sure, following is the code I run: source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/usr/local/freesurfer/subjects recon-all -i LT7616_3TS_Copy_0001.dcm -subjid test3
And I have attached two screenshots of what I get after running the code.
On Tue, Jun 28, 2016 at 4:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
you need to give us more information that that if you want us to help you. Send us the full command line you ran and the full screen output and log files for starters.
cheers Bruce
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
Thank you! When I recon-all my files, I get the following error:files are
not found to be different and cannot be sorted
Do you have any suggestions?
Thank you
Dorsa
On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: just give recon-all a single slice from the series with -i <slice file name>. It will figure out
the rest of them On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote: > Hi, > I am a little confused about how should I save my files to execute recon-all on > them. I have 240 slices of dicom format and I put them in a folder in my > subjects_dir. but I get errors when using recon-all on the folder containing the > MRIs. Can you help me with that? I really appreciate your help > > Thank you > > Dorsa > > On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Dorsa > > what specific models do you need? The 10-20 hours is to process the > data > from a single subject at a single timepoint. If you check out our > wiki > (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of > tutorials and > sample datasets and such > > cheers > Bruce > > On Mon, 27 Jun 2016, Dorsa Haji > Ghaffari wrote: > > > Hi, > > I am graduate student at the University of Michigan and I am > performing > > research on deep brain stimulation. I want to warp an anatomical > brain atlas > > to individual patient MRIs to get the patient specific brain models > out of > > it. I chose FreeSurfer to do this and I have installed it on my > computer. I > > realized that it takes 10-20 hrs to reconstruct the image. I wanted > to ask > > if that is the time for one image? or the whole series of images? > > I also wanted to ask if there is a step by step tutorial on how to > do this. > > > > Thank you > > > > Dorsa Ghaffari > > > > > > > > > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
