[Freesurfer] license key

Hello, I received a license key by email, but cannot find where in the license it should go. Thanks, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] inflated surface not appearing

Hi, I have run the process volume and create surface commands on a set of structural data, but when i go to edit segmentation, nothing comes up in the TkSurfer window. There are pictures in the TkEdit window, though. I have looked through my files and the surf folder has both lh and rh files in

[Freesurfer] Printing or saving TkSurfer image

Hello, Does anyone know how to print or save as an image, the infated brain surface as shown using TkSurfer? Thanks, Margaret ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fsfast parfiles

Hello, When writing par files for each functional run, do you match the timing of the stimuli to the ideal timing (starting at zero), the ideal adjusted timing for the 10 seconds of dummy scans (starting at 10 s), or the timing from the log files from Presentation? How much does this timing affec

[Freesurfer] FsFast file conversion/preprocessing

ar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank you so much, Margaret Duff ___ Freesurfer

Re: [Freesurfer] FsFast file conversion/preprocessing

l the number of slices. Does this resolve the difference? It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from? doug Margaret Duff wrote: > > Hi, I have 12 runs of functional data I a

Re: [Freesurfer] FsFast file conversion/preprocessing

unds like your bshorts are not being converted to AFNI properly. > > Can you send me your preproc-sess command-line and the location you are > > running it from? > > > > doug > > > > Margaret Duff wrote: > > > > > > Hi, I have 12 runs of fun

Re: [Freesurfer] FsFast file conversion/preprocessing

pace/troy ... > > doug > > > Margaret Duff wrote: > > > > hi, i am using bshort files. should i try bfloat? thanks, margaret > > > > On > > Thu, 4 Nov 2004, Doug Greve wrote: > > > > > > > > Hi Margaret, > > > > > &

[Freesurfer] fsfast stxgrinder-sess

s not used anymore? also, does anyone know if where i can find the fsfast manual, not just the tutorial manual? thanks, margaret duff ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] wmfill

Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not fou

Re: [Freesurfer] wmfill

than that. Can you send us log files from trying > to run mri_fill? Is it finding the cutting planes? Have you tried > specifying them manually? > > cheers, > Bruce > > On Tue, 30 Nov 2004, Margaret Duff wrote: > > > Hi, I keep getting an error message after I ru

Re: [Freesurfer] wmfill

t it could not find > $subject/mri/transforms/talairach.xfm for this volume. > > Tosa > > Margaret Duff wrote: > > >The log file is below. And at the end it says command finished, not that > >something went wrong. I am not sure about the cutting planes or how to >

Re: [Freesurfer] wmfill

in which the cc is disconnected and a horizontal slice above > the cerebellar peduncles where the pons is disconnected. > > cheers, > Bruce > > On Wed, 1 Dec > 2004, Margaret Duff wrote: > > > The log file is below. And at the end it says command finished, not that &

Re: [Freesurfer] wmfill

d ran recon-all -stage1 and "mri_fill" > created a very clean filled > volume. > > Tosa > > Margaret Duff wrote: > > >Hi, I tried to manually set the cutting planes, but I was unable to get > >the create surface to run. My subjects info is at >

Re: [Freesurfer] wmfill

ch coords - it looks like you > are using voxels coords. > > Bruce > > On Mon, 6 Dec 2004, Margaret Duff wrote: > > > Hi, I tried to manually set the cutting planes, but I was unable to get > > the create surface to run. My subjects info is at > > /space/troy/1/

Re: [Freesurfer] wmfill error

i had this problem recently. try using recon-all -stage one in a terminal window instead of process volume in csurf. or specify the corpus collosum and pons in the WMFill tab under Preferences->Expert Preferences in csurf. it probably cant find where to segment. you might want to check the archi

Re: [Freesurfer] wmfill error

erence on how to specify the corpus collosum and pons in the > WMFill under Preferences->Expert Preferences in csurf? > > Nam. > > >>> Margaret Duff <[EMAIL PROTECTED]> 12/22/04 12:10 PM >>> > i had this problem recently. try using recon-all -stage o

