the "file" and "ld" commands process the binaries. In this case it makes the "file" command say they are statically linked when infact it is dynamically linked. You can view this for yourself by running upx in reverse (upx -d mris_resample) and indeed you will see that it says dynamically linked. > > libboost1.41 is what comes by default on our centOS6_x86_64 platforms and it is what freesurfer builds against. All I can suggest is that you install the same version, or one very close to it. > > -Zeke > > > >> On 12/02/2013 02:50 PM, Martin Kavec wrote: >> Hi Zeke, >> >> Thanks for response. Well it was the first thing for me to try to compile boost on gentoo, which went fine. However the libraries were not compatible. Gentoo has 1.52 version, while the one needed is about 4 years old. >> >> When I do "ldd mris_resample" I get "not a dynamic executable" and when I do "file mris_resample" I get that it is a statically linked executable, stripped. I think something could have happened with when stripping the executable. I get the same output from file mris_rescale, but mris_rescale runs fine. >> >> I am using Freesurfer-5.3.0 for Centos6 x86_64. >> >> Thanks, >> >> Martin >> >> Sent from my iPad >> >>> On 2.12.2013, at 17:33, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: >>> >>> Martin, >>> >>> libboost is not a static library, it is a shared library. It comes by >>> default on centOS platforms and freesurfer compiles against it during >>> the the build process. Typing 'ldd mris_resample' and examining the >>> output confirms this: >>> >>> $>ldd mris_resample >>> linux-vdso.so.1 => (0x00007fffd2773000) >>> libboost_program_options.so.5 => >>> /usr/lib64/libboost_program_options.so.5 (0x00007fe2e588d000) >>> etc... >>> >>> Also, many of the freesurfer binaries do require the libboost library. >>> >>> Freesurfer works on most linux distribution, but we specifically build >>> on and support centOS platforms. We do not have Gentoo linux machines to >>> try and replicate your error but I am confident that if you get the >>> libboost libraries on your machine, the program will work properly. >>> >>> -Zeke >>> >>> >>> >>> >>>> On 11/28/2013 05:09 PM, Martin Kavec wrote: >>>> Hi Lilla, >>>> >>>> thanks for coming back. Unfortunately I was not able to compile >>>> appropriate boost for my operating system Gentoo linux. Nevertheless I >>>> do not understand why mris_resample misses the library if it should be >>>> statically linked. Other binaries do not need it. Could you please check >>>> if mris_resample in 64-bit linux version of CentOS is correct? >>>> >>>> Otherwise I cannot run cvs. >>>> >>>> Thanks a lot, >>>> >>>> Martin >>>> >>>> >>>> On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei >>>> <lzollei(a)nmr.mgh.harvard.edu <mailto:lzollei@nmr.mgh.harvard.edu>> wrote: >>>> >>>> >>>> This is a bit delayed response (my apologies) to an earlier question to >>>> the list: >>>> >>>> The boost library is installed by default on CentOS platforms. If a user >>>> gets the libboost error then they are using a different platform which >>>> doesn't have boost installed by default. On RedHat systems libboost >>>> can be >>>> installed by typing the follwing command: >>>> $>yum install boost-devel" >>>> >>>> The version of libboost that we use for our latest release is 1.41. >>>> >>>> Lilla >>>> >>>> --------------------------------------------- >>>> Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800 >>>> >>>> Hi guys, >>>> >>>> When running mri_cvs_register on linux (5.3.0), I get into problem with >>>> mris_resample, which cannot find libboost_programs_options.so.5. I >>>> installed >>>> the latest version of boost-1.52.0 for my system, but there are >>>> unresolved >>>> symbols. >>>> >>>> Which version is suitable for mris_resample? >>>> >>>> Thanks, >>>> >>>> Martin >>>> >>>> Sent from my iPad >>>> _______________________________________________ >>>> 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. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>

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Re: [Freesurfer] LONG stream questions
by Martin Reuter 02 Dec '13

