Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Re: [Freesurfer] patched version of mris_preproc for 5.1 user?
by Douglas N Greve 07 Feb '13

07 Feb '13

that link should work now doug On 02/07/2013 12:53 PM, Uri Hasson wrote: > Dear Doug, > > We're still using version 5.1 for a pipeline, and need to send > surface-based measures (volume, area, thickness) to a standard space > for whole-brain analysis. I read you had a patched version of > mris_preproc, but the link saw in an online post (below) doesn't work. > Is there another link to the utility? > > Thanks, > Uri > > D.G wrote: > --- > Hi Tetiana, thanks for the push. I've put a new version of mris_preproc > here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > This will implement the fix. > To "install" make a backup of mris_preproc in $FREESURFER_HOME/bin, then > move the new version. > You should re-run recon-all with -qcache (no need to rerun all of > recon-all). > > doug > --- > > -- 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] qdec and file "-qcache"
by Douglas N Greve 07 Feb '13

07 Feb '13

Hi Sophie, you can only run one subject at a time. What is your command for one subject? doug On 02/07/2013 11:41 AM, Sophie Maingault wrote: > Actually, I have more than 450 subjects but I will give an example with less > subjects (here 3 subjects). So the command line that I run is : recon-all -s > < t0001 t0002 t0003 > -qcache. > > Maybe I have to run this command line for each subject independently for > example first : recon-all -s < t0001 > -qcache and then recon-all -s < t0002 >> -qcache ...etc, until I did it with all my subjects ? > Is it ok or there are others symbols that you don't understand ? I begin > with Freesurfer so maybe I did some mistakes ! > > Sophie > > -----Message d'origine----- > De : freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Douglas N > Greve > Envoyé : jeudi 7 février 2013 17:33 > À : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] qdec and file "-qcache" > > Hi Sophie, can you cut and paste the actual command line that you are > using? I don't know what all the symbols mean. > doug > On 02/04/2013 08:15 AM, Sophie Maingault wrote: >> Hello everyone ! >> >> I want to use qdec so I tried to smooth the subjects with the >> following command: recon-all -s < t0001 … t0742 > -qcache (… = all my >> subjects !). The tutorial said that it takes about an hour but >> immediately a file was created : “-qcache” (2.95 Ko). Is it normal ? >> Does the process work or did I something wrong ? >> >> Thanks a lot for your help ! >> >> Sophie >> >> >> >> _______________________________________________ >> 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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annotating only certain regions
by Hemant Bokil 07 Feb '13

07 Feb '13

Hi all, Is there a way to get freesurfer to annotate only certain selected structures (e.g. basal ganglia). I suspect not, since the underlying model involves spatial relationships between labels, but thought I would ask. I am looking for any ways to speed up the annotation process. Thanks, Hemant

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qdec and file "-qcache"
by Sophie Maingault 07 Feb '13

07 Feb '13

Hello everyone ! I want to use qdec so I tried to smooth the subjects with the following command: recon-all -s < t0001 . t0742 > -qcache (. = all my subjects !). The tutorial said that it takes about an hour but immediately a file was created : "-qcache" (2.95 Ko). Is it normal ? Does the process work or did I something wrong ? Thanks a lot for your help ! Sophie

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Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas N Greve 07 Feb '13

