Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Validation of results
by Sinead Kelly 12 Aug '13

12 Aug '13

Dear freesurfer users, I would really appreciate if anybody could confirm that I have preformed my analysis correctly as I have very little experience with freesurfer and I want to make sure that my result is a true finding. Firstly, I am looking at the effect of a schizophrenia risk variant on cortical surface area in a large sample of healthy controls. a. I performed preprocessing on all of my subjects using *recon-all.* b. I then qcached my data (resampling it to the average subject -* fsaverage *) c. An FSGD file was then created for statistical analysis to look at differences between TT carriers and TG carriers with age and gender as covariates of no interest. Here is an example of the file I created: GroupDescriptorFile 1 Title MIR137 Class TTMale Class TTFemale Class TGMale Class TGFemale Variables Age Input CON3140 TGFemale 37 Input CON3891 TTFemale 33 Input CON4664 TTFemale 40 Input CON5591 TTMale 41 Input CON7009 TGMale 21 Input CON7024 TTMale 59 Input CON7038 TTMale 56 Input CON7050 TTMale 30 Input CON7054 TTMale 43 Input CON7055 TTMale 43 Input CON7072 TTFemale 41 d. I applied the following contrast: -0.5 -0.5 0.5 0.5 0 0 0 0 e. I followed the online tutorial by firstly running the *mris_preproc*script with *area.fwhm10.fsaverage* as my input file. Is this correct? (I ran this separately for the left and right hemisphere). f. I then ran the *mri_glmfi*t script followed by the *mri_glmfit-sim*script: *mri_glmfit-sim --glmdir rh.MIR137_area.glmdir --sim mc-z 5000 1.3 mc-z.abs --sim-sign abs --cwpvalthresh .999 --overwrite* (I ran this separately for each hemisphere) Does this look correct? When this ran I then checked the *mc-z.abs.sig.cluster.summary file:* ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.298 36614 541.01 -26.0 -53.1 62.2 0.77340 0.76580 0.78100 1177 superiorparietal 2 2.918 9004 1642.43 -8.5 9.7 65.2 *0.01020* 0.00840 0.01200 2790 superiorfrontal 3 2.626 126211 363.55 -30.3 -65.2 40.5 0.98580 0.98360 0.98800 817 inferiorparietal 4 2.441 6490 313.02 -30.5 -35.1 58.4 0.99660 0.99560 0.99760 693 postcentral 5 2.375 107140 1095.56 -10.9 -57.2 44.7 0.09720 0.09180 0.10260 2308 precuneus 6 2.347 132687 414.79 -38.6 2.1 24.8 0.95300 0.94920 0.95680 974 precentral 7 2.284 97632 1510.86 -41.4 -50.0 -14.4 *0.01820* 0.01580 0.02060 2446 fusiform 8 2.122 111909 365.94 -49.2 -29.5 -3.0 0.98480 0.98260 0.98700 837 superiortemporal 9 2.070 74111 444.95 -54.7 -42.0 6.3 0.92120 0.91620 0.92600 998 bankssts 10 1.809 85712 281.07 -57.0 -30.8 21.7 0.99860 0.99800 0.99920 598 supramarginal 11 1.796 121724 312.87 -10.0 64.3 6.5 0.99660 0.99560 0.99760 485 superiorfrontal I have two significant results here - does this look okay? Does this result indicate that surface area of the fusiform and superior frontal significantly differ between TT and TG carriers (corrected for multiple comparisons?). How can I check or report the statistics? Is it possible to extract the values and report descriptive as well as inferential statistics for the result? I would really appreciate if anyone can validate this for me as I have very little experience with freesurfer. Thank you for your help! Sinead Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Re: [Freesurfer] How to extract subjects' volume based on mask from spm?
by Douglas N Greve 09 Aug '13

