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Fw: Convert QDEC clusters on the MNI_152_T1 space
by Antonella Kis 27 Aug '12

27 Aug '12

Hi Doug, Many thanks for your help. Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on the MNI space since this is the template I use for my connectivity maps. I am not sure if I need to mention the label of my clusters for example the uncorrected clusters. Should I use the sig.mgh or I just run: mri_label2vol --label lh-precentral --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --o precentral-lh.nii Also what threshold should I use with mri_label2vol if this are my uncorrected clusters? How can I do this if as below I have two clusters in the same region? Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain > template? > > Thank you. > Antonella > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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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

2 2

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

2 1

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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