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 <fis...@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 <gr...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Surface statistics for PET >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <503806f3.50...@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@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -----Original Message----- >> From: freesurfer-request <freesurfer-requ...@nmr.mgh.harvard.edu> >> To: freesurfer <freesurfer@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@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-requ...@nmr.mgh.harvard.edu >> You can reach the person managing the list at >> freesurfer-ow...@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" <mhert...@chla.usc.edu> >> Subject: [Freesurfer] Control points and errors >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <7c6afe602753b44c84dc09c4d69f17b6a41...@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. --------------------------------------------------------------------- >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201208 >> 24/22eaa059/attachment-0001.html ------------------------------ >> Message: 2 >> Date: Fri, 24 Aug 2012 18:16:30 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] 3rd level surface analysis of fMRI data >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <5037fd3e.6080...@nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> Hi Susan, sorry for the delay. If you want to use a random fx model, then dont include any of the ffx options, so just >> /mri_glmfit --y xrun/lh.cope1.mgh --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/ >> doug >> On 08/22/2012 07:21 PM, Susan Alice McLaughlin wrote: >> > Hi, >> > >> > I?m a Freesurfer novice, and am confused about how to run a 3rd level > cross-subject analysis on the surface using as input cross-run .gfeats > from 10 subjects generated from a 2nd level analysis of fMRI data in FSL. >> > >> > Following the directions posted at > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I > have sampled the .gfeat copes and varcopes into standard surface > space, using /mris_preproc/. >> > >> > I would then go on to perform a 3rd level surface based analysis as > the instructions suggest, using: >> > >> > /mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh > >> > --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh > --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/ >> > >> > However, I want to use a random effects rather than fixed effects > analysis. How do I do this? I tried /--yrfxvar/ as opposed to > /--yffxvar/ but it didn?t work. And if I?m going to display the map > resulting from this analysi! s, do I need to correct for multiple > comparisons? >> > >> > Many thanks in advance, >> > >> > Susan McLaughlin >> > Doctoral Candidate >> > SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) >> > Dept. of Speech and Hearing Sciences >> > University of Washington >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.
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