09 Aug '13

Hi Mingxia, if you have a binarized map, then just use --id 1 with mri_cor2label (not need to for mri_binarize if it is already binary) doug On 05/21/2013 03:55 AM, zhang mingxia wrote: > Hi Doug, > > Thanks very much. A few more question after I read the description of > mri_cor2label. > > 1. there is a compulsory of mri_cor2label: --id (0-255). How can I > find the 'labelid'? > > 2. If I understand correctly, the final label will be made within > one particular 'labelid'. How if this mask is in more than one labels > (Sorry I haven't used Freesurfer for a long time, my understanding is > the labelids represent different regions. It may be wrong) ? > > 3. I have had the binarized mask created from spm, do I also need to > use mri_binarize? > > Mingxia > > > On Mon, May 20, 2013 at 6:51 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Try mri_binarize followed by mri_cor2label > doug > > > > > > On 05/20/2013 03:57 AM, zhang mingxia wrote: > > Dear Freesurfer experts, > > > > I analyzed functional data by spm and made a mask (analyze > format). I > > have also run recon-all of structural data. > > > > My question is: how to extract mean volume (from structural data) of > > the mask(from spm)? > > > > I only extracted volume(or thickness) of ROI of a label edited by > > myself and annotation file. If I can convert analyze format to a > label > > or annotation file, I can use that method. But how to convert > analyze > > format to a label or annotation? > > > > Or is there any easy way? > > > > Thanks in advance! > > > > Mingxia Zhang > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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/ > > _______________________________________________ > 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. > > -- 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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LME - lme_mass_FDR2 correction doesn't work
by Alex Hanganu 07 Aug '13

07 Aug '13

Hi Jorge, I got an error in the correction, and I can't find a way out. this is the cmd I use: ------------- /[Y,mri] = fs_read_Y('.../thickness-sm10.mgh'); Qdec = fReadQdec('.../LME.dat'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); ni = [2 2... 2]; X = [ones(length(M),1) M M(:,1).*M(:,2)]; [stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex); CM.C = [0 0 0 1]; fstats = lme_mass_F1(stats,CM); fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig'); nv = length(stats); Beta2 = zeros(1,nv); //Beta//4////= zeros(1,nv);// //for ....// //. .// //end; //Beta2_Beta//4//_sum = Beta2//+Beta4;// //mri1 = mri;// //mri1.vols//z(//4) = 1;// //fs//_write_Y(Beta2,mri1,'..../Beta2.mgh'//);// //[detvtx,sided_pval,pth//] = lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);// //fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');// // //??? Error using //===> reshape// //To RESHAPE the number of elements must not change.// // //Error in ==//> fs_write_Y at 21// //save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/ ------------- the cmd: /[detvtx ....//]/ didn't work, but there was no error message. I remember in the past this cmd took around 1 day to analyzebut now it didn't work at all. /fs_write_Y/ worked fine for Beta, alsothis time I used the /mri//1 //= mri/ cmd- so the /reshape /error shouldn't be associated with this. Please help ! best regards, Alex.

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Postdoctoral position: the brain connectome in twins populations
by Katell Mevel 07 Aug '13

07 Aug '13

Dear brain imaging fellows, One post-doc position is available in our group, the deadline is 30-08-2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND) (www.ki.se/kind) KIND is a competence center for research, development and education within the area of developmental psychopathology. The center is established in collaboration between Karolinska Institutet and Stockholm County Council, and aims at improving clinical practice, generating basic research, and spreading new knowledge to stakeholders. The Roots of Autism Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins being discordant for autism spectrum disorder and other neurodevelopmental disorders, e.g. ADHD. For the first time ever, twins are examined on multiple levels, among them functional and structural neuroimaging using MRI. Scanning is performed in the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750), and more than 45 pairs have now been examined. *** Duties As a post-doc, you will be mainly responsible for the acquisition and analyses of the multimodal neuroimaging data. This includes DTI, resting-state fMRI and structural T1, to be combined according to a brain connectome approach. This work will be done in close collaboration with the department of Clinical Neuroscience. The position also includes several other responsibilities, e.g. coordination of the neuroimaging works at KIND, involvement in international collaborations, administrative tasks, grant application and article writing. All the details about this position can be found here:https://ki.mynetworkglobal.com/en/what:job/jobID:24397/where:4/ Applications should be submitted here:https://ki.mynetworkglobal.com/what:login/jobID:24397/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best Regards, Katell MEVEL for KIND ________________________________ Katell Mevel | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B | 113 30 Stockholm +46 (0)8 514 52706 | +46 (0)721 980 350 katell.mevel(a)ki.se | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130><http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ______________________________________ Karolinska Institutet – a medical university

