[Freesurfer] Very strange error in surface reconstruction after a2-cp
Dear FS experts, I have a very strange error after running autorecon2-cp. I never saw this kind of error with previous versions of FS. I run recon-all -all on my subject, and obtained very good surface reconstructions, with the exception of few excluded wm voxels (see attachment called "before autorecon2-cp"). I added few control points throughout the entire image (for a total of 20 control points) and I run -autorecon2-cp -autorecon3 on the same subject. The output I obtain is very bad (see attachment called "after autorecon2-cp"). How is it possible that adding 20 control points causes such a surface distortions?!! I never had this error with previous FS versions. 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 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] Filipping issue
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 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] R: R: Filipping issue
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.
[Freesurfer] R: R: R: Filipping issue
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/ >> >> >&
[Freesurfer] R: R: R: R: Filipping issue
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.
[Freesurfer] R: R: R: R: R: Filipping issue
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.5xmi
[Freesurfer] R: R: R: R: R: R: Filipping issue
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 hav
[Freesurfer] Can -autorecon2-cp and -autorecon2-wm be run at the same time
Dear FreeSurfer experts, I am quite new to FreeSurfer and I am trying to analyze some patients. We run -autorecon2 step and we got some errors both in the intensitiy normalization and in the wm segmentation, so what we need to do now is both to add control points to the brainmask.mgz image and to slightly edit wm.mgz to fill holes. I am reading from the course slides the suggested workflow for running FreeSurfer, and it is suggested that 1) correction of intensitiy is performed (by adding control points and running of -autorecon2-cp) and 2) editing of wm is performed (by editing wm and running -autorecon2-wm). My question is: can I do both these steps together with a command line like: recon-all -s subject -autorecon2-cp -autorecon2-wm (after having done proper manual edits to both brainmask.mgz and wm.mgz) Or should I run only recon-all -s subject -autorecon2-cp, wait for the results of this step, check the wm output and proceed, if necessary, with -autorecon2-wm? I am asking this basically for saving time, but of course if it is not possible, we are proceeding with two separate steps Thank you for any advice Paola - DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permi...@hsr.it - www.5xmille.org ___ Freesurfer mailing list 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.
[Freesurfer] adding control points
Dear FS experts, we have run autorecon2 on a set of subjects and now we are in the process of manual editing adding control points. We read the tutorial about the manual editing; however, sometimes we have some doubts about adding or not adding control points in some regions. We had a look at the subject "bert" (included in FS distribution) to have a reference on what can be considered a "good" output and what is necessary to be edited. Can this subject be considered as a good one and used as reference, or do you have any additional reference subjects to look at? Thank you in advance Kind regards, Paola - DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permi...@hsr.it - www.5xmille.org ___ Freesurfer mailing list 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.
[Freesurfer] error in recon-all -autorecon3
Dear FS list, I am trying to finish my first analyses with freesurfer; however, I have some problems when running the last stages of recon-all. In summary what I did: 1) recon-all -autorecon1 (worked well) 2) some minor brain strip editing 3) recon-all -autorecon2 (worked well) 4) some editing both of white matter and adding some control points 5) Now I have run recon-all -autorecon2-cp -autorecon3, but I receive the following error (after many hours of post-processing): mris_volmask -label_left_white 2 -label_left_ribbon 3 -label_right_white 41 -label_right_ribbon 42 -save_ribbon -save_distance "subject_name" mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory recon-all exited with errors Apparently, cortical segmentation has been performed, since I see in the stats folder both ?h.aparc.stats and ?h.aparc.a2009s.stats files. Which additional output am I missing because of this error? Thank you for your help Paola Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY ___ Freesurfer mailing list 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.
[Freesurfer] .xdebug_tkmedit
Dear List, I installed version 5.0 of freesurfer on my Linux machine, when I tried to run tkmedit I got the attached error. Do you have any suggestion? Kind regards, Paola --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org .xdebug_tkmedit Description: Binary data ___ Freesurfer mailing list 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.
[Freesurfer] R: ICV differs systematically in repeated measurements
Dear Diederick, were all subjects acquired at point 1 with 1.5T and at point 2 with 3T? Or was the same subject acquired with the same scanner at both timepoints? In the first case, could it be simply a problem of scanner-related variability of ICV assessment (different scanner different sequence parameters different performance in assessing ICV)? Regards, Paola Valsasina _ Da: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Diederick Stoffers Inviato: lunedì 20 dicembre 2010 12.49 A: Freesurfer List Oggetto: [Freesurfer] ICV differs systematically in repeated measurements Hi all, I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks! Cheers, Diederick --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org ___ Freesurfer mailing list 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.
[Freesurfer] R: bad output of autorecon2 - is there any way to adjust it?
Dear Bruce Thank you for your answer. I tried to analyze these data both with FS 4.5 and with FS 5.0. Outputs are similar and bad in both cases. I think that the major problem is the quality of the starting sequence (3D FFE acquired on a Philips 3T), because I am running FS on another dataset (MP-RAGE from Siemens Avanto) and outputs are much better. Before starting FS pipeline, I also tried to segment starting images with SPM8, which produces as output also non-uniformity corrected images. I used these corrected images as input for FS, but outputs are bad also in this case. I would like that you look at my images, in order to have an expert opinion about feasibility of FS on these data. My original image (001.mgz) is 30 MB, whereas brainmask.mgz image is 10 MB. Can I send brainmask.mgz image by attachment? Or can I load the original image somewhere? Thank you in advance Best regards, Paola Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY -Messaggio originale- Da: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Inviato: martedì 28 dicembre 2010 14.01 A: Valsasina Paola Cc: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] bad output of autorecon2 - is there any way to adjust it? Hi Paola, that looks pretty bad. What version are you running? You can try using rhe expert opts to set the g/w intensities, or drop the dataset on our site and we'll take a look. cheers Bruce On Tue, 28 Dec 2010, Paola Valsasina wrote: > > > Dear Freesurfer experts, > > > > I have tried to analyze with Freesurfer a dataset of images acquired with a > 3D T1 sequence without inversion pulse (unfortunately, it is simply a FFE > sequence and not a MP-RAGE). Contrast between grey and white matter is not > optimal in this image, and when I run -autorecon2 step I obtain a very bad > output (attached). "white/grey" surface seems to be where the pial surface > is expected to be, and pial surface is in the middle of csf. > > > > In your opinion, is it possible to obtain meaningful results with these > images or not? Is there any setting of post-processing that I can change in > order to obtain better surfaces? > > Thank you for any suggestion > > Kind regards, > > Paola > > > > > --- > SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. > NON C'E' CURA SENZA RICERCA. > Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. > Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org > 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. --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Questions about Qdec
Dear FS list, I have a couple of questions about QDEC toolbox. 1) If I perform a multiple regression model and I obtain a significant cluster of correlation, is it possible to extract the corresponding regression coefficient, in order to report the strength of this correlation at that point? 2) Is it possible to perform some kind of masking? (e.g., to quantify correlation with a metric only within cortical areas that are different between groups?) 3) Is it correct that it is not possible to overlay the results of different qdec models on the same brain within qdec toolbox, but that we have to use a different tool (e.g. freeview?) to overlay multiple sig.mgh images at the same time? Thank you for any help Kind regards, Paola - Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmi...@hsr.it - www.5xmille.org ___ Freesurfer mailing list 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.
