Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

question about persession versus perrun motion correction
by Maryam Vaziri Pashkam 22 Jan '13

22 Jan '13

Hi Dough, This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line: *mkanalysis-sess \* * -analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* * -native -mcextreg -stc siemens -fwhm 0 \* * -event-related -paradigm para_cat.par -nconditions 5 \* * -spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* * * * * * And here is what I have in my analysis info analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3 I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1. M *

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Downsampling/decimating overlays (not surfaces)
by Nicola Toschi 22 Jan '13

22 Jan '13

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around.

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freesurfer@nmr.mgh.harvard.edu
by Nicola Toschi 22 Jan '13

22 Jan '13

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Re: [Freesurfer] question about persession versus perrun motion correction
by Douglas N Greve 22 Jan '13

22 Jan '13

Oh, right, I remember now (at least mostly). I fixed that for version 5.2. Maryam, it may be that the code is not actually using the persession data like it should. doug On 01/22/2013 03:19 PM, raij(a)nmr.mgh.harvard.edu wrote: > Hi Doug, > > There at least used to be a bug in the way perrun/persession was handled. > We exchanged emails about that about a years ago (see especially Tapsya's > emails). If I recall correctly we were never able to make this work > without rigging the file extensions etc (FS-FAST always defaulted to one > stream and/or one file extension regardless of which option was used). Not > sure if this is still a problem, but could be related to Maryam's email. > > Cheers, > > Tommi > > >> Hi Maryam, when you say that they are practically identical, I assume >> that there are at least some small differences indicating that something >> was different? And what are you comparing exactly? Eg, single subject or >> group? In principle, they should be pretty close to each other, it >> depends entirely on how much the subject moved between runs and how much >> smoothing you apply. If you have a well-behaved population, then there >> might not be much of a difference. If you reduce the smoothing to 0, >> then you might start to see more of an effect. >> >> doug >> >> >> On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote: >>> Hi Dough, >>> >>> This might be a very basic question: >>> I would like to compare the results of an analysis with the perrun and >>> persession motion correction. Here is my analysis line: >>> >>> >>> *mkanalysis-sess \* >>> >>> *-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \* >>> >>> *-native -mcextreg -stc siemens -fwhm 0 \* >>> >>> *-event-related -paradigm para_cat.par -nconditions 5 \* >>> >>> *-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2* >>> >>> * >>> * >>> * >>> * >>> * >>> And here is what I have in my analysis info >>> >>> analysis Cat_1 >>> mcstem fmc >>> fsd bold >>> runlistfile run_1.txt >>> TR 2 >>> RegDOF 6 >>> RawSpace volume native >>> mask brain >>> RawFWHM 0 >>> RawSTC siemens >>> UseB0DC 0 >>> inorm 100 >>> acfbins 30 >>> fixacf 1 >>> acffwhm 20 >>> acfsvd 0 >>> designtype event-related >>> nskip 0 >>> polyfit 2 >>> HPFCutoffHz 0 >>> HeteroGCor 0 >>> nconditions 5 >>> parname para_cat.par >>> RefEventDur 3 >>> timewindow 40.000000 >>> prestim 0 >>> TER 0.050000 >>> spmhrf 0 >>> stimulusdelay -1.00000000000000000000 >>> Condition 1 Condition01 >>> Condition 2 Condition02 >>> Condition 3 Condition03 >>> Condition 4 Condition04 >>> Condition 5 Condition05 >>> nuisreg mcextreg 3 >>> >>> >>> >>> I preprocessed my data once using the perrun option and once using the >>> persession option in two different directories and ran the analysis on >>> both of those data sets. The problem is when the analysis finished the >>> results where practically identical. I am not sure what is going on >>> and can't figure out if the analysis in both cases is done based on >>> the persession motion correction or they are both done based on the >>> perrun motion correction and how I can get the analysis to run in two >>> different ways. I am using freesurfer 5.1. >>> >>> M >>> * >> -- >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] long_mris_slopes / mris_calc problem
by O'Shea,Andrew 22 Jan '13

22 Jan '13

I was able to solve my problem in my earlier email included below. I downloaded a new verison of mris_calc made it executable with chmod +x FILE and then replaced it in the bin folder. I included this response in case anyone else runs into the same problem and does a search. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-int… ---- Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/02031… However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew

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What is "CSF" label is aseg.stats
by Sophie Maingault 22 Jan '13

22 Jan '13

Dear all, I read the others posts about CSF but I didn't find the information that I need. I would like to calculate total CSF and in the aseg.stats file there are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th Ventricle but what is CSF ? Because I read that freesurfer can't measure sulcus CSF so I don't understand what is the meaning of "CSF" alone. Thank you for your answer ! Sophie

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Re: [Freesurfer] Trouble with Initial Processing - Very Dark Images
by Dan LaFreniere 22 Jan '13

