Thank you Bruce for the piece of mind. The images were neurologically oriented (L=L) for analysis with SPM. Do you know if this helps at all? Thanks Pablo
Date: Wed, 25 Feb 2015 10:44:48 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analyze format Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: > Dear FS experts,I am trying to run recon-all on data with analyze format. I > am aware that this is not the best format, however I do not have DICOM or > NIFTI original data as this is a very old data from University of North > Carolina. > > When I run import the images with recon-all -i. I am getting the following > log below. Do you advice to proceed with recon-all -all or do you there is a > way I could obtain the mat file that freesurfer is asking? > Thank you > Pablo > recon-all -i 30225.img -s 30225 > > > mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > > mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > ----------------------------------------------------------------- > INFO: could not find /home/0116442s/FS_test/30225.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. > INFO: if not valid, please provide the information in > /home/0116442s/FS_test/30225.mat file > ----------------------------------------------------------------- > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /home/0116442s/FS_test/30225.img... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, 1) > k_ras = (0, 1, 0) > writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... > > #------------------------------------------ > > recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT > 2015 > done > > > > _______________________________________________ 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.
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