Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

Longitudinal Freesurfer & TRACULA quality control
by vbrunsch＠nmr.mgh.harvard.edu 17 Dec '13

17 Dec '13

Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per subject (2 cross-sectional runs, 2 long runs and the base). 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 folders per subject for the SBA? 2. Independent of the previous question, for the longitudinal version of TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer base folder only / additional folders? 3. In addition to the late visual check for well reconstructed pathways with freeview, is there another automated possibility to check the quality of the diffusion weighted images beforehand/do you think this is necessary? 4. On another note: If I understand correctly, in TRACULA bedpostX is used to reconstruct the pathways but then the mean over the voxels that were hit (by the MCMC sampling of the paths) of measures from the tensor model are taken as outputs. I wonder, is there also the possibility of using the partial volumes f1, f2,.. as output measures? Best, Vincent

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Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
by Bruce Fischl 12 Dec '13

12 Dec '13

yes, I think so. Why are you restarting? Or do mean start another one? On Tue, 26 Nov 2013, pablo najt wrote: > Thank you Bruce for your reply.Yes the computed has over 32 GB. > Let me check if I understood. > So far I have been running recon -all in a snow leopard for running as part > of the longitudinal stream. > If I want to re-start with this analysis in the FS 5.3 version for Centos > you are suggesting I can use the a new recon -all command (-openmp 8 flag to > recon-all)? > Thanks. > Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: pablonajt(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > Hi Pablo > > it also depends on how much ram it has. You should be able to run 1 > significantly faster using the -openmp 8 flag to recon-all, or 8 (if you > have enough ram, probably at least 32G) > > cheers > Bruce > > On Tue, 26 Nov 2013, pablo najt > wrote: > > > Dear Bruce,Last week I emailed with the question of how many recon -all > > separate subjects I could run in parallel with the FS version 5.3 for Cent > os > > 6. You answered that this depends on how many cores my machine has. > > I just found out that our workstation has two processors with 4 cores each > > (8 cores in total). > > Would you be able to tell me how many subjects could I run in parallel wit > h > > our workstation? > > Thank you for your support, > > Pablo > > > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > > From: fischl(a)nmr.mgh.harvard.edu > > To: pablonajt(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > Hi Pablo > > > > it depends on how many cores you have > > > > Bruce > > On Thu, 21 Nov 2013, pablo najt wrote: > > > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I > a > > m > > > wondering up to how many recon -all for separate subjects I can run in > > > parallel. With the version of Snow Leopard 32b I was running two at a ti > me > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > el > > ? > > > If so would this process still efficient or there is an optimum number? > > > Thank you, > > > Pablo > > > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > > From: zkaufman(a)nmr.mgh.harvard.edu > > > > To: garikoitz(a)gmail.com > > > > CC: pablonajt(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > > CentOS 6 > > > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > > CentOS6 build. > > > > > > > > -Zeke > > > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a > ny > > > > > reason to not use this version in your CentOS 6, if you have some ot > he > > r > > > > > requirements maybe Nick or Zeke could help you better, I am just an > us > > er > > > :) > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt(a)hotmail.com > > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > > > Dear Gari, > > > > > Thank you for the advice. One additional question. > > > > > Considering that I will start from scratch the processing in the > > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > > Thanks, > > > > > Pablo > > > > > > > > > > -------------------------------------------------------------------- > -- > > -- > > > > > From: garikoitz(a)gmail.com <mailto:garikoitz@gmail.com> > > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > > To: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > and CentOS 6 > > > > > > > > > > > > > > > Hi Pablo, > > > > > you shouldn't mix different OS-s or software version in the same > > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > > operating system version on anatomical volume and cortical thickness > > > > > measurements. /PloS one/, /7/(6), e38234. > > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > > it works too). > > > > > regards! > > > > > Gari > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt(a)hotmail.com > > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > > > Dear FS experts, > > > > > I am forwarding my question (please see below), in case it got > > > > > lost among the intense flow of messages. > > > > > Thank you for your consideration. > > > > > Pablo > > > > > > > > > > -------------------------------------------------------------------- > -- > > -- > > > > > From: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Date: Mon, 18 Nov 2013 16:38:41 +0000 > > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > and CentOS 6 > > > > > > > > > > > > > > > Dear FS experts, > > > > > I have a question about compatibility for running recon-all > > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > > wondering if I could process additional subjects in parallel > > > > > with this other machine that are also intended to be included in > > > > > the longitudinal stream. > > > > > Also, I am not sure about whether I should be installing in the > > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > > because of compatibility issues. > > > > > Thank you very much for your attention, > > > > > Pablo > > > > > > > > > > > > > > > _______________________________________________ Freesurfer > > > > > mailing list Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto: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. > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto: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. > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing > > > > > list Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto: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. > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.ed > u> > > > > > 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 > > > > > > > > > _______________________________________________ > > > > 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 informati > on > > 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 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] Fwd: white matter and pial surface don't track sulcus
by Darren Gitelman 06 Dec '13