02 Dec '13

Hi, so far that wiki page only had the commands for cross sectional runs. I added the commands for the longitudinal runs (see my mail and also the one for the surface mapping) to that page for future reference. Best, Martin On 12/02/2013 03:21 PM, Douglas N Greve wrote: > For #2 you can use the method described here > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > > On 12/02/2013 03:01 PM, Martin Reuter wrote: >> Hi Ivan, >> >> 1) it means that the voxel sizes across your images are different. Do >> mri_info on the images to see what's going on. Usually this is no >> problem if the differences are tiny. Just a warning. >> >> 2) yes, the longs are all in the same space as the base, you can map >> images to the rawavg from the cross runs with a single command: >> >> cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri >> >> mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \ >> -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \ >> -rt nearest aseg.mgz aseg-in-rawavg.mgz >> >> for other images (not segmentations, e.g. brainmask, use '-rt cubic' >> instead of nearest neighbor). >> >> Best, Martin >> >> >> On 11/22/2013 09:22 PM, Kirov, Ivan wrote: >>> Dear FreeSurfer group/Dr. Reuter, >>> >>> My questions are in regards to the LONG stream. >>> >>> My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>> >>> 1) Error message >>> During the creation of the BASE, I get the following error in the >>> beginning of the recon: >>>>>> WARNING: Image geometries differ across time, maybe due to >>> aquisition changes? >>> This can potentially bias a longitudinal study! Will >>> continue in 10s.<<<< >>> What should I be aware of in regards to this error? >>> >>> The images were all acquired using the same MPRAGE protocol. >>> All timepoints were fed MPRAGEs reconstructed in the axial >>> orientation, but some may have been reconstructed at an angle. I was >>> assured that this is not an issue for FreeSurfer, but could this be >>> the reason for the error? >>> >>> >>> 2) Conversion of LONG run aseg.mgz segmentations to native anatomical >>> space >>> >>> Executing the commands for converting aseg.mgz to native space (as >>> noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long >>> run (me1.long.me_base) does not convert. >>> >>> It seems to me that (unlike the cross runs) the long runs are all in >>> the same space (in the template/ base space?) and their rawavg.mgz >>> does not match that of the corresponding cross run. Some insight on >>> this would be appreciated. >>> >>> The question is how to convert an individual long run's aseg.mgz into >>> native anatomical space. Perhaps using the rawavg.mgz from the >>> corresponding cross run? >>> >>> Thank you very much! >>> Ivan >>> >>> -- >>> Ivan Kirov, PhD >>> Postdoctoral fellow >>> New York University School of Medicine >>> Center for Biomedical Imaging >>> 660 1st Ave, 4th floor, New York, NY 10016 >>> Tel: 212-263-3337 >>> Fax: 212-263-7541 >>> ------------------------------------------------------------ >>> This email message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain information that is >>> proprietary, confidential, and exempt from disclosure under >>> applicable law. Any unauthorized review, use, disclosure, or >>> distribution is prohibited. If you have received this email in error >>> please notify the sender by return email and delete the original >>> message. Please note, the recipient should check this email and any >>> attachments for the presence of viruses. The organization accepts no >>> liability for any damage caused by any virus transmitted by this email. >>> ================================= >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web :http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 02 Dec '13

