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30088 discussions

Total gray matter volume for aparc.2009?
by Yizhou Ma 16 Sep '13

16 Sep '13

Dear Freesurfer experts, I'm doing ROI analysis on surface area and gray matter volume using the aparc.2009 parcellation. Now that I wanted to use corresponding whole brain measures as covariates, I could not find whole brain gray matter volume measures in the aparc.a2009s.stats file. However, I find one in the aseg.stats file. Since I believe these two file use different approaches to estimate gray matter volume, I'm stuck with what I choose for the whole brain measure. Do I use the value in aseg.stats or do I add up the volumes of regions in aparc.a2009s.stats? And advice is appreciated. Thanks, Cherry

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Research Fellow/Postdoc in Pain Neuroimaging, University of Michigan, Ann Arbor, MI
by Alexandre Dasilva 16 Sep '13

16 Sep '13

Research Fellow/Postdoc in Pain Neuroimaging University of Michigan, Ann Arbor, MI The Headache and Orofacial Pain Effort (H.O.P.E.) requests applications for Research fellow/Postdoc to work on a TMD research program funded by NIH-NIDCR. The program uses neuroimaging to investigate central mu-opioid mechanisms of chronic TMD pain. Knowledge of Linux/UNIX operating systems as well as programming experience is required, as is a good level of comfort with novel computer applications and statistics. Previous research experience with positron emission tomography and/or MRI-based neuroimaging methods and analyses is also needed. We are seeking applicants with strong self-motivation to work in a highly creative, altruistic, and mentoring environment. The applicant will be exposed to other tech-innovations in chronic pain (e.g., migraine and cancer pain), such as: Neuroimaging/Neuronavigation: http://www.ns.umich.edu/new/multimedia/videos/21402-hologram-like-3d-brain-… Neuromodulation: http://www.jove.com/video/2744/electrode-positioning-montage-transcranial-d… Mobile Technology: http://www.ns.umich.edu/new/multimedia/videos/20960-new-mobile-app-helps-mi… H.O.P.E. is a multidisciplinary collaborative effort at University of Michigan to investigate the brain as a research and therapeutic target for headaches and orofacial pain disorders. The University of Michigan is an equal opportunity affirmative action employer. Initially a curriculum vitae and letter of intent should be sent to: Alexandre F. M. DaSilva, DDS, DMedSc Director, Headache and Orofacial Pain Effort (H.O.P.E.) TM Biologic & Material Sciences, School of Dentistry The Molecular & Behavioral Neuroscience Institute (MBNI) adasilva(a)umich.edu

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Repost family wise error rate correction
by Venkatesh Rajagopalan 16 Sep '13

16 Sep '13

Hi All, I am sorry to repost this message as I did not hear from you. I am wondering whether someone could tell me how I can do family wise error rate correction. I ran mri_glmfit with sim option and how I can perform the FWER correction using mri_surfcluster. Thanks Venkatesh Kessler Foundation is proud to be recognized as one of the Best Places to Work in New Jersey. The information in this transmission is intended for official use of the Kessler Foundation. It is intended for the exclusive use of the persons or entities to which it is addressed. If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited. If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.

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RE : RE : mri_glmfit_script.csh
by Stéphane Poulin 16 Sep '13

16 Sep '13

Ok, ________________________________________ De : Douglas Greve [greve(a)nmr.mgh.harvard.edu] Date d'envoi : 16 septembre 2013 11:42 À : Stéphane Poulin Objet : Re: RE : [Freesurfer] mri_glmfit_script.csh Hi Stephane, please post to the list and not to me separately. thanks! doug On 9/16/13 5:25 PM, Stéphane Poulin wrote: > Sorry Doug, > I have been using this script since my fellowship training at the Martinos and thought it was commonly used. > I have not used the mri_glmfit as explained in FS tutorials (ex https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) > In any case you can solve my issue just looking at the script (attached) it would be appreciated. If not, I'll get into the tutorials. > Thanks, > Stephane > > ________________________________________ > De : freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] de la part de Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Date d'envoi : 16 septembre 2013 10:25 > À : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] mri_glmfit_script.csh > > what is mri_glmfit_script.csh? Please send the actual mri_glmfit command line and terminal output. > doug > > On 9/16/13 3:58 PM, Stéphane Poulin wrote: >> Dear Freesurfer experts, >> >> If I want to correlate a variable with cortical thickness using mri_glmfit_script.csh, >> >> fsgd file >> >> GroupDescriptorFile 1 >> Title <name of the analysis> >> Class Main >> Variables <variable of interest> >> Input subject1 Main <results of subject 1 on variable of interest> >> … >> >> and contrast.mat >> >> 0 1 >> >> Question: red/yellow on the statistical surface map = positive correlation between cortical thickness and variable of interest (and blue negative correlation)? >> >> Thanks, >> >> Stephane >> >> _______________________________________________ >> 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] Significant clusters before and after Monte Carlo
by Anita van Loenhoud 16 Sep '13

