Re: [Freesurfer] error glm-fit-sim (message 11)

digest..." Today's Topics: 1. FW: RE: error glm-fit-sim (Caroline Beelen) 2. Re: output values of vertices on surface into a textfile (Sims, Sara A) 3. Re: output values of vertices on surface into a textfile (Bruce Fischl) 4. Re: output values of vertices on surface

[Freesurfer] FW: RE: error glm-fit-sim

D: <504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" What says that? What command are you running? What is the other terminal output? On 10/01/2018 04:54

[Freesurfer] error glm-fit-sim

External Email - Use Caution Dear FS, I followed the group analysis page for glm analysis and it worked fine until the final step. I'm using version 5.3. After performing glm-fit-sim it says "glm-fit done" (for all files), but when trying to open these it says: "Reading

Re: [Freesurfer] Manuel edits (message 5)

, Caroline Beelen -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens freesurfer-requ...@nmr.mgh.harvard.edu Verzonden: donderdag 18 mei 2017 18:00 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 159

[Freesurfer] manuel edits

r decision only based on wm intensity values? Thank you for your reply. Kind regards, Caroline Beelen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] visualize corrected results

Dear FS, I have a question on visualizing results from GLM analysis... How can I visualize corrected results in Freeview after having applied bonferroni/FDR correction (somewhere else)? I saw it is not possible (error: masking file missing) -and was told it is not necessary- to apply monte

Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 14

The error is: "Mapping unhit to unknown. Found 137851 unhit vertices". The file is made, but when trying to select it from the annotation tab in Freeview, Freeview crashes too. Regards, Caroline -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] myaparc

.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu<mailto:f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="windows-1252" what is your command line?

Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6

Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mapping error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your command line? On 8/3/16 6:00 AM,

[Freesurfer] mris_label2annot

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of

[Freesurfer] significance overlay Freeview

? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen > <caroline.bee...@kuleuven.be<mailto:caroline.bee...@kuleuven.be>> wrote: > > Dea

Re: [Freesurfer] significance overlay in freeview

is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.bee...@kuleuven.be> > wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather bas

[Freesurfer] significance overlay in freeview

Dear FS team, Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. I used the following command: freeview -f

[Freesurfer] GLM significance table

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example):

[Freesurfer] GLM significance table

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example):

[Freesurfer] 3 analyses questions

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on aparc.stats tables (my ROI's are few regions from DK-atlas). I tried to do the Monte Carlo simulation but get an error that a masking-file is missing. In general, how could I correct for

Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 29

and immediately > contact the sender. > > > ___ > 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.ha

[Freesurfer] wm parcellation

Dear FS team, Thank you for your answers before (email: WmParc). We now realize that we've formulated our question wrong, since our problem is mainly in creating the wmparc.a2009s.mgz file. We ran the following command: mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o

[Freesurfer] WmParc

Dear FS team, We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran the following command: mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by our subject) We get the following

Re: [Freesurfer] gnumeric file

Thu, 17 Mar 2016, Caroline Beelen wrote: > > Dear FS, > >   > > 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects > A01_T1 > > > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed > > by) > gnumeric lh.aparc.thickness.t

Re: [Freesurfer] gnumeric file

ouglas Greve Verzonden: woensdag 16 maart 2016 15:38 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] gnumeric file On 3/16/16 6:52 AM, Caroline Beelen wrote: Hi FS team, Sorry for these rather basic questions... I'm not sure whether the gnumeric file is an ascii file (see

Re: [Freesurfer] gnumeric file

hu, 17 Mar 2016, Caroline Beelen wrote: > Hi Bruce, > > Thank you very much! :) > I think somethings wrong with gnumeric indeed just discovered that gedit > works fine. > > As for 3, that would mean that the data are not in native space? I'm trying > to understand this

[Freesurfer] mean thickness

Dear Freesurfer team, Forgive me if this is a foolish question... I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated

Re: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

Dag Jolijn, Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens mij nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te gaan (zou wel nuttig zijn!). Al is het een beetje achter de feiten aan… Vriendelijke groet, Caroline Van:

Re: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

M U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 Le 12 févr. 2016 à 09:53, Caroline Beelen <car

[Freesurfer] Qdec

Dear Freesurfer experts, I just started using Freesurfer for performing MRI (T1)- group-based ROI analysis and managed to go through the first recon-all processing stream and making few manual edits. Then I followed first steps of the Qdec -procedure. However, there is a separate section on