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J_white
by Linn Mittlestein 06 Aug '13

06 Aug '13

Dear freesurfer experts, I am currently do group analysis in qdec, and I canot select jacobian white from the drop down menu, I thought this would be an option? Do I do have additional steps to get these values? Kind Regards, Linn

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Re: [Freesurfer] bvecs error from Tracula
by Z K 06 Aug '13

06 Aug '13

Hello Amir, According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are encountering a memory error? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: > Kindly find attached the recon-all.log > > > On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman(a)nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: > > Hello Amir, > > Thanks for that... could you also please provide the recon-all.log > file? It will be located in > $SUBJECT_DIR/subject_name/__scripts/recon-all.log > > -Zeke > > > On 07/24/2013 03:01 AM, amirhossein manzouri wrote: > > Hi, > The content is : > freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0 > Can it help? > > > On Mon, Jul 22, 2013 at 10:31 PM, Z K > <zkaufman(a)nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.__harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu>>> wrote: > > Hello Amirhossein, > > Can you please provide me with the contents of > build-stamp.txt in > the /Applications/freesurfer directory? > > -Zeke > > > On 07/22/2013 04:23 PM, amirhossein manzouri wrote: > > Hi, > Yes I am getting the memory error with version 5.3, > exactly the > one that > is reported in this link: > https://mail.nmr.mgh.harvard.____edu/pipermail//freesurfer/____2011-July/01… > > > <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/019392… > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html>> > Thanks, > > > On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu> > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>> > <mailto:ayendiki@nmr.mgh. > <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> > > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: > > > Hi Amirhossein - That fix applied only to the 5.1 > version. I'd > recommend using the 5.3 version for tracula. Are > you getting a > memory error, and if so with which version? > > Thanks, > a.y > > > On Mon, 22 Jul 2013, amirhossein manzouri wrote: > > Dear Anastasia, > I am trying to download the > dmri_5.1_snow_leopard.tar.__gz from > > FreeSurfer > website to solve memory problem but it is not > available. Would > you please > check the source to the link? > > > On Wed, Jul 17, 2013 at 5:51 PM, amirhossein > manzouri > <a.h.manzouri(a)gmail.com > <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com > <mailto:a.h.manzouri@gmail.com>__> > <mailto:a.h.manzouri@gmail.com > <mailto:a.h.manzouri@gmail.com> > > <mailto:a.h.manzouri@gmail.com > <mailto:a.h.manzouri@gmail.com>__>__>> wrote: > The format of my bval file was wrong so > I edited > your > file and > tried and it worked, also bvec should be in > three columns > as you > have mentioned before. > > > On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu> > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>> > <mailto:ayendiki@nmr.mgh. > <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> > > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: > > Good to hear! Can you please share with > all of > us what was > wrong with your original files? It may help > others who > have the same problem in the future. > Thanks! > > On Wed, 17 Jul 2013, amirhossein > manzouri wrote: > > Thanks Anastasia, > IT HELPED! > > > On Tue, Jul 16, 2013 at 5:25 PM, > Anastasia > Yendiki > <ayendiki(a)nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>> > <mailto:ayendiki@nmr.mgh. > <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> > > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>>>> > > wrote: > > Hi Amirhossein - I'm > attaching sample > files. > > a.y > > On Tue, 16 Jul 2013, > amirhossein > manzouri wrote: > > Hi Anastasia, > I have tried both , > 3-row and > 3-column format and still > wrong bvecc and bval > from flip4fsl. Could > you please > send me a sample of your > original files so I > can compare? > > > On Mon, Jul 15, 2013 > at 7:44 PM, > Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>> > <mailto:ayendiki@nmr.mgh. > <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> > > <mailto:ayendiki@nmr.mgh.__harvard.edu > <mailto:ayendiki@nmr.mgh.harvard.edu>>>> > > wrote: > > Hi Amirhossein > - Are your > original bvecs/bvals in > 3-row format > instead of > 3-column format? > > > http://surfer.nmr.mgh.harvard.______edu/fswiki/FsTutorial/____Tracula > > > > <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula > <http://harvard.edu/fswiki/FsTutorial/__Tracula> > > > <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula>>> > > Thanks, > a.y > > On Mon, 15 Jul > 2013, > amirhossein manzouri wrote: > > Dear Experts, > I am > running trac-all > -prep -c dmrirc on my > DWI > data. > After flip4fsl > step I get the attached > bval > and bvec > file which > the bvec one is wrong so > the > process exits > with > error in dtifit. > I have also attached > original > bvec and > bval. > > -- > Best regards, > > Amirhossein Manzouri > > > > > > > > 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 > <http://www.partners.org/____complianceline> > <http://www.partners.org/____complianceline > <http://www.partners.org/__complianceline>> > > > <http://www.partners.org/____complianceline > <http://www.partners.org/__complianceline> > <http://www.partners.org/__complianceline > <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. > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > ___________________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.__harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer > > > <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > -- > Best regards, > Amirhossein Manzouri > > > > > > -- > Best regards, > Amirhossein Manzouri > >

