On 05/21/2014 08:30 AM, Paola Valsasina wrote: > Dear Doug, > > thank you so much for your help, it worked! now I pre-processed the flipped > images and estimated my GLM model. > > I had a look at my results with tksurfer, as explained in the xhemi tool > page (e.g., tksurfer fsaverage_sym lh inflated -aparc -overlay "my > results"/sig.mgh) > > I have now two (probably trivial) questions: > 1) the default threshold of the overlay is the same as in qdec? And how can > I change this threshold for visualization purposes? I'm not sure if the default is the same, I think it is. To change the threshold, Configure->Overlay > 2) how can I obtain a list of clusters surviving to the threshold (i.e., the > analogous of the "Find Clusters and Go to Max" button in Qdec)? Run mri_glmfit-sim. At this point it is the same as any other group analysis. See the tutorial and lecture notes doug > > Thank you in advance > Kind regards > Paola > > > Paola Valsasina, MSc > Research Fellow > Neuroimaging Research Unit (Director Prof. M. Filippi) > Institute of Experimental Neurology, Division of Neuroscience, > Scientific Institute and University "Vita-Salute" San Raffaele > Via Olgettina 60, 20132 Milan, Italy > -------------------------------------------------------------------------- > IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO > PERCHE' QUI LA RICERCA DIVENTA CURA. > CF 07636600962 > SE NON QUI, DOVE? > Info: 5xmi...@hsr.it - http://www.5xmille.org/ > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > -----Messaggio originale----- > Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Inviato: lunedì 19 maggio 2014 19.56 > A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu > Oggetto: Re: R: R: R: R: R: [Freesurfer] Filipping issue > > Instead of --surfreg try using --srcsurfreg > > doug > > On 05/14/2014 04:37 AM, Paola Valsasina wrote: >> Dear Doug, >> >> thank you for your answer. I added --target fsaverage_sym but it still >> fails: >> >> MRISread($SUBJECTS_DIR/fsaverage_sym/surf/lh.fsaverage_sym.sphere.reg): >> could not open file. >> >> This seems to happen because in the folder "fsaverage_sym/surf" there is > no >> "lh.fsaverage_sym.sphere.reg"; in this folder there is a file called >> "lh.sphere.reg" or a file called "lh.ni.sym.b40.i30.sphere.reg". >> Which one is the correct file? >> >> Thank you again >> Best regards, >> >> Paola >> >> >> Paola Valsasina, MSc >> Research Fellow >> Neuroimaging Research Unit (Director Prof. M. Filippi) >> Institute of Experimental Neurology, Division of Neuroscience, >> Scientific Institute and University "Vita-Salute" San Raffaele >> Via Olgettina 60, 20132 Milan, Italy >> >> -------------------------------------------------------------------------- >> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >> PERCHE' QUI LA RICERCA DIVENTA CURA. >> CF 07636600962 >> SE NON QUI, DOVE? >> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >> >> Disclaimer added by CodeTwo Exchange Rules 2007 >> http://www.codetwo.com >> >> -----Messaggio originale----- >> Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Inviato: martedì 13 maggio 2014 21.12 >> A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu >> Oggetto: Re: R: R: R: R: [Freesurfer] Filipping issue >> >> >> Sorry, in both of those mris_preproc commands add >> >> --target fsaverage_sym >> >> doug >> >> >> On 05/13/2014 09:48 AM, Paola Valsasina wrote: >>> Dear Doug, >>> >>> I am trying to run "mris_preproc" as you indicated, but it fails with the >>> following error: >>> >>> MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could >>> not open file. >>> >>> Why is target file searched in the "fsaverage" folder? I was expecting it >> is >>> searched in the "fsaverage_sym" folder? >>> >>> Thank you in advance >>> Kind regards >>> Paola >>> >>> >>> Paola Valsasina, MSc >>> Research Fellow >>> Neuroimaging Research Unit (Director Prof. M. Filippi) >>> Institute of Experimental Neurology, Division of Neuroscience, >>> Scientific Institute and University "Vita-Salute" San Raffaele >>> Via Olgettina 60, 20132 Milan, Italy >>> > -------------------------------------------------------------------------- >>> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >>> PERCHE' QUI