[Freesurfer] recon-all exiting with errors

Hello, I am trying to run recon-all but it seems to have some problems during nu_correct. I am using the command recon-all -subjid SM2C1tal -stage1, my subjectsdir is /space/troy/1/users/FREESURFER, and I am getting the error, Can't locate MNI/Startup.pm in @INC. then it says all the stuff @INC

[Freesurfer] Preproc-sess failed during smoothing

Hi, I was trying to preprocess some functional data using the command preproc-sess -fwhm 6 -sf sessid -df sesspar. My subjects study directory is located at /space/troy/1/users/FREESURFER/SM2C2_fsfast/study. The command made it through motion correction, then during smoothing gave me this error:

[Freesurfer] averaging brains over two sessions

Hello, I am trying to reconstruct brains of patients who had one structural scan during each of 2 visits, a month apart. I averaged the two images together, but since they are from different visits, they look very badly lined up. It looks like there is one image and another image overlaid and sh

Re: [Freesurfer] averaging brains over two sessions

On Wed, 2 Feb 2005, Margaret Duff wrote: > > > Hello, I am trying to reconstruct brains of patients who had one > > structural scan during each of 2 visits, a month apart. I averaged the > > two images together, but since they are from different visits, they look > > ver

Re: [Freesurfer] averaging brains over two sessions

lign, due to differences in shims, > read-out directions and bandwidth. Reconning with a single image is > certainly doable (we've done hundreds), but is more labor intensive. > > cheers, > Bruce > > On Wed, > 2 Feb 2005, Margaret Duff wrote: > > > Hello, I am tr

[Freesurfer] Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found.

Hi, During running recon-all, I get this line INFO: Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found. I looked in my /tmp folder and I have a mritotal_7563 folder but no mritotal_5659 folder. Will this affect my recon-all processing? This error also appears in my orig.euler files. I

[Freesurfer] -notalairach option not working

Hello, I am running the line recon-all-nmr -notalairach -stage1 -stage2 -subjid SM2C3 from SUBJECTS_DIR /space/troy/users/2/mikesfolder and in the std-env. The recon-all-nmr program is still creating a bad talairach transform that overwrites the good one I just made. So, the recon-all-nmr kee

[Freesurfer] ERROR: nu_correct

Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like

Re: [Freesurfer] ERROR: nu_correct

. On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote: Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C

Re: [Freesurfer] defining labels

You have to use the aparc.annot file that is in your label folder in your subjects folder. That would be $SUBJECTS_DIR/subjid/label. It is made during recon-all-nmr -stage4b. Hope this helps, margaret On Thu, 23 Jun 2005, Kirk, Gregory wrote: Hello, I remember a message from Bruce

Re: [Freesurfer] defining labels

oh sorry, i was think of the -a file. not sure about the label file. margaret On Thu, 23 Jun 2005, Margaret Duff wrote: You have to use the aparc.annot file that is in your label folder in your subjects folder. That would be $SUBJECTS_DIR/subjid/label. It is made during recon-all-nmr

[Freesurfer] segmentation fault during mri_convert

Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from that. i dont know exa

Re: [Freesurfer] segmentation fault during mri_convert

-0400, Margaret Duff wrote: Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from tha

[Freesurfer] ERROR:nu_correct

Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: - Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0

Re: [Freesurfer] ERROR:nu_correct

v1.4, from 1.0.4), and I hadn't fully tested against all the binary/platform/machine dependencies, which can be quite complicated and exasperating! Let me know how things work. Sorry for the delay. Nick On Thu, 2005-08-25 at 12:14 -0400, Margaret Duff wrote: Hello, I am running the co

[Freesurfer] mris_euler_number

Hi, I am running the command recon-all -subjid SM2C4_autoreconall -autorecon2 on troy, with subjects directory being /space/troy/1/users/FREESURFER. I just got this error message, which I have never gotten before: - Euler Number rh Fri Sep 9 02:03

[Freesurfer] slight head wrapping using tkregister2

Hi, When I am looking at a brain using tkregister2 to see how well the talairach lines up, it seems like the brain is leaving the viewing window and gets cut off. This is especially apparent using the sagittal view and additionally, a white rounded blob(maybe the nose) appears behind the brai