Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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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Repost: updating the tables and volumes associated with aseg.mgz
by silver47＠gmx.com 15 Sep '13

15 Sep '13

Hi, Sorry to repost, but I'm seeking some advice on updating the tables and volumes associated with aseg.mgz. I have completed the cortical analysis on a number of subjects and now would like to review and edit (if needed) aseg.mgz My strategy is to not cause any changes to the surfaces already completed and involves running: recon-all -subjid subject -surfsegedit to fix the aseg, using info from the surfaces. Followed by manual editing (if needed) of aseg.mgz, then recon-all -subjid subject -aparc2aseg -segstats -wmparc to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, and stats/wmparc.stats Does this look right? Are there any other considerartions? Thanks, P.

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Ploting convolved stimuli with actual stimuli
by Aser A 15 Sep '13

15 Sep '13

Hi all, Using the output from OptSeq, is there a possible ( easy ^u^ ) way of plotting in the same graph the presentation of stimuli with their convolution? So basically, I created my design using OptSeq. To make it nicer, I want to plot this. I am not aware of freesufer and I use SPM. In SPM it just shows the convolved stimuli without showing sticks of the stimuli. I have attached a picture taken from the genetic program that helps creating or optimizing fMRI designs just to show you what I mean or I want. I have also attached an excel file contains the output from OptSeq. Thanks Aser

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Interpretation of interaction effect in qdec
by Yang, Daniel 15 Sep '13

15 Sep '13

Hi FreeSurfer experts, Let's say I have two class variables: Sex (female, male) Dx (patient, control) I see that the analysis results show the following: Does the average thickness, accounting for Dx, diff between female and male? Red means: female > male Does the average thickness, accounting for Sex, diff between patient and control? Red means: patient > control Is there a Sex-Dx interaction in the mean thickness? Red means either (a) the female > male effect is stronger in patient (vs. control); or (b) the patient > control effect is stronger in female (vs. male) Is my interpretation correct? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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family wise error rate correction
by Venkatesh Rajagopalan 15 Sep '13

15 Sep '13

Hi All, I am trying to compare my VBM results from FSL with cortical thickness changes using freesurfer. I would like to perform permutation based FWER correction to see cortical thickness changes. The reason to do FWER correction is I used randomise in FSL with FWER correction so I want to keep my statistical approach the same between FSL and Freesurfer to compare VBM and cortical thickness changes. I extensiviely searched the archives but could not find an answer so posting this message I ran the following command mris_preproc --fsgd deisgn_all.fsgd --cache-in area.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.all_gps.area.10.mgh mri_glmfit --y lh.all_gps.area.10.mgh --fsgd deisgn_all.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.all_gps.glmdir --sim perm 5000 1.3 csd1 --fwhm 7 --surf I do not know how to run the mri_surfcluster command. I read few posts and tried running the following mri_surfcluster --src sig.mgh --csd csd-group.3.diff.csd --ocp sig_cluster.mgh but I did not see any cortical thickness changes wheres I did see cortical thickness changes when simply using FDR option in the tksurfer. Kindly let me know where I am making the mistake. Any help will be greatly appreciated. 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: [Freesurfer] [martinos-tech]
by Douglas N Greve 15 Sep '13

