Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Fwd: Surface statistics for PET
by Daniel Tarquinio 26 Aug '12

26 Aug '12

Hi Bruce, I'm sorry I didn't ask the correct question - I was able to generate the .mgh file with mri_vol2surf without problem. The issue was that "qsurfer" gives me an error stating it couldn't find the .w file. According to usage it needs a file ending in -?h.w. Is there a way to use a .mgh file with qsurfer, or is there a better way to view inflated functional data than with qsurfer? Thank you again, Daniel Sent from my iPhone On Aug 26, 2012, at 12:50 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > sure, use mgh as the output format of mri_vol2surf. > > cheers > Bruce > On Sun, 26 Aug 2012, Daniel Tarquinio wrote: > >> Thank you Doug, that worked perfectly. >> Regarding the .w file, to view the functional data inflated I used this >> tutorial: >> http://poc.vl-e.nl/distribution/manual/fsl-3.2/freesurfer/index.html >> Is there a workaround to view inflated functional data mapped using >> mri_vol2surf with a .mgh file? >> Thank you again, >> Daniel >> Message: 6 >> Date: Fri, 24 Aug 2012 18:57:55 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Surface statistics for PET >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <503806F3.50807(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> You can use mri_segstats for this, something like >> mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat >> where lh.pet.mgh is the surface-sampled pet >> BTW, unless you need a .w for something, use a .mgh file (the .w is becoming obsolete). >> doug >> On 08/23/2012 07:27 PM, Daniel Tarquinio wrote: >> > I would like to calculate average PET intensities for specific labels > (using the aparc.annot label files). >> > >> > I have coregistered and used mri_vol2surf to assign PET values to the > FS generated surface, and viewed the results using qsurfer. >> > >> > The next step is to take the values from the .w files and calculate > label-specific stats. I've tried mris_anatomical_stats but I don't > think this is the right command. >> > >> > Any advice? >> > >> > Thank you in advance, >> > Daniel >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -----Original Message----- >> From: freesurfer-request <freesurfer-request(a)nmr.mgh.harvard.edu> >> To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Sat, Aug 25, 2012 12:00 pm >> Subject: Freesurfer Digest, Vol 102, Issue 27 >> Send Freesurfer mailing list submissions to >> freesurfer(a)nmr.mgh.harvard.edu >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-request(a)nmr.mgh.harvard.edu >> You can reach the person managing the list at >> freesurfer-owner(a)nmr.mgh.harvard.edu >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> Today's Topics: >> >> 1. Control points and errors (Herting, Megan) >> 2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve) >> 3. Re: In Qdec, what does the 'area' mean within 'Measure' menu >> in 'Design' tab (Jeff Sadino) >> 4. Re: problem with tksurfer (Douglas N Greve) >> 5. Re: In Qdec, what does the 'area' mean within 'Measure' menu >> in 'Design' tab (Douglas N Greve) >> 6. Re: Surface statistics for PET (Douglas N Greve) >> 7. Re: mri_segstats error (Douglas N Greve) >> 8. Re: qdec analyses without interaction effect (Douglas N Greve) >> 9. tracula trac-all error malloc_error_break (Cat Chong) >> 10. Re: creating labels, new atlas (Bruce Fischl) >> 11. Re: creating a gca file from .mgz files (Bruce Fischl) >> 12. Re: Control points and errors (Bruce Fischl) >> ---------------------------------------------------------------------- >> Message: 1 >> Date: Fri, 24 Aug 2012 18:45:54 +0000 >> From: "Herting, Megan" <mherting(a)chla.usc.edu> >> Subject: [Freesurfer] Control points and errors >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Message-ID: >> <7C6AFE602753B44C84DC09C4D69F17B6A41058(a)CHLAEXMBH01.LA.AD.CHLA.ORG> >> Content-Type: text/plain; charset="us-ascii" >> Hi, >> I have been using freesurfer on a large dataset and I am having some trouble >> . Sometimes the temporal lobes are not fully covered, so I will go back to add >> a few control points based on the recommendations of freesurfer (voxels that a >> re <110 and not next to a gray matter voxel) and send it through again. This wi >> ll often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to f >> ix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another >> method? >> Thank you! >> Megan >> --------------------------------------------------------------------- >> CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidentia >> l >> 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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Re: [Freesurfer] Surface statistics for PET
by Daniel Tarquinio 26 Aug '12