06 Dec '13

Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Check the aseg and see if it was labeled ventricle (and make sure it > really isn't). You may need to edit the aseg > > > > On Sep 16, 2012, at 5:19 PM, Darren Gitelman <d-gitelman(a)northwestern.edu> > wrote: > > Hi > > I have run into an issue that I'm not sure how to correct. What happens > is that in some subjects the surfaces don't seem to properly track sulci > coming off the medial part of temporo-occipital cortex. Please see green > arrows on the attached image. > > In fact the tutorial on topological defects shows an image with a > similar issue, but fixing it is not discussed. > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?actio… > > I have checked and these are sulci and not the occipital extent of the > lateral ventricle. > > Perhaps it is not a problem, or if it is then how to approach fixing it? > > Thank you, > Darren > -- > Darren Gitelman, MD > Northwestern University > 710 N. Lake Shore Dr. > Abbott 11th Floor > Chicago, IL 60611 > Ph: (312) 908-8614 > Fax: (312) 908-5073 > > <3809-error.png> > > _______________________________________________ > 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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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possible pial surface editing
by Gennan Chen 05 Dec '13

05 Dec '13

Hi! All, We ran into a few cases which the wm matter surface is pretty decent but pial surface did not go far enough to include all gray matter. Is there a way to fix this? Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts
by Douglas N Greve 04 Dec '13

04 Dec '13

Hi Sue, that looks correct. I think it is an open question as to whether you should use the corrected maps or use the uncorrected and then correct the final map. Maybe someone else can chime in. doug On 10/23/2013 09:49 AM, Susan Ruiz wrote: > Hi Doug, > > This is /very/ helpful. > > Procedurally, would this be the correct approach? > > For positive % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.pos.sig.cluster.nii > condBvFix.th3.pos.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i > condBvFix.th3.pos.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii > > For negative % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.neg.sig.cluster.nii > condBvFix.th3.neg.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i > condBvFix.th3.neg.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii > > Note that for positive activation differences I would use sign=pos for > each condition vs fixation during mri_glmfit-sim, and for > "deactivation" clusters I use sign=neg for each condition vs fixation > during mri_glmfit-sim. BUT for both cases I use sign=pos for condition > A vs. condition B. > > Thanks so much! > > Best, > ~Sue > > > > On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Sue, I agree that they are not the same thing. There is not a > single > flag that will do what you want. What you are describing is a post-hoc > test. So you look for places where A != B, then within those > voxels you > do posthoc tests. You can implement this with a conjunction analysis > where you set up threeway conjunction A>B and A>0 and B>0. You can do > this with the --conjunt option to mri_concat > doug > > > On 10/21/2013 02:13 PM, Susan Ruiz wrote: > > Hi all, > > > > When running a functional analysis and comparing two experimental > > conditions, we observed that there are some voxels/vertices > where both > > condition A and condition B have a positive % signal change from > > baseline, and condition A has greater activity than condition B. > > > > In other regions, both condition A and condition B have negative % > > signal change from baseline, but condition B has a greater absolute > > value % signal change (thus relative to baseline condition B has > more > > "deactivation"--a term I am using since you all know what I mean > even > > if the term itself is imperfect). > > > > Since, in both cases, the % signal change is technically > condition A > > > condition B, the between-conditions maps do not distinguish > these two > > scenarios. FS-FAST sees these as being the same. Is there a way to > > tell FS-FAST to cluster these scenarios separately? Is there a > > compelling reason why I should not consider these different > > situations? It seems to me that the interpretation of what's taking > > place in these two scenarios is not identical. Agree or > disagree? Can > > FS-FAST distinguish these with a flag I don't know about? > > > > Thank you, > > ~Sue > > > > -- > > * * ** *** ***** ******** ************* > > Susan Mosher Ruiz, Ph.D. > > Research Scientist > > Boston University School of Medicine > > Laboratory of Neuropsychology > > VA Boston Healthcare System > > smosher(a)bu.edu <mailto:smosher@bu.edu> <mailto:smosher@bu.edu > <mailto:smosher@bu.edu>> > > * * ** *** ***** ******** ************* > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > ------------------------------------ > > Yahoo! Groups Links > > <*> To visit your group on the web, go to: > http://groups.yahoo.com/group/martinos-tech/ > > <*> Your email settings: > Individual Email | Traditional > > <*> To change settings online go to: > http://groups.yahoo.com/group/martinos-tech/join > (Yahoo! ID required) > > <*> To change settings via email: > martinos-tech-digest(a)yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com> > martinos-tech-fullfeatured(a)yahoogroups.com > <mailto:martinos-tech-fullfeatured@yahoogroups.com> > > <*> To unsubscribe from this group, send an email to: > martinos-tech-unsubscribe(a)yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com> > > <*> Your use of Yahoo! Groups is subject to: > http://info.yahoo.com/legal/us/yahoo/utos/terms/ > > > > > -- > * * ** *** ***** ******** ************* > Susan Mosher Ruiz, Ph.D. > Research Scientist > Boston University School of Medicine > Laboratory of Neuropsychology > VA Boston Healthcare System > smosher(a)bu.edu <mailto:smosher@bu.edu> > * * ** *** ***** ******** ************* > __._,_.___ > Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwa21mMTlwBF9TA…> > Reply to sender > <mailto:smosher@bu.edu?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlZjd2ZDVnBF9TA…> > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5844;_ylc=X3oDMTM0a2Nkb…> > (3) > > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcXY1cjhnBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkdW8xcWpkBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://info.yahoo.com/legal/us/yahoo/utos/terms/> • > Send us Feedback > <mailto:ygroupsnotifications@yahoogroups.com?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Fwd: Minimum Dti directions and odf
by Salil Soman 02 Dec '13