16 Sep '13

Hi Doug, Thanks for your reply. I was using 1.3 for visualization and 2 for simulation. So that's probably where it went wrong? When I set both thresholds to 2, significant clusters after Monte Carlo were also there before the simulation. Just to double-check: can the values associated with these significant clusters be different before and after Monte Carlo? For example, before Monte Carlo the value of the rostralmiddlefrontal was -4.42, after Monte Carlo it's -2.19. That's normal, right? Thanks again, Anita

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mri_glmfit_script.csh
by Stéphane Poulin 16 Sep '13

16 Sep '13

Dear Freesurfer experts, If I want to correlate a variable with cortical thickness using mri_glmfit_script.csh, fsgd file GroupDescriptorFile 1 Title <name of the analysis> Class Main Variables <variable of interest> Input subject1 Main <results of subject 1 on variable of interest> … and contrast.mat 0 1 Question: red/yellow on the statistical surface map = positive correlation between cortical thickness and variable of interest (and blue negative correlation)? Thanks, Stephane

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Re: [Freesurfer] recon all question
by Rashmi Singh 16 Sep '13

16 Sep '13

I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This is why I need total brain volume measurements. Do you suggest that its not a good idea to use mri-binarize of brain.mgz for calculating it? Earlier freesurfer experts had suggeted me to use this option. Rashmi _______________________ ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura. cheers Bruce On Fri, 13 Sep 2013, Rashmi Singh wrote: > Thank you Bruce ! > mri_binarize was suggested to me by the freesurfer group, so now I am a little concerned when you say that this has not been assessed for accuracy. May you suggest how otherwise do you get the total brain volume ( which you suggest is more accurate), as this measurement is not present in the freesurfer output stat files. > > May you please elaborate a little more the steps of using T2-FlAIR for recon all or suggest me where I can find the detail information ( may be on the website). While scanning we do collect T2-FLAIR that is linked with T1 for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a -T2Flair swicht? > Sorry, with a background of molecular biology and being a novice in image analysis, it really takes me time and lots of effort to understand imaging and its analysis. Your guidance is appreciated. > Thanks, > > Rashmi > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, September 13, 2013 8:46 AM > To: Rashmi Singh > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] recon all question > > 1. I don't think I know anyone who has done this, and we haven't assessed > it for accuracy. > > 2. The best thing to do is get a T2-FLAIR and run it with the -T2Flair > switch after recon-all is done. This does a great job avoiding dura > > cheers > Bruce > > > On Fri, 13 Sep 2013, Rashmi Singh wrote: > >> Hey Bruce, >> I have two more questions. >> 1) I was suggested to use mri_binarize with brain.mgz to get the total brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume. >> >> 2)I learnt that using T2 weighted image along with T1 weighted image from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer. >> May the FreeSurfer experts guide me through this. >> >> Thanks, >> Rashmi >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Thursday, September 12, 2013 5:27 PM >> To: Rashmi Singh >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon all question >> >> Hi Rashmi >> >> putting them in the orig folder with those numbers will get recon-all to >> do motion correction and averaging. >> >> cheers >> Bruce >> On Thu, 12 Sep 2013, Rashmi Singh wrote: >> >>> >>> Hello Freesurfer experts, >>> I am doing volumetrics study. During the scan we get 2-3 mprage per >>> scan for a subject. >>> While running the FreeSurfer, if I want to use the three mprages for >>> that subject as an input file, may I just keep the three mgz files >>> (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple >> recon >>> all command :=Recon-all -s (subject file name) -all or do I need to have >>> some additional l flags so that recon all command will use the three T1 >>> images to get one output file? >>> Thanks, >>> Rashmi >>> >>> >> >> >> 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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Significant clusters before and after Monte Carlo
by Anita van Loenhoud 16 Sep '13

16 Sep '13

Hi all, When I do a group analysis and check significant clusters after performing a Monte Carlo, I see significant areas that were NOT significant before doing a multiple comparisons correction. Specifically, after Monte Carlo, the parstriangularis is significant, while this area was not significant in the first place (before Monte Carlo). I'm confused; how could that be possible? Am I doing something wrong? Thank you! Anita