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Re: [Freesurfer] qdec question: discrepancy in sig. clusters (Douglas Greve)
by Maria Kharitonova 05 Aug '13

05 Aug '13

Hi Doug, Thanks. Per your advice, I'm trying to visualize output in tksurfer but it would help me to do what the different overlays refer to. Could you clarify what the differences are between: mc-z.abs.tho20.sig.cluster.mgh vs mc-z.abs.tho20.sig.ocn.mgh vs mc-z.abs.tho20.sig.vertex.mgh I think .ocn.mgh draws the regions that I see output in the terminal when I run qdec, but am not 100% sure. I searched the archives/tutorials and couldn't find the explanation of these different files. Thanks! Maria > > > Message: 14 > Date: Fri, 26 Jul 2013 13:47:41 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] qdec question: discrepancy in sig. clusters > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51F2B63D.6020706(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Maria, can you tar up the qdec output folder and send it to our file > drop? I'm traveling now, so it might be the 1st week of august before I > can take a look. You can also go into the qdec output folder and run > tksurfer to show you the results. > > doug > > > On 7/26/13 1:37 PM, Maria Kharitonova wrote: >> Hello, >> >> I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole. >> >> Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. >> >> Can you please help me reconcile the 2 types of output? Thanks! >> >> *** terminal output: >> >> # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh >> # Frame Number 0 >> # srcsubj fsaverage >> # hemi rh >> # surface white >> # annot aparc >> # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final >> # Minimum Threshold 2 >> # Maximum Threshold infinity >> # Threshold Sign abs >> # AdjustThreshWhenOneTail 1 >> # CW PValue Threshold: 0.05 >> # Area Threshold 0 mm^2 >> # CSD thresh 2.000000 >> # CSD nreps 10000 >> # CSD simtype null-z >> # CSD contrast NA >> # CSD confint 90.000000 >> # Overall max 4.75828 at vertex 134555 >> # Overall min -2.56762 at vertex 93241 >> # NClusters 4 >> # Total Cortical Surface Area 65020.8 (mm^2) >> # FixMNI = 1 >> # >> # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot >> 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal >> 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal >> 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal >> 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral >> >> Simulation complete. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > ------------------------------ > > Message: 15 > Date: Fri, 26 Jul 2013 13:56:13 -0400 > From: Satrajit Ghosh <satra(a)mit.edu> > Subject: Re: [Freesurfer] Freesurfer surface circle of pre-defined > size > To: sarahp(a)nmr.mgh.harvard.edu > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+A4wO=cfM+7MnCVi-GvadUT5s4NFNGASU_+DS4nUStUoQ4frQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hi sarah, > > you'll get a much quicker response posting PySurfer related questions to: > > nipy-devel(a)neuroimaging.scipy.org > > cheers, > > satra > > On Fri, Jul 26, 2013 at 12:57 PM, <sarahp(a)nmr.mgh.harvard.edu> wrote: > >> Hello Freesurfer Experts, >> >> We would like to use PySurfer's function plot_label_foci.py to >> automatically create circular labels of a pre-defined radius (eg. 14mm) on >> the fsaverage surface of freesurfer. >> >> What are the specified units of "n_steps" in the command line argument >> "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', >> n_steps=50"? >> >> Thank you, >> Sarah >> _______________________________________________ >> 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] function that do the same step like qcache?
by Bruce Fischl 05 Aug '13