LA RICERCA DIVENTA CURA. >>> CF 07636600962 >>> SE NON QUI, DOVE? >>> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >>> >>> Disclaimer added by CodeTwo Exchange Rules 2007 >>> http://www.codetwo.com >>> >>> -----Messaggio originale----- >>> Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >>> Inviato: martedì 29 aprile 2014 18.25 >>> A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu >>> Oggetto: Re: R: R: R: [Freesurfer] Filipping issue >>> >>> >>> You can't use qdec for this, you will have to use mris_preproc, >>> mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the >>> tricky one in that you will have to run mris_preproc twice then merge >>> the two data sets. >>> >>> For the subjects that you want the left hemisphere, run mris_preproc as >>> "normal" >>> >>> mris_preproc --hemi lh --meas thickness --surfreg >>> fsaverage_sym.sphere.reg --s subject1 --s subject2 --o >> subjects.lh.sm00.mgh >>> For the right hemi subjects run >>> >>> mris_preproc --hemi lh --meas thickness --surfreg >>> fsaverage_sym.sphere.reg --s subject3/xhemi --s subject4/xhemi --o >>> subjects.rh.sm00.mgh >>> >>> Note above that you still specify --hemi lh but that the subject name >>> changes to subject/xhemi >>> >>> Now concatenate the two files together >>> >>> mri_concat subjects.lh.sm00.mgh subjects.rh.sm00.mgh --o > subjects.sm00.mgh >>> Then proceed with smoothing, etc. When you do the glm, make sure that >>> your FSGD file has the proper order of subjects (above it would be >>> subject1, subject2, 3, 4) >>> >>> doug >>> >>> >>> >>> On 04/29/2014 12:07 PM, Paola Valsasina wrote: >>>> Dear Doug, >>>> >>>> I registered with surfreg the hemispheres I would like to analyze. How >>>> should I proceed now for the final statistical vertex-wise analysis? >>>> Should I smooth the surfaces and perform between-group comparison with >>> qdec? >>>> Thank you in advance >>>> Paola >>>> >>>> Paola Valsasina, MSc >>>> Research Fellow >>>> Neuroimaging Research Unit (Director Prof. M. Filippi) >>>> Institute of Experimental Neurology, Division of Neuroscience, >>>> Scientific Institute and University "Vita-Salute" San Raffaele >>>> Via Olgettina 60, 20132 Milan, Italy >>>> >> -------------------------------------------------------------------------- >>>> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >>>> PERCHE' QUI LA RICERCA DIVENTA CURA. >>>> CF 07636600962 >>>> SE NON QUI, DOVE? >>>> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >>>> >>>> >>>> Disclaimer added by CodeTwo Exchange Rules 2007 >>>> http://www.codetwo.com >>>> >>>> -----Messaggio originale----- >>>> Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >>>> Inviato: martedì 22 aprile 2014 18.20 >>>> A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu >>>> Oggetto: Re: R: R: [Freesurfer] Filipping issue >>>> >>>> >>>> You can register just the hemisphere you want to fsaverage_sym. But if >>>> you have a subject whose right hemi you want, you would run the surfreg >>>> with --rh, but later you would specify that you want the lh of >>> subject/xhemi >>>> doug >>>> >>>> On 04/22/2014 12:04 PM, Paola Valsasina wrote: >>>>> Sorry, I didn't note I was replying to you only.. >>>>> Anyway, thank you for the reply! So I will apply the command I > mentioned >>>> to >>>>> you in my previous e-mail to create flipped RH and LH surfaces for the >>>>> subjects with the right hemisphere affected. >>>>> Should I register to the fsaverage_sym atlas also the subjects I don't >>>> want >>>>> to flip (i.e., those with the left hemisphere affected), to pool them >>>>> together in the statistic with the flipped subjects? >>>>> Thank you again >>>>> Paola >>>>> >>>>> Paola Valsasina, MSc >>>>> Research Fellow >>>>> Neuroimaging Research Unit (Director Prof. M. Filippi) >>>>> Institute of Experimental Neurology, Division of Neuroscience, >>>>> Scientific Institute and University "Vita-Salute" San Raffaele >>>>> Via Olgettina 60, 20132 Milan, Italy >>>>> >>>>> > -------------------------------------------------------------------------- >>>>> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >>>>> PERCHE' QUI LA RICERCA DIVENTA CURA. >>>>> CF 07636600962 >>>>> SE NON