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? 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)? 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