22 Jan '13

Hey Falk, Much appreciated for your reply on this! Fortunately I was able to correct the issue by contacting our MRI tech - he suggested we use his nifti files instead and the results turned out a lot better. I emailed Bruce but forgot to include the freesurfer mailing list in the CC. Here is an attached screenshot of my final results with the nifti files for the record. Thanks again for the replies! I'm sure I'll be contacting the experts down the road. Cheers, Dan On Tue, Jan 22, 2013 at 4:06 AM, "Falk Lüsebrink" <falk.luese(a)gmx.net>wrote: > Hey Dan, > > Bruce might be right about the SNR, but you could try to adjust the > parameters of the inhomogeneity correction in the N3 algorithm. > > You could either use the following command line: > recon-all -autorecon1 -mprage -nuintensitycor-3t -i <data> -s <subject> > > Or if this still isn't good enough, try changing the parameters of the N3 > manually (e.g. distance and fwhm): > SUBJ=ab11 > > recon-all -motioncor -talairach -tal-check -i <data> -s $SUBJ > > mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o > $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.5 > --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm > > recon-all -mprage -normalization -skulstrip -s $SUBJ > > If the skullstrip looks fine continue by using this: > recon-all -mprage -autorecon2 -autorecon3 -s $SUBJ > > Best, > Falk > > > -------- Original-Nachricht -------- > > Datum: Mon, 21 Jan 2013 22:39:29 -0500 > > Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > An: Dan LaFreniere <lafreniere.dj(a)gmail.com> > > CC: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Betreff: Re: [Freesurfer] Trouble with Initial Processing - Very Dark > Images > > > Wow, that's a huge bias field! Control points will help uniformity, but > > the snr may not be good enough for good results > > Bruce > > > > > > > > On Jan 18, 2013, at 11:09 AM, Dan LaFreniere <lafreniere.dj(a)gmail.com> > > wrote: > > > > > Hey all, > > > > > > I'm very new to Freesurfer and am having some issues with the initial > > processing of our MPRAGE dicom files. So far, I'm able to get initial > > -autorecon1 steps to work but once this has finished and I open my > brainmask.mgz > > files and the brain is incredibly dark in inferior regions. So much so > that > > the skull strip appears to be removing large chunks of anterior temporal > > lobes. What remains of the temporal lobes is incredibly dark with grey > matter > > almost indistinguishable from CSF. > > > > > > I would really like to look into freesurfer for cortical thickness > > analysis of subcortical regions since it seems like such an awesome > program but > > I have really been struggling to get a decent looking brain. It's > probably > > noteworthy that these brains have always been quite dark but I'm usually > > able to correct them to a point where they're pretty good in other > programs. > > > > > > I have read about a few solutions to the problem but am having trouble > > implementing them. One suggestion was to use the -mprage flag; > > unfortunately, I'm not sure how to run this or when. Another suggestion > was to use > > control points but I don't yet have the red and blue segmentation > boundary lines > > - I'm using tkmedit FoM04_KA brainmask.mgz -aux T1.mgz to view the > files. > > For reference, this is the line I use to run autorecon1: Recon-all > > -autorecon1 -subjid FoM04_KA > > > > > > Does anyone have any suggestions as to what I could do? It would be > > greatly appreciated. I've attached a screenshot to illustrate. Also, we > used a > > 4.7T Varian scanner with 0.375/0.375/1mm voxels. I believe we used a > > gradient echo multislice sequence. In addition, all subjects' data have > been > > obtained so there is no chance of changing sequences… > > > > > > Best wishes, > > > > > > Dan > > > > _______________________________________________ > > > 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 > > > > > > 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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Re: [Freesurfer] (no subject)
by Douglas N Greve 22 Jan '13

22 Jan '13

That should not happen. Concentrating on the Mac for a moment, please send the recon-all.log files for both runs. doug On 01/22/2013 10:36 AM, Varghese Chikku wrote: > Many thanks Doug, > I forgot to mention,I ran same patient,same time point,twice on > Mac and VM and the results varied each time.So why is it happening > though I am using the same machine and same set of images. > Cheers, > Chikku -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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qdec
by Catherine Bois 22 Jan '13

22 Jan '13

Hi, I am considering using qdec, however due to our large dataset (and different individuals having been in charge at different times) I just realized that the folders fsaverage etc are "missing". As these are necessary for the qdec use, is there anything else I can do? Eg a command line to just generate the fsaverage for all my subjects? Thank you for your help -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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22 Jan '13

Dear FS-experts, I'm trying to follow the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get volumetric stats etc on a functional ROI derived from marsbar. The tutorial looks all clear to me, however, I have already problems at the first step. If I want to view the ROI I see a big orange square instead of the specific region. This almost fills the whole brain. command: tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5 I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > "Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong? Thanks in advance! Best wishes, Cédric ------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn(a)uva.nl W http://home.medewerker.uva.nl/p.c.m.p.koolschijn/ ------------------------------------------------------------

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Freesurfer January 2013