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Re: [Freesurfer] Freesurfer Digest, Vol 115, Issue 20
by Lijia Wang 16 Sep '13

16 Sep '13

Hi, Two quick questions: 1) How to draw an open border on activation surface map? 2) How to set False Discovery Rate of one subject? Thanks, On Sun, Sep 15, 2013 at 12:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > 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. Re: Resolved, crash during longitudinal process when it run > mri_ca_register during CA reg. (Knut J Bjuland) > 2. Re: Tracula and Qdec (Alan Francis) > 3. Re: recon all question (Harms, Michael) > 4. Re: Tracula and Qdec (Anastasia Yendiki) > 5. Re: Tracula and Qdec (Alan Francis) > 6. mapping extracted MNI152 ROIs to individual subjects (Paul Beach) > 7. Getting around a design matrix with zero columns (ye tian) > 8. Re: mapping extracted MNI152 ROIs to individual subjects > (Thomas Yeo) > 9. Re: Interpretation of interaction effect in qdec (ye tian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 13 Sep 2013 19:11:28 +0200 > From: Knut J Bjuland <knutjorgen(a)outlook.com> > Subject: Re: [Freesurfer] Resolved, crash during longitudinal process > when it run mri_ca_register during CA reg. > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <BLU0-SMTP155871B1490571BAB6BB181C33B0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Closed, not bug in Freesurfer. > > > On 09/12/2013 10:31 PM, Knut J Bjuland wrote: > > When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all > > -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can > > send the rest of the log. > > Knut J > > > > > > > > > > #-------------------------------------- > > #@# CA Reg Thu Sep 12 19:59:01 CEST 2013 > > /cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri > > > > mri_ca_register -nobigventricles -T transforms/talairach.lta > > -align-after -mask > > brainmask.mgz norm.mgz > > /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a > > ll_2008-03-26.gca transforms/talairach.m3z > > > > not handling expanded ventricles... > > using previously computed transform transforms/talairach.lta > > renormalizing sequences with structure alignment, equivalent to: > > -renormalize > > -regularize_mean 0.500 > > -regularize 0.500 > > using MR volume brainmask.mgz to mask input volume... > > reading 1 input volumes... > > logging results to talairach.log > > > > > > ======= NUMBER OF OPENMP THREADS = 1 ======= > > reading input volume 'norm.mgz'... > > reading GCA > > > '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... > > label assignment complete, 0 changed (0.00%) > > det(m_affine) = 1.55 (predicted orig area = 5.2) > > label assignment complete, 0 changed (0.00%) > > freeing gibbs priors...done. > > average std[0] = 5.0 > > **************** pass 1 of 1 ************************ > > setting smoothness coefficient to 0.039 > > blurring input image with Gaussian with sigma=2.000... > > 0000: dt=0.000, rms=0.932, neg=0, invalid=96777 > > > > > > > > > > > > > > > > > > > > > > > > On 09/12/2013 10:14 AM, Knut J Bjuland wrote: > >> Hi, > >> I have run recon-al longitudinal process on abel cluster with this > >> command recon-all -base @filename@_template -tp @filename@ -tp > >> @filename@v2 -all -debug. However, it crashed or is killed when it > >> ran mri_ca_register. > >> I have looked through the log, and I have not found a reason for it > >> being killed even tough I added -debug. The cluster is running sbatch > >> and CentOS release 6.4. Are there any debug options I can add or are > >> there any debugversion of mri_ca_register I can download? This happen > >> every time I run the program. I have asked for 8g ram when ran the > >> program. > >> > >> Best regards > >> Knut J?rgen Bjuland > >> > >> > >> _______________________________________________ > >> 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 > > > > > > 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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Getting around a design matrix with zero columns
by ye tian 15 Sep '13

15 Sep '13

Dear Freesurfers, I am studying how the practice of meditation affects cortical thickness. I have two types of meditations, and I also know for how many years each mediator has meditated. Therefore, ideally I would like my categorical factor to be meditation (control, meditation1 and meditation2), and continuous factor to be the number of years of meditation. This design, of course, has a problematic column of zeros, which corresponds to the slope of the control (a non-meditator has meditated for 0 years). Does freesurfer has a way out of this problem? For example, I have came across pseudoinverse methods in literature? Any suggestion is highly appreciated. Thank you very much! Sincerely, Ye

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