02 Dec '13

Hi David - I am not convinced that all the regisrtrations have worked well for this subject. The fact that some of the coordinates of the control points, which are mapped from template to individual space, are negative in individual space (see INFO messages in log file), means that some part of the brain in templated space is mapped outside the field of view in individual DWI space. Can you send any screenshots that show the quality of the DWI to anatomical and DWI to MNI registrations? Thanks, a.y On Mon, 2 Dec 2013, David Soto wrote: > hi - thanks , not sure though...the no_dif brain maskseems ok, if that is > what you meant... > > I did re-run the processing and > in the last run I can not see the WARN you mentioned > the latest preprocessing output from the preprocessing can be > found here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt > > the dlabel/diff output got stuck with the > rh.ilf_AS_avg33 which only contains thee _mni_bbr_cpts_5.txt but nothing > else > > thanks so much > > ds > > > > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi David - Sorry for the delayed response due to traveling. > > There's a warning about the right ILF in the log file that may > offer a > clue: > > WARN: Initial control point 37 56 -6 is not in DWI volume - is > DWI cropped? > WARN: Replacing with closest point in volume (37 56 0) > WARN: Initial control point 38 45 -1 is not in DWI volume - is > DWI cropped? > WARN: Replacing with closest point in volume (38 45 0) > WARN: Initial start point 37 56 0 is not in start ROI > WARN: Replacing with closest point in start ROI (31 56 0) > > Is the brain mask cropped on either end of the right ILF? You > mentioned > that you already checked the registration of the FA map to the > template > space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's > nothing > wrong there. > > a.y > > On Sat, 16 Nov 2013, David Soto wrote: > > > Thanks! > > for some weird unknown reason > > the log for the preprocessing file of this > > subject is unusually big (2.8 megabytes) > > please get it from this link > > https://dl.dropboxusercontent.com/u/8209026/Archive.zip > > cheers > > ds > > > > > > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi David - This log only shows output from the -path > step and > > not from the -prep step. The file that's missing should > be > > created during the -prep step, so there's no way to > figure out > > what went wrong without seeing the output from the > > pre-processing. > > > > Please cc the freesurfer list on your reply. > > > > Thank you, > > a.y > > > > > > On Sat, 16 Nov 2013, David Soto wrote: > > > > Thanks, please see attachedI only noticed this > > ERROR: Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_ > avg > > 33_m > > ni_bbr_cpts_5_std.txt > > cheers > > DS > > > > > > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi David - Can you please send us the > > trac-all.log file for this > > subject? > > Without seeing where it stopped and what > error > > messages there > > are it's > > hard to guess what's going on. > > > > Thanks, > > a.y > > > > On Fri, 15 Nov 2013, David Soto wrote: > > > > > Hi - > > > trac-all completed in all my Ps except one > > > and I noticed that the dlabel/diff output > > does not contain > > all the files > > > > > > I assessed whether it could be do to poor > > registration, by > > checking > > > the aparc+aseg > > > file and looks allright > > > > > > I also checked the registration of FA maps > > to standard space > > by > > > freeview -v > > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > > dtifit_FA.bbr.nii.gz > > > and seems fine > > > > > > also > > > > > > freeview -v brain_anat_orig.nii.gz > > lowb_brain.nii.gz > > > > > > which also seems fine > > > > > > any ideas pls? > > > > > > thanks! > > > > > > ds > > > > > > > > > > > > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia > > Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > I suspect the current problem is > > caused by poor > > registration. > > > Have you checked the aparc+aseg > and/or > > the registration > > from > > > diffusion to anatomical and from > > anatomical to MNI? > > > > > > On Fri, 16 Aug 2013, David Soto > > wrote: > > > > > > > > > > > > -- > > > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > -- > http://www1.imperial.ac.uk/medicine/people/d.soto/ > >

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Re: [Freesurfer] LONG stream questions
by Martin Reuter 02 Dec '13