QUI, DOVE? >>>>> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >>>>> >>>>> >>>>> Disclaimer added by CodeTwo Exchange Rules 2007 >>>>> http://www.codetwo.com >>>>> >>>>> -----Messaggio originale----- >>>>> Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >>>>> Inviato: martedì 22 aprile 2014 17.56 >>>>> A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu >>>>> Oggetto: Re: R: [Freesurfer] Filipping issue >>>>> >>>>> >>>>> Hi Paola, please remember to post to the list and not to us personally. >>>>> thanks! I would still use the xhemi tools for this. If you have N >>>>> subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. >>>>> You can then just pick the ones you want to analyze further >>>>> doug >>>>> >>>>> On 04/22/2014 08:34 AM, Paola Valsasina wrote: >>>>>> Dear Doug, >>>>>> >>>>>> We have followed your suggestion and we performed the recon-all >> analysis >>>>> for >>>>>> all study subjects (till autorecon3) on non-flipped images. >>>>>> >>>>>> I am now reading the instructions on the wiki about the xhemi tool, > but >>> I >>>>> am >>>>>> not 100% sure they apply to our case. >>>>>> >>>>>> The wiki instructions describe a comparison between LH and RH within >>>>>> subjects (i.e., an analysis of cortical asymmetry), whereas we would >>> like >>>>>> simply to L-R flip the final surfaces of patients having a RH damage, >> so >>>>>> that all patients have the damage in the LH. >>>>>> Then, we would like to compare them with control subjects. >>>>>> >>>>>> For this purpose, is it sufficient to register the patients lesioned > in >>>>> the >>>>>> RH to the symmetric template with the --xhemi option? >>>>>> >>>>>> (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) >>>>>> >>>>>> Then, how do we perform final statistical analysis? >>>>>> >>>>>> Thank you in advance for any suggestion! >>>>>> Kind regards >>>>>> Paola >>>>>> >>>>>> >>>>>> >>>>>> Paola Valsasina, MSc >>>>>> Research Fellow >>>>>> Neuroimaging Research Unit (Director Prof. M. Filippi) >>>>>> Institute of Experimental Neurology, Division of Neuroscience, >>>>>> Scientific Institute and University "Vita-Salute" San Raffaele >>>>>> Via Olgettina 60, 20132 Milan, Italy >>>>>> >>>>>> >> -------------------------------------------------------------------------- >>>>>> IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO >>>>>> PERCHE' QUI LA RICERCA DIVENTA CURA. >>>>>> CF 07636600962 >>>>>> SE NON QUI, DOVE? >>>>>> Info: 5xmi...@hsr.it - http://www.5xmille.org/ >>>>>> >>>>>> >>>>>> Disclaimer added by CodeTwo Exchange Rules 2007 >>>>>> http://www.codetwo.com >>>>>> >>>>>> -----Messaggio originale----- >>>>>> Da: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Douglas N >>>>> Greve >>>>>> Inviato: giovedì 13 febbraio 2014 21.50 >>>>>> A: freesurfer@nmr.mgh.harvard.edu >>>>>> Oggetto: Re: [Freesurfer] Filipping issue >>>>>> >>>>>> >>>>>> Definitely #2. You should use the xhemi tools >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >>>>>> First run them through recon-all as normal, then follow the steps on >> the >>>>>> wiki. Contact the list again to get instructions for the final >> analysis. >>>>>> doug >>>>>> >>>>>> >>>>>> On 02/13/2014 08:23 AM, Paola Valsasina wrote: >>>>>>> Dear List, >>>>>>> >>>>>>> we are starting the analysis of cortical thickness for a group of >>>>>>> patients who have only one side affected. The majority of patients >>>>>>> have the left hemisphere affected, but some patients have the right >>>>>>> hemisphere affected. In order to do a group analysis, we would like > to >>>>>>> flip the images of some patients, so that the affected side is left >>>>>>> for all subjects. >>>>>>> >>>>>>> Which is the best way to do this: >>>>>>> >>>>>>> 1)flip the 001.mgz volume and perform the entire recon-all pipeline >>>>>>> with flipped images; >>>>>>> >>>>>>> or >>>>>>> >>>>>>> 2)perform the recon-all pipeline with the non-flipped volumes and > flip >>>>>>> only the final surfaces for statistical purposes? >>>>>>> >>>>>>> Thank you for any suggestion >>>>>>> >>>>>>> Kind regards >>>>>>> >>>>>>> Paola >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > > > 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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