02 Dec '13

Hi, I hope all is well. Was wondering if any of had heard of an explicit minimum number of DTI directions necessary for using odf / hardi modeling ? I have run a couple of data sets of 30 directions (+ 5 b0) through TRACULA, and have run this same data through diffusion toolkit using the hardi / odf model, with reasonable looking results. I was wondering if there was any specific reason why using these models with 30 directions would be considered in appropriate? Thanks! Sal

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Volume differences after corrections
by Garikoitz Lerma-Usabiaga 01 Dec '13

01 Dec '13

Hi list, I obtained cortical thickness and volumetric results before and after correcting them for defects. I just did some wm edits and mostly controls points in the top of the head (some subjects had less signal so I put control points in order to allow for a good surface reconstructions). When comparing the values: EXPECTED - Same volume values for subcortical structures, i.e.: same thalamic volume before and after - Different CT values in the edited areas and only for the edited subjects, i.e.: lh_paracentral_thickness - Different volumetric values only for the edited subjects in, for example: lhCortexVol, CortexVol, CorticalWhiteMatterVol NOT EXPECTED - Same values for EstimatedTotalIntraCranialVol. I was controlling thalamic values with the eTIV, (using Raz 2005's formula)*, but before and after correcting almost half of the subjects, obviously, I obtain the same results. - Should I use a different value other than the eTIV? - Is normal that the eTIV doesn't change but the rest of the values are changing? The brain is definitely different after the control points, it grows a little bit upwards. any information on this will be appreciated! thanks, Gari PS: * Volume (adj) = Vol(rawi)-b*(ICV(i)-mean ICV), where b is the slope of regression of an ROI volume on ICV

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Within group hemisphere comparison in QDec
by krista kelly 30 Nov '13

30 Nov '13

Hello, I need to do a within group hemisphere comparison to see if there are any hemisphere asymmetries in a patient group. I would like to do this in QDec or if possible, somehow do it in freesurfer without using Qdec. I asked this question two years ago and you mentioned that you were working on this and it should be available soon. Has there been any progress? Thanks! Krista

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how to recon-all multiple participants simultaneously? thanks
by chen kanwisher 29 Nov '13

29 Nov '13

Dear Freesurfers, I'd like to ask how could we recon-all multiple participants at the same time? My laptop has a 32G ram and a 8-core-intel-Core-i7 CPU, i expect it could speed up the surface construction by running several participants simultaneously. When i use the following command: 'foreach i (1 2 3....);recon-all -subjid sub$i -all -openmp8;end', each participant needs 4-5 hours. Although this is much faster than the typical time consumption as stated in freesurfer wiki, i notice only 3 out my 32G working memory is used under such command. So I am wondering if there are some other ways to make full use of the working memory and make the surface construction go even faster. I have tried to open 8 terminal windows, each for a separate participant, and for each window, the command was like this, 'recon-all sub01 -all openmp 8'. It turned out the analysis ran extremely slow, none of the subjects finished even after 36 hours, the CPU was 100% used, but still no more than 7 of the 32G working memory was occupied. So, question, is it possible for me to make the analysis more quickly, and if so, how？ Looking forward to your informations, and thank you a lot! Chen

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Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs
by Anita van Loenhoud 29 Nov '13

29 Nov '13

Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita

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Freesurfer November 2013