26 Aug '12

Thank you Doug, that worked perfectly. Regarding the .w file, to view the functional data inflated I used this tutorial: http://poc.vl-e.nl/distribution/manual/fsl-3.2/freesurfer/index.html Is there a workaround to view inflated functional data mapped using mri_vol2surf with a .mgh file? Thank you again, Daniel Message: 6 Date: Fri, 24 Aug 2012 18:57:55 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Surface statistics for PET To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <503806F3.50807(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You can use mri_segstats for this, something like mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat where lh.pet.mgh is the surface-sampled pet BTW, unless you need a .w for something, use a .mgh file (the .w is becoming obsolete). doug On 08/23/2012 07:27 PM, Daniel Tarquinio wrote: > I would like to calculate average PET intensities for specific labels > (using the aparc.annot label files). > > I have coregistered and used mri_vol2surf to assign PET values to the > FS generated surface, and viewed the results using qsurfer. > > The next step is to take the values from the .w files and calculate > label-specific stats. I've tried mris_anatomical_stats but I don't > think this is the right command. > > Any advice? > > Thank you in advance, > Daniel > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -----Original Message----- From: freesurfer-request <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Sat, Aug 25, 2012 12:00 pm Subject: Freesurfer Digest, Vol 102, Issue 27 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Control points and errors (Herting, Megan) 2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve) 3. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Jeff Sadino) 4. Re: problem with tksurfer (Douglas N Greve) 5. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Douglas N Greve) 6. Re: Surface statistics for PET (Douglas N Greve) 7. Re: mri_segstats error (Douglas N Greve) 8. Re: qdec analyses without interaction effect (Douglas N Greve) 9. tracula trac-all error malloc_error_break (Cat Chong) 10. Re: creating labels, new atlas (Bruce Fischl) 11. Re: creating a gca file from .mgz files (Bruce Fischl) 12. Re: Control points and errors (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Aug 2012 18:45:54 +0000 From: "Herting, Megan" <mherting(a)chla.usc.edu> Subject: [Freesurfer] Control points and errors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <7C6AFE602753B44C84DC09C4D69F17B6A41058(a)CHLAEXMBH01.LA.AD.CHLA.ORG> Content-Type: text/plain; charset="us-ascii" Hi, I have been using freesurfer on a large dataset and I am having some trouble. Sometimes the temporal lobes are not fully covered, so I will go back to add a few control points based on the recommendations of freesurfer (voxels that are <110 and not next to a gray matter voxel) and send it through again. This will often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to fix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another method? Thank you! Megan --------------------------------------------------------------------- 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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creating labels, new atlas
by Jeff Thompson 25 Aug '12

25 Aug '12

Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there another way? Thank you, Jeff Thompson

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tracula trac-all error malloc_error_break
by Cat Chong 24 Aug '12

24 Aug '12

Hello Experts, I get the following error when running trac-all: *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice I am using the update for trac-all that was recommended, but it still isn't working. I would be grateful for any suggestions. cheers, cat below is the trac-all log: Loading cortex mask from /Applications/freesurfer//trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(78737) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice Cannot allocate memory Darwin fmris-Mac-Pro-2.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Aug 24 15:37:39 MST 2012

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Re: [Freesurfer] mri_segstats error
by Blazey, Tyler 24 Aug '12

24 Aug '12

Hi Doug, Thanks for the quickly reply. The new version of mri_segstats works fine. I noticed after running it though that all the volumes are slightly different than those reported by previous version. I think it might have something to do with the partial volume correction, as the results are the same when I do not use the --pv flag. Is this expected behavior? And if so, is the new version more accurate? Thanks again, -Tyler ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Surface statistics for PET
by Daniel Tarquinio 24 Aug '12

24 Aug '12

I would like to calculate average PET intensities for specific labels (using the aparc.annot label files). I have coregistered and used mri_vol2surf to assign PET values to the FS generated surface, and viewed the results using qsurfer. The next step is to take the values from the .w files and calculate label-specific stats. I've tried mris_anatomical_stats but I don't think this is the right command. Any advice? Thank you in advance, Daniel

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Re: [Freesurfer] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab
by Jeff Sadino 24 Aug '12

24 Aug '12

Hello FreeSurfers, I am following up on a previous question by another poster: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21700.html In here, Doug says that the mris_preproc script was patched to help with mapping the surface area to a common space, but Doug also hints that it might also help with the volume. I am using FreeSurfer 5.0.0, mris_preproc release date 10-13-09, Revision 1.53. If I want to do a qdec analysis in fsaverage space on just the thickness and volume, can I go ahead with files previously created using my current mris_preproc, or do I need to download the updated one at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc? We also have some people using FreeSurfer 5.1.0, mris_preproc release date 5-17-11, Revision 1.59.2.1. Do they need to update their mris_preproc script? Thank you very much, Jeff Sadino

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Re: [Freesurfer] problem with tksurfer
by Douglas N Greve 24 Aug '12

