[Freesurfer] request

this the correct link to upload files and folders? https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Sorry to bother you all but this would be extremely helpful given that I experienced a similar problem in several subjects of this sample. Thanks in advance, Pietro -- Pietro De Rossi

Re: [Freesurfer] request

ok. is it possible to upload the whole subject folder? 2013/11/11 Louis Nicholas Vinke > Hi Pietro, > Yes, the filedrop would be fine or you can upload using ftp. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > -Louis > > > On Mon, 11 Nov

Re: [Freesurfer] request

ok thanks! 2013/11/11 Louis Nicholas Vinke > Yes, just tar/zip it up first. > > > On Mon, 11 Nov 2013, pietro de rossi wrote: > > ok. is it possible to upload the whole subject folder? >> >> >> 2013/11/11 Louis Nicholas Vinke >> Hi Pietro, &

[Freesurfer] Files uploaded

HI, I succesfully uploaded the files. Thanks in advance for your help! Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'A

[Freesurfer] (no subject)

Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS

Re: [Freesurfer] your mail

l points and rerunning. The norm.mgz is passed to mri_pretess to > create the wm.mgz. You can see there is overlap between the hyper-intense > voxels on the norm and the voxels not being included in the wm mask, which > leads to major errors in the wm surface. > -Louis > > On Fri, 15 Nov

[Freesurfer] problems with control points

several times but it didn't work... Could you please have a look? Any suggestion would be greatly appreciated :-) Thanks in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neurosc

Re: [Freesurfer] problems with control points

sing a poor wm surf initialization and further problems > downstream. Filling in the gaps on several slices seems to have done the > trick. Snapshot attached. > -Louis > > On Thu, 13 Feb 2014, pietro de rossi wrote: > >> Dear FreeSurfers, >> I have uploaded a

[Freesurfer] setenv command not found

d not found How can I solve the problem? It never happened on the Mac I was previously working on... Thanks -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di

Re: [Freesurfer] setenv command not found

sorry. I've just realized that I must switch the shell to tcsh the problem is that it doesn't let me do that. sorry for bothering :-) 2014-02-27 8:44 GMT+01:00 pietro de rossi : > Dear Freesurfers, > > I am using Freesurfer version 5.1 on Linux-centos4_x86_

Re: [Freesurfer] setenv command not found

done. 2014-02-27 10:31 GMT+01:00 pietro de rossi : > sorry. I've just realized that I must switch the shell to tcsh > > the problem is that it doesn't let me do that. > > sorry for bothering :-) > > > 2014-02-27 8:44 GMT+01:00 pietro de ros

[Freesurfer] Question about Intracranial Volume

timated by FreeSurfer 5.1 has a bad quality and is not reliable. However, neither the reviewer provides any evidence, nor I could find any... Is there any evidence for this? Thanks in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di

Re: [Freesurfer] Question about Intracranial Volume

e testing a somewhat different > hypothesis (that local atrophy is faster than whole-brain atrophy, as > opposed to whether atrophy exists at all) > > cheers > Bruce > > > > On Mon, 11 Jan 2016, pietro de rossi wrote: > > Dear FreeSurfers, >> I am editing a paper on

Re: [Freesurfer] Question about Intracranial Volume

> hypothesis (that local atrophy is faster than whole-brain atrophy, as > opposed to whether atrophy exists at all) > > cheers > Bruce > > > On Mon, 11 Jan 2016, pietro de rossi wrote: > > > Dear FreeSurfers, > > I am editing a paper on subcortical volum

Re: [Freesurfer] editing topological defect

k. > > cheers > Bruce > > > > On Mon, 12 Aug 2013, pietro de rossi wrote: > > Hi freesurfers, >> >> I have a problem editing a topological defect given that it is >> represented by cortex non included within the pial boundary >> without white matte

[Freesurfer] problems with aparcstats2table

eird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (

Re: [Freesurfer] problems with aparcstats2table

Douglas N Greve ha scritto: > > Is it failing on one particular subject? > > > On 08/29/2013 09:38 AM, pietro de rossi wrote: >> Dear FreeSurfers, >> >> I am extracting thickness values through the aparcstats2table command >> line. >> >&

Re: [Freesurfer] problems with aparcstats2table

fine for the left hemisphere (same list of subjects). Sorry for bothering and thanks again for your help, Pietro 2013/8/29 Douglas N Greve > > What is your command line? Try it on a single subject to see if it fails > doug > > > > > On 08/29/2013 02:00 PM, Pietro

Re: [Freesurfer] problems with aparcstats2table

subject...there are some processing defects (i.e. the superior temporal girus is not well segmented despite editing). Could that be the problem? Thanks 2013/9/2 pietro de rossi > Hi Doug, > > my command line is > > aparcstats2table --subjects subject1 subject2 subject3 --hem