07 Feb '13

it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. thanks doug On 02/04/2013 07:26 AM, Richter, Julia wrote: > This doesn't work either (see attachment) :( > > -----Ursprüngliche Nachricht----- > Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 31. Januar 2013 20:29 > An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec > > The threshold must be in the form of -log10(pthreshold). So, if you want pthreshold=.05, then use 1.3 doug > > > > On 01/31/2013 07:37 AM, Richter, Julia wrote: >> Dear Doug, >> >> thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. >> >> Looking forward to your answer, >> >> Best, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve >> Gesendet: Mittwoch, 30. Januar 2013 17:16 >> An: Richter, Julia; free surfer >> Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec >> >> Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters >> >> doug >> >> On 1/30/13 8:09 AM, Richter, Julia wrote: >>> No it is not...or I just do not find it. >>> >>> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? >>> >>> Many thanks, Julia >>> >>> -----Ursprüngliche Nachricht----- >>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve >>> Gesendet: Dienstag, 29. Januar 2013 18:46 >>> An: freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec >>> >>> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >>> doug >>> >>> >>> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>>> Dear FreeSurfer experts, >>>> >>>> I did a group analysis in qdec, found several significant clusters and >>>> would now like to extract the mean cortical thickness of each >>>> significant cluster. I know that I have to run mri_glmfit-sim to do >>>> this, but I do not understand which commands I need to get the >>>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>>> >>>> Any ideas? Any help is appreciated. J >>>> >>>> Best wishes, Julia >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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/ >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >> _______________________________________________ >> 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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DOSS and FDR in QDec
by Sean Hatton 07 Feb '13

07 Feb '13

Hi FreeSurfers, These should be a simple questions but they have been bugging me. 1. I have two diagnostic groups that I want to compare controlling for gender and age. I am entering them in Qdec with diagnosis and gender as discrete factors and age as continuous (n=89). If I use DODS I get non-sig result after FDR, but I am not sure if this is modelling back to age 0 – I have demeaned the age to try to get the mean age value but get the same results. I read that to overcome this you can use DOSS where I do get a significant results after FDR, but the results are exactly the same as the age-thickness correlation (I.e. There is no diagnostic effect, it is all age-related). Can you advise the best way to control for age and gender. 2. Can you control for FDR over both hemispheres? 3. After FDR, how can you adjust the heat bars so that you can approapriately compare between statical maps? Thank you!

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BEDPOSTX - seychelles option
by Susan Kuo 07 Feb '13

07 Feb '13

Hi FreeSurfer community, I would like to run '-bedp' with TRACULA, to run the bedpostx option. I see from the *./subjID/scripts/trac-all.cmd* file that the actual command issued was *bedpostx_seychelles*, which allows for the PBS queueing system running on seychelles and is used by the Martinos Center folks to parallelize computation. I have 2 questions regarding this modification: 1 - Can I switch to strictly *bedpostx*? Is there a text file I can alter to reflect changes to the commands issued? I believe *trac-all.cmd* is actually created at runtime, not prior. 2 - I work at NIH and have the Biowulf cluster to work with. Can I parallelize bedpostx on Biowulf (which uses a Altair's PBS Pro batching system) with TRACULA's *trac-all -bedp* command, or any of *trac-all*? Thank you for your attention! Susie Kuo

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Re: [Freesurfer] Xhemi questions
by Gabriel Gonzalez Escamilla 07 Feb '13

07 Feb '13

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white matter hyperintensities
by Linn Mittlestein 07 Feb '13

07 Feb '13

Dear freesurfer experts, I have a question regarding white matter hyperintensities (ie values above 110)..if these are included in the brainmask accurately, ie as white matter when it is indeed white matter, does hyperintensities still cause problems, and if so why? Regards Linn

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longitudinal processing with -FLAIRpial
by Charles Malpas 07 Feb '13

07 Feb '13

Dear Freesurfer Ninjas, I have been playing around with the new beta version, and am very interested in the -FLAIRpial option. I have been using this successfully on cross-sectional runs, but would like to extend it to cross sectional runs. I have played around with trying to get this to work, including copying FLAIRconf.mgz to the longitudinal run directions (subjid.long.template) and the recon-alll -long command with -FLAIRpial. Although this runs, it produces cortical thickness estimates that appear underestimated on visual inspection. Is there a better way to incorporate -FLAIRpial on longitudinal runs? Is it even possible at this stage? Many thanks for your time, - Charles -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas(a)student.unimelb.edu.au Skype: charles.malpas

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Freesurfer February 2013