24 Aug '12

Hi Maryam, it seems very strange that one hemisphere looks ok but other looks bad. In fact, I'd say that it cannot happen. The differences are not likely to be due to version. Can you double check that the tksurfer commands for the lh and rh are the same (except for lh and rh, of course) doug On 08/22/2012 09:13 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > I am having a problem with tksurfer overlay function. I ran one > analysis in freesurfer 5.1 on a mac machine and I cannot properly load > it on the surface. The analysis was performed in the native space. > When I use tksurfer to load the analysis on the surface using the > overlay function I dont get an error but the output image just shows > small dots on the surface instead of patches of activity. It looks > like the registration is not correct. I checked the registration on > the volume and it looks fine to me. This only happens with one of my > subject and only on his left hemisphere. I have attached two tif > images called lhnative.tif and rhnative.tif that show the results. I > also ran the analysis on the surface for both left and right > hemisphere, and it looks fine (lhsurf.tif and rhsurf.tif files attached). > Any Idea how to solve this problem? My guess is that the error is in > the registration of anatomical volume to anatomical surface in the > left hemisphere of this specific subject, but I dont know how to solve > this issue. > > here is the code that I use to load the data on the surface: > > tksurfer teal_tiger_kcb lh inflated -curv -overlay > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > Just a note that the recon-all was performed in freesurfer 4.5 and the > analysis on freesurfer 5.1. Any chance this might have caused the error? > > Thanks, > Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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3rd level surface analysis of fMRI data
by Susan Alice McLaughlin 24 Aug '12

24 Aug '12

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Re: [Freesurfer] Tracula question
by Anastasia Yendiki 23 Aug '12

23 Aug '12

This probably means that bedpostx didn't process all the slices in your DWIs. Someone else reported something like that recently, not sure what may be causing it, but since it's independent of trac-all, I'd check on the FSL list archives. On Thu, 23 Aug 2012, Natalia Sánchez wrote: > they are not. The z dimension of the bedpost images is 52 (from FSL) and for > the dmri FS images it is 72. > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Can you please check that the x-y-z dimensions of the bedpostx > output files are the same as the dimensions of the DWIs? > > On Thu, 23 Aug 2012, Natalia Sánchez wrote: > > Thanks for your response!Attached are the requested files > > The error occurs here are shown on my terminal: > Loading b-valuesfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr > i/bv > als > Loading gradientsfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr > i/bv > ecs > Segmentation fault > Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu > 10.8.0 Darwin Kernel > Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia - I'd need to see at which point in the > processing > the error occurs, since this is a very generic error > message. > Can you please include your trac-all.log and dmrirc? > > Thanks, > a.y > > On Thu, 23 Aug 2012, Natalia Sánchez wrote: > > Hi Anastasia!I finally made tracula -prep work > without errors, using the 1mm > T1 MNI template (i tried using the 2mm one but > the > vertices for registering > white matter came out as NaN). However, I was > not > able to get bedpost to > work. After looking at other posts on the FS > archive, I think the reason why > -bedp does not work is because of my FSL > version. I > tried running bedpost on > FSL and then just copying those files on my > dmri.bedpost folder and using > those files for reconstructing the white > matter > tracts. However, I get a > "Segmentation Fault" error. Do you have any > idea > what this error may mean? > > My dpath folder is empty and I my trac-all.log > file > has no errors related to > -path > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement > Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 5:05 PM, Anastasia > Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia - This is an error that will > occur > if lowb_brain_mask > does not exist. The command that > generates > lowb_brain_mask is > "bet" - can you find that line in the > log file > and run it > directly on the command line and see if > you > get an error? > > On a separate note, have you opted to > use a > DWI mask instead of > an anatomical mask by setting > usemaskanat = 0? > If not, then it > may be that it's trying to use the DWI > mask > b/c it can't find > the anatomicals, in which case I'd check > if > SUBJECTS_DIR has > been set properly and a freesurfer recon > of > the same subject > exists there. But this is a separate > issue than the DWI mask not being > generated. > > Hope this helps, > a.y > > On Fri, 10 Aug 2012, Natalia Sánchez > wrote: > > The required files were not generated. > > the error occurs at > > rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subject > s > /Justin/cJD/dlabel/mni/low > b_brain > _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/ > d > mri/mni/dtifit_F > A.fl > t.nii.gz --ncpts 5 --trunc --debug > ERROR: fio_pushd: > > > /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni > ERROR: Must specify brain mask volume > for > output subject > > does the brain mask have to be input > manually > in the > configuration file, or > is this part of the pre-processing? > since I > set the bet > thr to 0.23 in the > config file i thought the brain mask was > also > created > during the > preprocessing stage. Attached is my log > file. > > I am familiar with FSL but I am using > Free > surfer since i > think automating > the entire process, including tracking > is a > great > advantage, but I'm just > starting to get the hang of it > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical > Engineering & > Physical Therapy and Human Movement > Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 4:28 PM, > Anastasia > Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > dtifit_FA.fl > t.nii.gz > > > > > > > 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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Freesurfer August 2012