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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 16, 2020 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
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:
External Email - Use Caution 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.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have not seen that file appear. Can you re-upload it?
On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
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:
* External Email - Use Caution * 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> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
External Email - Use Caution
Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.
Thanks,
Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 9:12 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 16, 2020 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
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:
External Email - Use Caution 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.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into.
On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.
Thanks,
Laura
*From: *"Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, June 18, 2020 at 9:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
I have not seen that file appear. Can you re-upload it?
On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
* External Email - Use Caution * Hi Douglas, OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry! Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem 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: * External Email - Use Caution * 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> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Thanks Douglas. I could send other problem data sets too if it would help. Just let me know.
Thanks, Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 19, 2020 at 6:10 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.
Thanks,
Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 9:12 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 16, 2020 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
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:
External Email - Use Caution 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.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface)
On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
Thanks Douglas. I could send other problem data sets too if it would help. Just let me know.
Thanks,
Laura
*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 19, 2020 at 6:10 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into.
On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
* External Email - Use Caution * Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz. Thanks, Laura *From: *"Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Thursday, June 18, 2020 at 9:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Hi Douglas, OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry! Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem 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: * External Email - Use Caution * 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> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Interesting – I never did any editing directly on the original brain.finalsurfs.mgz. I only did cerebellar edits on the brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz. Looks like those edits copied over somehow.
Regardless, it sounds like this will be easy to correct. Where can I find an unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that into the processing stream?
Thanks, Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, June 22, 2020 at 12:13 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface) On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Thanks Douglas. I could send other problem data sets too if it would help. Just let me know.
Thanks, Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 19, 2020 at 6:10 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.
Thanks,
Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 9:12 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 16, 2020 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
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:
External Email - Use Caution 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.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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If you run this, it will create a new brain.finalsurfs and rerun just what you need to rerun recon-all -s subject -autorecon2 -nogcareg -nocalabel -nonormalization2 -autorecon3
On 6/22/2020 1:20 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
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Interesting – I never did any editing directly on the original brain.finalsurfs.mgz. I only did cerebellar edits on the brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz. Looks like those edits copied over somehow.
Regardless, it sounds like this will be easy to correct. Where can I find an unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that into the processing stream?
Thanks,
Laura
*From: *"Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, June 22, 2020 at 12:13 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface)
On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
* External Email - Use Caution * Thanks Douglas. I could send other problem data sets too if it would help. Just let me know. Thanks, Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 19, 2020 at 6:10 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz. Thanks, Laura *From: *"Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Thursday, June 18, 2020 at 9:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Hi Douglas, OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry! Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem 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: * External Email - Use Caution * 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> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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OK thanks. Do you recommend that I re-run this for every subject that I did these cerebellar edits on since it ended up editing brain.finalsurfs.mgz? I have a handful of other data sets where it didn’t affect the longitudinal surfaces, but upon further inspection it’s clear that those cross-sectional edits within the cerebellum carried over to brain.finalsurfs.mgz in the longitudinal data sets.
Also, I’m still not sure how the edits I made on the brain.finalsurfs.manedit.mgz volumes got transferred over to the original. Do you have any suggestions for how this happened and how to avoid doing this in the future?
Thanks, Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 23, 2020 at 10:18 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
If you run this, it will create a new brain.finalsurfs and rerun just what you need to rerun recon-all -s subject -autorecon2 -nogcareg -nocalabel -nonormalization2 -autorecon3
On 6/22/2020 1:20 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Interesting – I never did any editing directly on the original brain.finalsurfs.mgz. I only did cerebellar edits on the brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz. Looks like those edits copied over somehow.
Regardless, it sounds like this will be easy to correct. Where can I find an unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that into the processing stream?
Thanks, Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, June 22, 2020 at 12:13 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface) On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Thanks Douglas. I could send other problem data sets too if it would help. Just let me know.
Thanks, Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 19, 2020 at 6:10 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.
Thanks,
Laura
From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 9:12 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution Hi Douglas,
OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry!
Laura
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, June 16, 2020 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Stream Problem
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:
External Email - Use Caution 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.EDUmailto:dgreve@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, June 12, 2020 at 10:35 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Laura, it looks like there is a bug in v6 that does not transfer the edits correctly. This is fixed in v7, but I'm looking into getting you a version of mri_mask that will work in v6. doug
On 6/23/2020 1:49 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
OK thanks. Do you recommend that I re-run this for every subject that I did these cerebellar edits on since it ended up editing brain.finalsurfs.mgz? I have a handful of other data sets where it didn’t affect the longitudinal surfaces, but upon further inspection it’s clear that those cross-sectional edits within the cerebellum carried over to brain.finalsurfs.mgz in the longitudinal data sets.
Also, I’m still not sure how the edits I made on the brain.finalsurfs.manedit.mgz volumes got transferred over to the original. Do you have any suggestions for how this happened and how to avoid doing this in the future?
Thanks,
Laura
*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, June 23, 2020 at 10:18 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Longitudinal Stream Problem
If you run this, it will create a new brain.finalsurfs and rerun just what you need to rerun recon-all -s subject -autorecon2 -nogcareg -nocalabel -nonormalization2 -autorecon3
On 6/22/2020 1:20 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
* External Email - Use Caution * Interesting – I never did any editing directly on the original brain.finalsurfs.mgz. I only did cerebellar edits on the brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz. Looks like those edits copied over somehow. Regardless, it sounds like this will be easy to correct. Where can I find an unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that into the processing stream? Thanks, Laura *From: *"Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Monday, June 22, 2020 at 12:13 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface) On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Thanks Douglas. I could send other problem data sets too if it would help. Just let me know. Thanks, Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 19, 2020 at 6:10 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into. On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Sorry I’m not sure why it didn’t upload. I just tried it again. danielianall.tar.gz - Should include all parts. EM2 is the cross-sectional. EM is the base. EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz. Thanks, Laura *From: *"Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Thursday, June 18, 2020 at 9:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem I have not seen that file appear. Can you re-upload it? On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote: * External Email - Use Caution * Hi Douglas, OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry! Laura *From: *"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, June 16, 2020 at 10:10 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Longitudinal Stream Problem 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: * External Email - Use Caution * 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> <mailto:dgreve@MGH.HARVARD.EDU> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, June 12, 2020 at 10:35 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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Danielian, Laura (NIH/NINDS) [E] -
Douglas N. Greve