02 Dec '13

Hi Ivan, 1) it means that the voxel sizes across your images are different. Do mri_info on the images to see what's going on. Usually this is no problem if the differences are tiny. Just a warning. 2) yes, the longs are all in the same space as the base, you can map images to the rawavg from the cross runs with a single command: cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \ -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \ -rt nearest aseg.mgz aseg-in-rawavg.mgz for other images (not segmentations, e.g. brainmask, use '-rt cubic' instead of nearest neighbor). Best, Martin On 11/22/2013 09:22 PM, Kirov, Ivan wrote: > Dear FreeSurfer group/Dr. Reuter, > > My questions are in regards to the LONG stream. > > My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > 1) Error message > During the creation of the BASE, I get the following error in the > beginning of the recon: > >>>WARNING: Image geometries differ across time, maybe due to > aquisition changes? > This can potentially bias a longitudinal study! Will continue > in 10s.<<<< > What should I be aware of in regards to this error? > > The images were all acquired using the same MPRAGE protocol. > All timepoints were fed MPRAGEs reconstructed in the axial > orientation, but some may have been reconstructed at an angle. I was > assured that this is not an issue for FreeSurfer, but could this be > the reason for the error? > > > 2) Conversion of LONG run aseg.mgz segmentations to native anatomical > space > > Executing the commands for converting aseg.mgz to native space (as > noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long > run (me1.long.me_base) does not convert. > > It seems to me that (unlike the cross runs) the long runs are all in > the same space (in the template/ base space?) and their rawavg.mgz > does not match that of the corresponding cross run. Some insight on > this would be appreciated. > > The question is how to convert an individual long run's aseg.mgz into > native anatomical space. Perhaps using the rawavg.mgz from the > corresponding cross run? > > Thank you very much! > Ivan > > -- > Ivan Kirov, PhD > Postdoctoral fellow > New York University School of Medicine > Center for Biomedical Imaging > 660 1st Ave, 4th floor, New York, NY 10016 > Tel: 212-263-3337 > Fax: 212-263-7541 > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of > the intended recipient(s) and may contain information that is > proprietary, confidential, and exempt from disclosure under applicable > law. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you have received this email in error please notify the > sender by return email and delete the original message. Please note, > the recipient should check this email and any attachments for the > presence of viruses. The organization accepts no liability for any > damage caused by any virus transmitted by this email. > ================================= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Re: [Freesurfer] talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0
by Koene Van Dijk 02 Dec '13

02 Dec '13

Yes, that's correct! Thanks for the follow up ~koene On 12/2/13 2:27 PM, Louis Nicholas Vinke wrote: > Hi Koene, > It looks like Nick copied that volume over on 11/27. Thanks for > pointing that out. > -Louis > > On Tue, 26 Nov 2013, Koene Van Dijk wrote: > >> Hi there, >> >> We've been using this local version of Freesurfer: >> /cluster/freesurfer/centos6_x86_64/stable5 >> >> And this file was relevant: >> /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca >> >> >> We want to switch to the newest version of Freesurfer at the beginning >> of a new study but we can't find that "talairach_mixed_with_skull.gca" >> file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory. >> >> Is it possible to also include the "talairach_mixed_with_skull.gca" >> file in: >> /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/? >> >> Thanks, >> >> Koene >> >> > >

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Linear regression
by stdp82＠virgilio.it 02 Dec '13

02 Dec '13

Hi list, I have some questions, please. I performed linear regression by qdec to find the regions where the cortical thinning correlates with neuropsychological test (NPS), taking in account 3 nuisance factors. A- I individuated some posterior regions and now I'd like to build a table with partials correlations of individuals ROIs with NPS. How can I obtain the values for each region? B- I'd like to obtain the covariance matrix of the regression made between cortical thickness, group and covariates. How can I do it? C- Is there a specific reference for qdec? Thank you very much, Stefano