15 Sep '13

Hi Suzanne, I'll cc the FS list so others can benefit ... On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > I have two follow-up questions to enhance my own understanding of > Freesurfer. I know that MC simulations take into account the > smoothness of the data. I noticed that the smoothing factor of my > surface maps is quite high (around 8/9 fwhm), even though I applied a > smoothing factor of 5 during pre-processing. Can you explain to me why > the final maps have such a high fwhm? Is this because of the > transformations that are necessary to create the surfaces? The final measured FWHM is a composite of the smoothing you applied plus any smoothness that may already be in the data. Eg, when the surfaces are created, there is a smoothness constraint that can cause smoothness in the surfaces. The gyrification index has very high smoothenss. For fMRI, there is already natural smoothness in the data plus smoothness added due to interpolation when sampling to the surface. > > Another question concerns the relationship between voxels and > vertices. Does one voxel corresponds to one vertex, or is the > relationship different? This may be a very stupid question, but I > thoroughly searched the wiki and the web without finding a > straightforward answer. Vertices and voxels are different entities. A voxel is a 3D box, a vertex is essentially a 2D triangle on the surface. The surface is made from a volume, of course. Initially, the square face of a voxel is divided into two triangles of equal size. The location of the vertices are then adjusted to get a better fit. Oftentimes, we use the term voxel and vertex interchangeably because each just represents a data point either on the surface or in the volume. > The next question is, if I want to apply a liberal threshold to my > data that is similar to say p < .005; k > 20, then how do I produce > this using the minarea flag in the mri_surfcluster command? I'm not sure what you mean by p < .005. Is that a vertex-wise threshold (ie, the cluster-forming threshold) or cluster-wise? What is k? If you want to correct for multiple comparisons, then you can run mri_glmfit-sim. Once you select a cluster-wise and cluster-forming thresholds (and given the FWHM and search space), the critical clustersize can be determined. doug > > Thanks in advance for your answers! > Suzanne > > > On Tue, Sep 3, 2013 at 3:57 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Suzanne, the pre-computed data is for a full hemisphere. if you > have > a smaller search space, then the whole hemi results will be too > conservative. In that case, you should run mri_glmfit-sim without the > --cache and with --sim as indicated in your command line (which looks > correct to me). The simulations can take a while. If you send me your > label, I can compute cached tables for you, so you don't have to keep > running 10000 iterations of mri_glmfit-sim > > doug > > > On 09/02/2013 12:04 PM, Suzanne Oosterwijk wrote: > > [Attachment(s) <#TopText> from Suzanne Oosterwijk included below] > > > > Hi all, > > > > I have a question about the Monte Carlo simulation in Freesurfer. I > > would like to run a simulation to define the minimum cluster > size in a > > specific collection of vertices (say within a ROI label). After > > running a masked glmfit the pre-cached simulation doesn’t seem to > > correct for the smaller number of vertices; the text files > produce the > > same results. I also ran a full simulation to see whether that > made a > > difference, and then I got different results. I just want to > make sure > > that this is because the smaller volume was applied and not simply > > because the “real” simulation can differ from the pre-cached data. > > Attached are the different output files, the cached MC with > mask, the > > cached MC without mask, the simulation with mask and a normal > cluster > > search within the mask (which demonstrates that there are > > sub-threshold clusters). > > > > Below is my code, > > > > foreach s (f_fear_c_fear f_disg_c_disg f_mf_c_mf f_notc_c_notc) > > > > pushd ${s} > > > > mri_glmfit --surf fsaverage lh --y ces.nii.gz --osgm --glmdir > > glm.masked --label > > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/network_labels/FP_DN_network.label > > > > mri_glmfit-sim --cache 2.3 pos --sim-sign pos --cwpvalthresh .05 > > --glmdir glm.masked > > > > mri_surfcluster --sign pos --hemi lh --in glm.masked/osgm/sig.mgh > > --thmin 2.3 --thmax infinity --minarea 50 --subject fsaverage --sum > > glm.masked/osgm/cluster_pos_23.sum --o > > ./glm.masked/osgm/sig.cluster_pos_23.mgh --annot aparc > > > > cd .. > > > > end > > > > > > I used this code to run the simulation: > > > > mri_glmfit-sim --glmdir glm.masked --sim mc-z 10000 2.3 mc-z.pos.23 > > --sim-sign pos > > > > Thanks in advance for responding! > > > > Suzanne > > > > -- > 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://docs.yahoo.com/info/terms/ > > -- 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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Optseq2 design question - series of events
by John Ryan 15 Sep '13

15 Sep '13

Hi all - I'm trying to design my first event related experiment, and I'm having trouble figuring out how to best optimize the design...wondering if you have any insights: I have two conditions (milkshake and water). Each condition has several events in order: Participants get a squirt of milkshake (4s) then swallow (jittered?) then a rinse of water (no interest) then swallow (jitter again?). In the other condition, they just get a squirt of water and a swallow. In order to model all of this, would I need to put in every event that's taking up time as an event, and then just do an event contrast comparing the two conditions of interest (receipt of milkshake/water)? Or would I make the "events" be long enough to encompass all the actions that are taking place during that event (even though I'm just interested in the first 4s when the person is receiving a taste)? thanks for any tips.

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