I have your data, but it does not have the base image. Can you upload that as well?
On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
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Hi Douglas,
I just upload the files as danielian.tar.gz. I didn’t notice any damage or artifact on this particular brain or the others that had this same problem. This subject is a healthy control and most of the subjects (3 of 4) that are having this problem are healthy. For each we used 2 T1s for the original cross-sectional input. The cross was reconstructed fine as was the base and the 2 other longitudinal timepoints for this same subject. The same is the case with the others I’m having trouble with – all of the their other timepoints are fine for the cross/base/longitudinal surfaces. The warped surfaces are always lower posterior (cerebellum adjacent) and sometimes also temporal. Upper cortical and frontal regions are unaffected.
Thanks for your help!
Laura
*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
Hard to tell from just that view. Was there a lot of brain change with that time point? Or was there an MRI artifact? If no to both, then you can upload all the cross, the base, and that one long. Follow instructions below (you can make one tarball for all subjects)
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subjects.tar.gz ./subject1 ./subject2 Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subjects.tar.gz Send an email that the file has been and the name of the file.
On 6/9/2020 6:32 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
* External Email - Use Caution * Hi, I’ve finished processing a data set that included longitudinal data and I’m having a problem with a small percentage of the longitudinal timepoints. To review what I’ve done, I edited all of the individual (cross-sectional) timepoints until the wm and pial surfaces were correct, then created the base and edited that until it looked good, and then created the longitudinal files for each cross-sectional timepoint. Most of these did not need editing and some needed slight edits to either wm or brainmask which corrected the longitudinal surfaces. However, in a small handful of cases, the wm/pial surfaces were so distorted that editing would not fix the problem. In these cases, longitudinal surfaces were very different from both the original cross-section and base. I’ve tried to attach a file that shows an example – it might only affect a small portion of the brain but in these cases I don’t think I could edit it to improve the surfaces. In the example I attached, red/blue are from the long file and pink/lt blue are from the base. Do you have any suggestions for why this might be happening and how to fix it? I’m running v6.0. Thanks! Laura Danielian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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