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Douglas N Greve 02 Dec '13

02 Dec '13

Hi Clark, I think Approach A should work ok. As you imply, there could be different scalings, so take that into account somehow. A slightly modified approach would be do define a different set of conditions for each subject in the paradigm file. They create a contrast with mkcontrast-sess that averages over subjects while testing the contrast you are interested in. Does that make sense? doug On 12/02/2013 12:27 PM, Clark Fisher wrote: > Hi Doug (and other Freesurfers), > > Hope you had a pleasant Thanksgiving. My thread last left off before > everyone left for the holidays. I just wanted to re-raise this > question, as it's still a pressing one for me. > > Thanks, > Clark > > > On Nov 27, 2013, at 11:06 AM, Clark Fisher <cfisher(a)rockefeller.edu > <mailto:cfisher@rockefeller.edu>> wrote: > >> Hmm, it looks like my formatting didn't survive the internet (at >> least in my e-mail program). . I'm going to try it one more time (I'm >> going to include the complete original message). >> >> Hi Doug, >> >> I sidestepped the registration issue because I am performing the >> analysis on 5 ROIs per subject (5x1x1 volumes), which are aligned by >> design. I'm doing this using the lab's semi-manual NHP processing >> stream, so usual assumptions you have about which FS-fast steps have >> been performed may not hold. >> >> Just to clarify things, I'll try to outline where I stand more >> completely. >> >> I have a block design study with 3 subjects, and ~30 runs per >> subject. Each run contains every condition occurs twice in each run. >> These runs have been collected over 2-3 days for each subject. Within >> each subject, I aligned all of the different sessions and combined >> them into a single metasession. Within these 3 metasessions, I >> defined ROIs, and created new ROI volumes by averaging the time >> courses within each ROI. From here I have taken 2 approaches. >> >> Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), >> which are pre-aligned with each other, into a single bold folder. >> Run selxavg3-sess on this data using my contrasts of interest. >> >> Approach B: Keep the ROI volumes from each subject in their own bold >> folder, and run selxavg3-sess 3 times (once for each subject). Then I >> used mri_glmfit to attempt fixed effects meta-analysis. Here there's >> another split. >> Approach B.1: I ran the contrasts for each individual subject, then >> used mri_glmfit --osgm on the ces and cesvar volumes of each contrast >> to test for significance of the contrast over the group. This does >> not work for F-tests. >> Approach B.2: I ran an omnibus contrast on each subject separately, >> and use the ces and cesvar for each condition in each subject. I >> assembled this for input to mri_glmfit. The fsgd file looks roughly >> like: >> >> GroupDescriptorFile 1 >> Class Subj1 >> Class Subj2 >> Class Subj3 >> Variables Condition1 Condition2 Condition3Condition4 >> Input Subj1-Cond1 Subj1 1 0 0 0 >> Input Subj1-Cond2 Subj1 0 1 0 0 >> Input Subj1-Cond3 Subj1 0 0 1 0 >> Input Subj1-Cond4 Subj1 0 0 0 1 >> Input Subj1-Cond00 Subj1 0 0 0 0 >> Input Subj2-Cond1 Subj2 1 0 0 0 >> Input Subj2-Cond2 Subj2 0 1 0 0 >> Input Subj2-Cond3 Subj2 0 0 1 0 >> Input Subj2-Cond4 Subj2 0 0 0 1 >> Input Subj2-Cond00 Subj2 0 0 0 0 >> Input Subj3-Cond1 Subj3 1 0 0 0 >> Input Subj3-Cond2 Subj3 0 1 0 0 >> Input Subj3-Cond3 Subj3 0 0 1 0 >> Input Subj3-Cond4 Subj3 0 0 0 1 >> Input Subj3-Cond00 Subj3 0 0 0 0 >> >> Approach B.2 (continued): I then define contrasts comparing >> conditions (Condition1 vs Condition2, etc.) and run these contrasts >> using mri_glmfit --C. With this method, I have no problem defining F >> contrasts (what they are actually testing is another question). >> >> My actual experiment is a 6 condition, 2x3 factorial design. The 2 >> contrasts of interest that I need an F test for are one of the main >> effects (these contrasts are shown without the 3 leading columns of >> zeros for the different subjects): >> 1 1 -1 -1 0 0 >> 1 1 0 0 -1 -1 >> >> and the interaction effect: >> 1 -1 -1 1 0 0 >> 1 -1 0 0 -1 1 >> >> I switched to Approach B because I want to scale the condition betas >> per-subject before running the analysis across all subjects (this is >> to correct for potentially different levels of a contrast agent). I >> was worried that if I scaled the raw time courses that are the input >> to Approach A, that the normalization step built into selxavg3-sess >> would interact with my manual normalization in ways that would be >> difficult to figure out. With approach B, I can directly scale the >> contrast ces and cesvars (B.1) or betas (B.2) for each subject. >> >> >> OK, given all of that background information, what is the best way