[Freesurfer] questions about recon-all pipelines

advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Depar

Re: [Freesurfer] questions about recon-all pipelines

t import your *.dcm files with the command >> >> recon-all -i first_dicom_image_name.dcm -s subjID >> >> Then when you process your data you would type >> >> recon-all -s subjID -autorecon1 -autorecon2 >> >> or whatever steps you are using. >> >&

[Freesurfer] output problem after recon-all

medit [name_of_folder_with_dcm_files] norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt the scans look all the sameit is like the last scan I processed was overwritten on the previous onesdoes it make sense? thank you very much, Pietro -- Pietro De Ross

Re: [Freesurfer] output problem after recon-all

c the list on these emails? Your command line should be: > > recon-all -i -s > -all > > cheers > > Bruce > > > On Thu, 27 Sep 2012, pietro de rossi wrote: > > the command line was >> >> recon-all -autorecon1 -autorecon2 -subjid name_of_folder_with

Re: [Freesurfer] output problem after recon-all

Thank you very much Bruce! it's working. 2012/9/27 Bruce Fischl > no, it represent the name of the folder that FS will create to put the > results of the analysis in. The -i should be the full path to one file in > the correct (T1-weighted) dicom series > > On Thu, 27 Sep 2

[Freesurfer] processing scans on more than one computer

n the same computer (even if I set the new folder as the SUBJECTS_DIR) I'm not able to run tksurfer and tkmedit for those subjectsam I doing anything wrong? is it just that once you've processed the scans the proc_folders cannot be moved? thanks, Pietro -- Piet

Re: [Freesurfer] processing scans on more than one computer

tro > > you should be able to. When you say you can't run tksurfer/tkmedit what > happens? Can you send us screen output? > > Bruce > > On Tue, 2 Oct 2012, pietro de rossi wrote: > > Dear FreeSurfer experts, >> I'm processing scans on three different computers

Re: [Freesurfer] processing scans on more than one computer

I've just figured that out.the storage device icon is on the desktop but the actual path to the storage device is differentvery silly :-) sorry for bothering 2012/10/2 pietro de rossi > Ok, this is what happened after I moved the folders to a storage device > (M

[Freesurfer] set a breakpoint in malloc_error_break to debug Bus error in recon-all

vance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neu

Re: [Freesurfer] set a breakpoint in malloc_error_break to debug Bus error in recon-all

oon, but in the interim I would suggest you track down the cause > of your huge defect and correct it either with control points, or by > editing the wm.mgz > > cheers > Bruce > > > > On Mon, 15 Oct 2012, pietro de rossi wrote: > > Hi free surfer users and developers

Re: [Freesurfer] set a breakpoint in malloc_error_break to debug Bus error in recon-all

opological defects in temporal lobe. should I repost the email? Sorry for bothering, Pietro 2012/10/15 Bruce Fischl > Hi Pietro, > > yes, possibly. Subject motion can cause this to happen. > > > cheers > Bruce > On Mon, 15 Oct 2012, pietro de rossi wrote: > > Thanks

[Freesurfer] direct repositioning

Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences,

Re: [Freesurfer] direct repositioning

regenerate the thickness maps) > > cheers > Bruce > > > > On Wed, 24 Oct 2012, pietro de rossi wrote: > > Hi FreeSurfer people, >> I'm considering editing through direct repositioning in freeview (under >> tools->reposition surface) for some scans

Re: [Freesurfer] direct repositioning

thanks! cheers 2012/10/24 Bruce Fischl > look in the recon-all -help output > > On Wed, 24 Oct 2012, pietro de rossi wrote: > > ok, >> how do I get a list of all the commands after mrsi_make_surface? >> >> 2012/10/24 Bruce Fischl >> Hi Pietro,

[Freesurfer] exporting aseg.stats values

users/derossip/desktop/Subjects_ABC_Proc/501/stats/aseg.stats Building the table.. Writing the table to aseg.vol.sample.table Nowwhere can I physically visualize the data? Thank you verymuch, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Fa

Re: [Freesurfer] exporting aseg.stats values

Thanks a lot! 2012/11/19 Douglas N Greve > It should be in the current directory. > doug > > On 11/19/2012 12:47 PM, pietro de rossi wrote: > > Hi FreeSurfer users and developers, > > > > I'm trying to export aseg.stats values for a preliminary analysis. I

[Freesurfer] error loading datatable in qdec

...there are 20 subjects in my data table and not just 19... is there a way I can solve this? thanks, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di

[Freesurfer] medial prefrontal cortex

values. Is there a way to do this without drawing a ROI to use in a group-analysis by adec/fsdg? Thanks in advance for your help, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze

[Freesurfer] problems with license

Dear Experts, I'm sorry to bother you with a very silly question but...I'm trying to setup free surfer on my Mac and I'm having problems due to the fact that it keeps giving me errors saying that I don't have a valid license I've received the email with the three line license after the download