[Freesurfer] Control points: possible bug (only tested in 5.3)

Hi list, I've been creating control points and I got the following error: MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat): could not open file No such file or directory I created the /tmp/ folder by hand and then it created the control.dat file prope

Re: [Freesurfer] mris_preproc --qdec-long problem

Hi I updated mris_preproc (for both the --qdec and --qdec-long flags) and now it can also read \r (old mac) files. It can also deal with empty lines in the files. This will be in the next release, if anyone else gets stuck, request an updated version of mris_preproc from us. thanks, Martin

[Freesurfer] FS-FAST - ERROR: mapping surfaces

I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part whe

[Freesurfer] mris resample: Command not found. This error is permanent after new patch download

Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found.Darwin iMac I have performed my

Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download

Hi Stefano probably you want to put mris_resample in $FREESURFER_HOME/bin, which should be in your path cheers Bruce On Fri, 7 Jun 2013, std...@virgilio.it wrote: Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0 writing registered surface to/Applicati

Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download

Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, std...@vi

[Freesurfer] R: Re: mris resample: Command not found. This error is permanent after new patch download

Hi Zeke, thank you very much. I have download a file that named "unknown". I should rename it as "mris_resample"? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent afte

Re: [Freesurfer] Parameterization Optseq

Dear Doug, Thank you for your e-mail. Please find attached our command line. We felt that the first two lines of code should essentially yield the same timing of events. In the first we included the fixed duration of the fix (1.0) in our event duration (4.0) and meant to ask for extra null events

[Freesurfer] R: Re: R: Re: mris resample: Command not found. This error is permanent after new patch download

Ok, now I think that I have downloaded the correct file. I try to rerun trac-all -prep and at the end I'll send you a feedback. Thanks, Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 7-giu-2013 18.18 A: Cc: Ogg: Re: [Freesurfer] R: Re: mris resample: Command not f

Re: [Freesurfer] AR2 Error

Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve wrote: > > OK, this is a known problem when running recon-all with -autorecon1 >

Re: [Freesurfer] AR2 Error

Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately? Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning wrote: > Hi Doug-- > > Running: > > recon-all -s freesurfer -autorecon2 -autorecon3 > > produ

Re: [Freesurfer] Xhemi question

Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding x

Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces

Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 b

Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces

Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007 Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits?

Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces

On 06/07/2013 02:24 PM, preci...@nmr.mgh.harvard.edu wrote: > Thanks Doug, > I did make some manual edits to wm.mgz and brainmask.mgz then reran the > subject a couple times using: > recon-all -autorecon2-wm -subjid subj007 > > Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? No,

Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces

Hi Ronny you should have run recon-all -autorecon2-wm -subjid subj007 -autorecon3 at this point you should be fine running -make all. It should retain all your manual edits cheers Bruce On Fri, 7 Jun 2013, preci...@nmr.mgh.harvard.edu wrote: > Thanks Doug, > I did make some manual edits to

[Freesurfer] subfield algorithm and subject intensity differences

I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundari

Re: [Freesurfer] subfield algorithm and subject intensity differences

Hi Josh it depends on intensity differences if it can find them as well as boundary/geometry. cheers Bruce On Fri, 7 Jun 2013, Joshua Lee wrote: > I'm trying to understand Leemput's subfield algorithm better as implemented > in Freesurfer. Does the algorithm make use of intensity differences

Re: [Freesurfer] subfield algorithm and subject intensity differences

Dear Josh, at this point, and given that the boundaries between these subfields cannot really be seen in 1mm T1 scans, the algorithm assumes that all the subfields other than fimbria and fissure share the same image intensity properties. Therefore, using your own words: "depend only on outward bo

Re: [Freesurfer] subfield algorithm and subject intensity differences

Thanks Bruce and Eugenio, Suppose I had two identical images of a subject, but in one image I reduced the contrast of internal lamina while leaving the rest of the image intact...just removing internal intensity differences, but leaving the outer boundary contrast intact. Would the images result

[Freesurfer] Hypointense lesions

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

Re: [Freesurfer] AR2 Error

you need to include the -autorecon3 flag simultaneously with the -autorecon1 and -autorecon2 flags. On 06/07/2013 05:45 PM, Erin Browning wrote: > > It fails before ar3 runs. > > On Jun 7, 2013 2:54 PM, "Douglas N Greve" > wrote: > > > There is no indicati

[Freesurfer] environment variable FREESURFER_HOME

Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer: /Applications/freesurfer I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFree

Re: [Freesurfer] AR2 Error

The recon-all.log fail indicates that you did not use the -autorecon3 flag. In any event, I'm trying to get you a new version of mri_segstats, but it looks like our snowleopard build has not gone through since I made the change. I'll try again over the weekend or on Monday. doug On 06/07/2013

Re: [Freesurfer] environment variable FREESURFER_HOME

There should be a file called ".cshrc" in your home directory. Add the two lines to that file. -Zeke On 06/07/2013 05:53 PM, pablo najt wrote: > Can anyone advice me on how to set the environment variable > FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? > > My directo

[Freesurfer] Installation trouble on Macbook Air (no such file or directory)

I am new to Unix and FreeSurfer, and I am having some trouble installing FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just fine, and when I start the installation steps, I'm instructed to add some lines to my .cshrc or .tcshrc files in my home directory. Can anyone point me to