to >> approach this? Should I: >> a) Try to scale the time courses that go into Approach A >> b) Work with Approach B.1, and live without knowing the significance >> of my main/interaction effects (not a nice thought) >> c) Work with Approach B.2 >> d) Take some other tack >> >> If I take Approach B.2, would any violation within-subject >> independence decrease my power, or artificially inflate my >> significance? Some loss of power could be acceptable. >> >> Thanks for reading all of the way through this (twice now), >> Clark >> >> >> >> On Nov 26, 2013, at 11:13 PM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >>> >>> Clark, it sounds like what you did (ie, combine different subjects >>> into one folder) would be tricky to analyze correctly because FSFAST >>> will try to register them to the same subject. I could think of a >>> way to do it, but it would be complicated. What is the test that you >>> want to do? An F test is usually something like a logical "or" >>> between two conditions. The RM ANOVA won't do this, but a simple >>> ANOVA would. The problem is that the DOF would be off because it >>> would assume that each data point came from a different subject, and >>> it would not take into account the covariance in the measurements >>> from a single subject. Another approach would be to do separate >>> tests for each condition at the group level, then do a type of >>> conjunction analysis to implement the OR. Let me know if you want to >>> pursue that approach. >>> >>> doug >>> >>> >>> >>> On 11/26/13 4:02 PM, Clark Fisher wrote: >>>> Thanks again, >>>> >>>> I have 3 subjects, and want to tests for effects using data >>>> collected across all 3 subjects. The multiple sessions for each >>>> subject have already been concatenated into a single BOLD folder (3 >>>> folders total: 1 for each subject). I have actually already >>>> performed the fixed effects analysis by concatenating all 3 >>>> subjects into a single bold folder and re-running the first level >>>> analysis. While that works, I now want to try to normalize the >>>> data for each subject to minimize the variability introduced by the >>>> contrast agent we use, and that would be easier to do by >>>> normalizing the outputs of the first level analysis. If I wanted to >>>> normalize per-subject and then combine them into a first level >>>> analysis, what would be the best way to do this? >>>> >>>> My naive assumption would have been that using glmfit for this >>>> should be very similar to the repeated measures ANOVA example that >>>> is on the wiki >>>> (http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) >>>> Rather than time points for each subject, I will have the beta from >>>> each condition for each subject. In both cases (multiple time >>>> points from a single subject and multiple conditions from a single >>>> subject/set of runs), the within-subject measurements are not >>>> independent. How is my situation different? >>>> >>>> Cheers, >>>> Clark >>>> >>>> >>>> On Nov 26, 2013, at 1:41 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>>> >>>>> Are the different input to glmfit different runs within a session >>>>> or across sessions? Either way, for within subject analysis, can >>>>> you put all of the runs into a single "bold" folder? Then it >>>>> automatically does the FFX analysis across runs, which can include >>>>> an F-test. The problem is that glmfit expects all the inputs to be >>>>> independent, which conditions within a run will not be. >>>>> doug >>>>> >>>>> >>>>> On 11/25/2013 01:35 PM, Clark Fisher wrote: >>>>>> Thanks Doug, >>>>>> >>>>>> I had forgotten that my roadblock was actually in isxconcat_sess, >>>>>> not mri_glmfit. This worked out great. >>>>>> >>>>>> Following this up, how would you recommend calculating the >>>>>> fixed-effects significance of a complex (within subject) contrast >>>>>> with mri_glmfit? For simple contrasts, I have been calculating >>>>>> the contrast at the single subject level, then performing an osgm >>>>>> fixed-effects analysis on the output ces and cesvar volumes for >>>>>> each subject. However, I have some 2D F-contrasts that don't >>>>>> output ces volumes (naturally). >>>>>> >>>>>> One possibility would be to concatenate the ces and cesvar from >>>>>> the omnibus contrasts of each subject, set up an appropriate fsgd >>>>>> (as in >>>>>> http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) and >>>>>> then define the contrasts at the level of mri_glmfit with .mtx >>>>>> files. Would that be the way to go? >>>>>> >>>>>> Thanks, >>>>>> Clark >>>>> -- >>>>> 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 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> >>>>> >>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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