Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution Thank you so much Yujing! On Fri, Sep 1, 2023 at 5:45 PM Huang, Yujing wrote: > External Email - Use Caution > > Try just one dash. Flair image needs to be provided with -flair image>. > > > > Here are explanation and examples of -T2, -FLAIR, -T2pial, -FLAIRpial > flags: > > > > “ > > T2 OR FLAIR TO IMPROVE PIAL SURFACES > > > > Pial surfaces can be improved using the different contrast in T2 or FLAIR > > images. The original pial surfaces without T2/FLAIR data are saved as > > ?h.woT2.pial or ?h.woFLAIR.pial, and new ?h.pial surfaces are created. > One > > example where this is useful is when there is dura in the brainmask.mgz > that > > isn't removed by skull stripping. The flags for these commands are: > > > > -T2 or -FLAIR > > (Specify the path to the T2 or FLAIR image to use) > > -T2pial or -FLAIRpial > > (Create new pial surfaces using T2 or FLAIR images) > > > > An example of running a subject through Freesurfer with a T2 image is: > > > > recon-all -s subjectname -i /path/to/input -T2 /path/to/T2_input -T2pial > -all > > > > T2 or FLAIR images can also be used with Freesurfer subjects that have > already > > been processed without them. Note that autorecon3 should also be re-ran to > > compute statistics based on the new surfaces. For example: > > > > recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 > > “ > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alan Francis > *Sent:* Friday, September 1, 2023 5:11 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] T2 FLAIR Images > > > > *External Email - Use Caution* > > I tried the following command with the --flair flag but it did not work: > > > [DMK6P4G6FJ1G:~/SUBJECTS/NCANDA_S00033] alanfrancis% recon-all -s S00033 > -i t1.nii.gz -i t2.nii.gz --flair -all > ERROR: Flag --flair unrecognized. > > > > Could you please tell me where the --flair flag is slotted? > > > > thanks, > > > > Alan > > > > On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve > wrote: > > *External Email - Use Caution* > > Sorry, you need to pass it to recon-all with --flair or --T2 > > On 8/21/2023 1:19 PM, Alan Francis wrote: > > *External Email - Use Caution* > > Hi Doug: > > > > Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the > T2.nii.gz as 002.mgz. So will the following command work? > > > > mri_convert t2.nii.gz --flair 002.mgz > > > > or is it: > > > > mri_convert --flair t2.nii,gz 002.mgz > > > > Thanks, > > > > Alan > > > > On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve > wrote: > > *External Email - Use Caution* > > How did you set up the T2? Did you set 001.mgz to be the T1 and the > 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the > FLAIR with the --flair flag. recon-all will register them together. Or do > you just want to register them outside of recon-all? > > On 8/14/2023 2:46 PM, Alan Francis wrote: > > *External Email - Use Caution* > > Good evening Doug et all: > > > > I am trying to coregister T1 and T2 images and run the recons. However, > the T2's are giving me an error message. Please see below: I opened the T2 > image on Freeview. It looks normal. I tried running a second brain. Same > problem. Appears normal on Freeview but recons wont run. > > > > So I tried running the recons on the T1 alone and it ran without problems. > > > > Thanks, > > > > Alan > > > > [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid > NCANDA_S00042/ > fs-check-version --s NCANDA_S00042 --o > /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 > Mon Aug 7 16:06:21 CDT 2023 > > setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS > cd /Users/alanfrancis/SUBJECTS > /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o > /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 > -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 > /Applications/freesurfer/7.4.1/bin/fs-check-version > > freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 > $Id$ > Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 > 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 > pid 9192 > Current
Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution Try just one dash. Flair image needs to be provided with -flair . Here are explanation and examples of -T2, -FLAIR, -T2pial, -FLAIRpial flags: “ T2 OR FLAIR TO IMPROVE PIAL SURFACES Pial surfaces can be improved using the different contrast in T2 or FLAIR images. The original pial surfaces without T2/FLAIR data are saved as ?h.woT2.pial or ?h.woFLAIR.pial, and new ?h.pial surfaces are created. One example where this is useful is when there is dura in the brainmask.mgz that isn't removed by skull stripping. The flags for these commands are: -T2 or -FLAIR (Specify the path to the T2 or FLAIR image to use) -T2pial or -FLAIRpial (Create new pial surfaces using T2 or FLAIR images) An example of running a subject through Freesurfer with a T2 image is: recon-all -s subjectname -i /path/to/input -T2 /path/to/T2_input -T2pial -all T2 or FLAIR images can also be used with Freesurfer subjects that have already been processed without them. Note that autorecon3 should also be re-ran to compute statistics based on the new surfaces. For example: recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 “ Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alan Francis Sent: Friday, September 1, 2023 5:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2 FLAIR Images External Email - Use Caution I tried the following command with the --flair flag but it did not work: [DMK6P4G6FJ1G:~/SUBJECTS/NCANDA_S00033] alanfrancis% recon-all -s S00033 -i t1.nii.gz -i t2.nii.gz --flair -all ERROR: Flag --flair unrecognized. Could you please tell me where the --flair flag is slotted? thanks, Alan On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: External Email - Use Caution Sorry, you need to pass it to recon-all with --flair or --T2 On 8/21/2023 1:19 PM, Alan Francis wrote: External Email - Use Caution Hi Doug: Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the T2.nii.gz as 002.mgz. So will the following command work? mri_convert t2.nii.gz --flair 002.mgz or is it: mri_convert --flair t2.nii,gz 002.mgz Thanks, Alan On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: External Email - Use Caution How did you set up the T2? Did you set 001.mgz to be the T1 and the 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the FLAIR with the --flair flag. recon-all will register them together. Or do you just want to register them outside of recon-all? On 8/14/2023 2:46 PM, Alan Francis wrote: External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run. So I tried running the recons on the T1 alone and it ran without problems. Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 # #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCAND
Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution I tried the following command with the --flair flag but it did not work: [DMK6P4G6FJ1G:~/SUBJECTS/NCANDA_S00033] alanfrancis% recon-all -s S00033 -i t1.nii.gz -i t2.nii.gz --flair -all ERROR: Flag --flair unrecognized. Could you please tell me where the --flair flag is slotted? thanks, Alan On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve wrote: > External Email - Use Caution > > Sorry, you need to pass it to recon-all with --flair or --T2 > > On 8/21/2023 1:19 PM, Alan Francis wrote: > > External Email - Use Caution > Hi Doug: > > Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the > T2.nii.gz as 002.mgz. So will the following command work? > > mri_convert t2.nii.gz --flair 002.mgz > > or is it: > > mri_convert --flair t2.nii,gz 002.mgz > > Thanks, > > Alan > > On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve > wrote: > >> External Email - Use Caution >> How did you set up the T2? Did you set 001.mgz to be the T1 and the >> 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the >> FLAIR with the --flair flag. recon-all will register them together. Or do >> you just want to register them outside of recon-all? >> >> On 8/14/2023 2:46 PM, Alan Francis wrote: >> >> External Email - Use Caution >> Good evening Doug et all: >> >> I am trying to coregister T1 and T2 images and run the recons. However, >> the T2's are giving me an error message. Please see below: I opened the T2 >> image on Freeview. It looks normal. I tried running a second brain. Same >> problem. Appears normal on Freeview but recons wont run. >> >> So I tried running the recons on the T1 alone and it ran without >> problems. >> >> Thanks, >> >> Alan >> >> [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid >> NCANDA_S00042/ >> fs-check-version --s NCANDA_S00042 --o >> /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 >> Mon Aug 7 16:06:21 CDT 2023 >> >> setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS >> cd /Users/alanfrancis/SUBJECTS >> /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o >> /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 >> -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 >> /Applications/freesurfer/7.4.1/bin/fs-check-version >> >> freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 >> $Id$ >> Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 >> 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 >> pid 9192 >> Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 >> Subject does not have a bstampfile, copying >> /Applications/freesurfer/7.4.1/build-stamp.txt >> Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 >> No constraints on version because REQ=UnSet and FsVerFile=NotThere >> #@#% fs-check-version match = 1 >> fs-check-version Done >> INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS >> Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 >> Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 >> 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 >> # >> #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 >> Found 2 runs >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz >> Checking for (invalid) multi-frame inputs... >> Checking for (invalid) multi-frame inputs... >> #--- >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042 >> \n mri_robust_template --mov >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 >> --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit >> --inittp 1 --fixtp --noit --iscale --iscaleout >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt >> --subsample 200 --lta >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n >> 7.4.1 >> >> --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz >> as movable/source volume. >> --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz >> as movable/source volume. >> Total: 2 input volumes >> --average: Using method 1 for template computation. >> --template: Using >> /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output >> volume. >> --satit: Will estimate SAT iteratively! >> --inittp: Using TP 1 as target for initialization >> --fixtp: Will map everything to init TP! >> --noit: Will output only first template (no iterations)! >> --iscale: Enabling intensity scaling! >> --iscaleout: Will perform intensity scaling and output results >> --subsample: Will subsample if size is larger than 200 on all axes! >>
Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution Sorry, you need to pass it to recon-all with --flair or --T2 On 8/21/2023 1:19 PM, Alan Francis wrote: External Email - Use Caution Hi Doug: Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the T2.nii.gz as 002.mgz. So will the following command work? mri_convert t2.nii.gz --flair 002.mgz or is it: mri_convert --flair t2.nii,gz 002.mgz Thanks, Alan On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve wrote: External Email - Use Caution How did you set up the T2? Did you set 001.mgz to be the T1 and the 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the FLAIR with the --flair flag. recon-all will register them together. Or do you just want to register them outside of recon-all? On 8/14/2023 2:46 PM, Alan Francis wrote: External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run. So I tried running the recons on the T1 alone and it ran without problems. Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 # #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source
Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution Hi Doug: Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and the T2.nii.gz as 002.mgz. So will the following command work? mri_convert t2.nii.gz --flair 002.mgz or is it: mri_convert --flair t2.nii,gz 002.mgz Thanks, Alan On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve wrote: > External Email - Use Caution > > How did you set up the T2? Did you set 001.mgz to be the T1 and the > 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the > FLAIR with the --flair flag. recon-all will register them together. Or do > you just want to register them outside of recon-all? > > On 8/14/2023 2:46 PM, Alan Francis wrote: > > External Email - Use Caution > Good evening Doug et all: > > I am trying to coregister T1 and T2 images and run the recons. However, > the T2's are giving me an error message. Please see below: I opened the T2 > image on Freeview. It looks normal. I tried running a second brain. Same > problem. Appears normal on Freeview but recons wont run. > > So I tried running the recons on the T1 alone and it ran without problems. > > Thanks, > > Alan > > [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid > NCANDA_S00042/ > fs-check-version --s NCANDA_S00042 --o > /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 > Mon Aug 7 16:06:21 CDT 2023 > > setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS > cd /Users/alanfrancis/SUBJECTS > /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o > /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 > -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 > /Applications/freesurfer/7.4.1/bin/fs-check-version > > freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 > $Id$ > Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 > 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 > pid 9192 > Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 > Subject does not have a bstampfile, copying > /Applications/freesurfer/7.4.1/build-stamp.txt > Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 > No constraints on version because REQ=UnSet and FsVerFile=NotThere > #@#% fs-check-version match = 1 > fs-check-version Done > INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS > Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 > Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 > 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 > # > #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 > Found 2 runs > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #--- > /Users/alanfrancis/SUBJECTS/NCANDA_S00042 > \n mri_robust_template --mov > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 > --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt > --subsample 200 --lta > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta > /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n > 7.4.1 > > --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as > movable/source volume. > --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz > as template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enabling intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on all axes! > --lta: Will output LTA transforms > Setting iscale ... > reading source > '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... > converting source > '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... > MRItoBSpline degree 3 > reading source > '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... > converting source > '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... > MRItoBSpline degree 3 > ERROR: MultiRegistration::loadMovables: images have different voxel sizes. > Currently not supported, maybe first make conform? > Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375,
Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution How did you set up the T2? Did you set 001.mgz to be the T1 and the 002.mgz to be the T2FLAIR? If so, that will not work. You should pass the FLAIR with the --flair flag. recon-all will register them together. Or do you just want to register them outside of recon-all? On 8/14/2023 2:46 PM, Alan Francis wrote: External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run. So I tried running the recons on the T1 alone and it ran without problems. Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 # #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] T2 FLAIR Images
External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run. So I tried running the recons on the T1 alone and it ran without problems. Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 # #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] T2 FLAIR images
External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 # #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023 -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] T2/FLAIR images longitudinal stream
Hi Donald, the T2/FLAIR should also work for longitudinal processing (just pass -T2pial along in cross and long). Long grabs the image from the cross run and improves it surfaces. Best, Martin On 04/30/2013 06:46 PM, MCLAREN, Donald wrote: Martin and others, As the T2/FLAIR image is only available for cross-sectional processing; if we are doing a longitudinal study, is there any advantage of using the T2/FLAIR image? Will the improved pial surface can transferred to the base and long surfaces? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] T2/FLAIR images longitudinal stream
Martin and others, As the T2/FLAIR image is only available for cross-sectional processing; if we are doing a longitudinal study, is there any advantage of using the T2/FLAIR image? Will the improved pial surface can transferred to the base and long surfaces? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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.