05 Aug '13

can you cc the list so that others can answer or see the answer? You need to specify the source and target subjects with --srcsubject and --trgsubject cheers Bruce On Mon, 29 Jul 2013, fatma zribi wrote: > mri_surf2surf --hemi lh --s s000_open_brain_sanlm_+TIR_normlalized --sval curv --src_type curv --fwhm 10 --trg_type curv --tval > curv.10 > > > 2013/7/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > what is your full command line? You can smooth and map with it (use -fwhm-src or fwhm-trg to smooth in either the > source or target space) > On Mon, 29 Jul 2013, fatma zribi wrote: > > Dear Bruce, > I have tried mri-surf2surf, it makes the result (smoothed curv for example) with the same dimension of > the subject. But I would > like a smoothed file with the dimesion of fsaverage. > > Thank you for your help. > > With best regards, > > Fatma > > > 2013/7/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > you can use mri_surf2surf within subject I believe, but Doug can confirm (although he's traveling > so it may be a > bit). You can also do it interactively in tksurfer. > > cheers > Bruce > > > On Mon, 29 Jul 2013, fatma zribi wrote: > > Dear Bruce, > > Would you mind tell me if there is a function of freesurfer that I can use to do the same > step of > qcache to smooth and > interpolate in the fsaverage one subject > with mri_surf2surf I can smooth only or align one subject with an average. > thank you for you help. > with best regards, > Fatma > > > > > 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] dPSD and ev duration
by Ella Hinton 05 Aug '13

05 Aug '13

Hi Doug Thanks for your email. I gave your suggestion a try - reduced the dPSD to 0.5 (as well as adjusted the PSDMAX, and no. of volumes to reflect the new TR - see full command line below). Unfortunately the efficiency is way down (0.03) and the VRF you previously suggested should be between 20-40 is 4.5! I now wonder if Optseq is trying to tell me this is now a bad design!! Would be very grateful for any ideas for improvement? optseq2 --ntp 240 --tr 2.5 --psdwin 0 20 0.5 --ev hf 3 50 --ev lf 3 50 --ev nf 3 50 --nkeep 3 --o test14 --nsearch 10000 --focb 100 many thanks Ella Date: Sun, 28 Jul 2013 23:33:07 -0400 From: greve(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dPSD and ev duration Hi Ella, it has an internal clock that events have to be syncrhonized to. Try setting the dPSD to 0.5 doug On 7/28/13 4:05 PM, Ella Hinton wrote: Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella _______________________________________________ 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. _______________________________________________ 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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tksurfer problem - annotation of vertices
by Sinead Kelly 05 Aug '13

05 Aug '13

Dear freesurfer users, I am having a problem visualizing results using tksurfer using the following command: tksurfer fsaverage lh inflated -annot lh.MIR137_area.glmdir/MIR137_test/mc-z.abs.sig.ocn.annot -fthresh 2 -curv -gray & Please also see the terminal output stating that the vertices do not have an annotation. I do not have much experience with freesurfer - is there a way to resolve this? Thank you for your help! Sinead [kellys37@tcin-n01 Freesurfer_data]$ setting fthresh to 2.0000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data checking for nofix files in 'inflated' Reading image info (/projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage) Reading /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: Reading header info from /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 12 entries read (originally none) Found embedded color table in annotation. 149719 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/support/tcin/apps/freesurfer/5.2.0/tktools/tksurfer.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_common.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_wrappers.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Freesurfer July 2013