Re: [Freesurfer] Working with MEMPRAGE
Thanks Bruce. On Mon, Jul 15, 2013 at 4:52 PM, Bruce Fischl wrote: > Hi Alan > > to use the 4 echoes you want to compute the rms. I think something like > > mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz > > should do the trick (then use mprage_rms.mgz as the input to recon-all) > > cheers > Bruce > > > > On Mon, 15 Jul 2013, Alan Francis wrote: > > Hi Jonathan, FreeSurfer folks: >> >> Did you have success in combining 4 echoes of MEMPRAGE images into one? I >> went through the archives and it appears to me that you would use: >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the >> scan >> has been through the recon all process. My question is did you use >> mri-concat to combine the 4 echoes into one? >> >> thanks, >> >> Alan >> >> >> On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt >> wrote: >> Bruce, >> >> how is it that I might load multiple surfaces, loading lh after >> having loaded rh makes the other disappear. this is loading >> manually, not from the command line >> On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: >> >> > Hi all, >> > >> > last question promise. Successfully completed >> mris_make_surfaces for both hemispheres. in my day-to-day >> editing I open tkmedit thusly: >> > >> > tkmedit brainmask.mgz -aux >> $SUBJECTS_DIR/subjid/mri/wm.**mgz -surface >> $SUBJECTS_DIR/subjid/surf/lh.**white -aux-surface >> $SUBJECTS_DIR/subjid/surf/rh.**white -aparc+aseg >> > >> > this works for mprage subjects. In evaluating and possibly >> editing MEMPRAGE subjects, which surfaces should I have opened >> in tkmedit, as there seem to be many more this time around. >> > >> > best, >> > jon >> > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >> > >> >> Hi Kayle >> >> >> >> it's been a long time since I wrote that code and we've only >> run it a few >> >> times. If you upload your subject directory I'll take a look >> >> >> >> cheers >> >> Bruce >> >> On Sat, 11 May >> >> 2013, Kayle Sawyer wrote: >> >> >> >>> Hi all, >> >>> >> >>> I tried to use the 4-echo MEMPRAGE dura detection for >> mris_make_surfaces, but I'm not sure if it worked. The terminal >> output, including commands, is attached. It was run with version >> freesurfer-Linux-centos6_x86_**64-stable-v5.3.0-BETA-**20130509. >> >>> >> >>> On the original recon, in the rh, there is a segment of dura >> marked as grey inside the pial line, at 94 111 169. The surfaces >> did not appear to change substantially after I reran >> mris_make_surfaces with the -dura flag specifying the 4-echo >> MEMPRAGE, which I placed in the mri directory. You can see the >> before and after for yourself on the attached screenshots, or if >> you have NMR access, here: >> >>> /space/ficus/6/users/SNEF_**edits/OB01_orig/ >> >>> /space/ficus/6/users/SNEF_**edits/OB01_orig_dura/ >> >>> >> >>> I saw this output from mris_make_surfaces for the rh, so >> maybe -dura did correct a different defect? >> >>> 7 non-cortical segments detected >> >>> only using segment with 1900 vertices >> >>> >> >>> Any help would be appreciated, because we have over 130 >> brains and the fewer manual corrections, the better! >> >>> >> >>> Thanks, >> >>> -Kayle >> >>> >> >>> >> >>> >> >>> >> >>> From: Douglas Greve >> >>> Date: Thu, May 9, 2013 at 8:44 PM >> >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >> >>> To: freesurfer@nmr.mgh.harvard.edu >> >>> >> >>> >> >>> >> >>> the dcmunpack command is right. You should make sure to >> analyze only the >> >>> RMS in recon-all (ie , that is the only volume that goes >> into mri/orig &
Re: [Freesurfer] Working with MEMPRAGE
Hi Alan to use the 4 echoes you want to compute the rms. I think something like mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz should do the trick (then use mprage_rms.mgz as the input to recon-all) cheers Bruce On Mon, 15 Jul 2013, Alan Francis wrote: Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one? thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > Hi all, > > last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: > > tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg > > this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. > > best, > jon > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > >> Hi Kayle >> >> it's been a long time since I wrote that code and we've only run it a few >> times. If you upload your subject directory I'll take a look >> >> cheers >> Bruce >> On Sat, 11 May >> 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>> >>> On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: >>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>> >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? >>> 7 non-cortical segments detected >>> only using segment with 1900 vertices >>> >>> Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! >>> >>> Thanks, >>> -Kayle >>> >>> >>> >>> >>> From: Douglas Greve >>> Date: Thu, May 9, 2013 at 8:44 PM >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> the dcmunpack command is right. You should make sure to analyze only the >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>> doug >>> >>> >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> Hi Kayle >>>> >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>> >>>> cheers >>>> Bruce >>>> On Thu, >>>> 9 May 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have t
Re: [Freesurfer] Working with MEMPRAGE
Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one? thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt wrote: > Bruce, > > how is it that I might load multiple surfaces, loading lh after having > loaded rh makes the other disappear. this is loading manually, not from the > command line > On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > > > Hi all, > > > > last question promise. Successfully completed mris_make_surfaces for > both hemispheres. in my day-to-day editing I open tkmedit thusly: > > > > tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz > -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface > $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg > > > > this works for mprage subjects. In evaluating and possibly editing > MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there > seem to be many more this time around. > > > > best, > > jon > > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > > > >> Hi Kayle > >> > >> it's been a long time since I wrote that code and we've only run it a > few > >> times. If you upload your subject directory I'll take a look > >> > >> cheers > >> Bruce > >> On Sat, 11 May > >> 2013, Kayle Sawyer wrote: > >> > >>> Hi all, > >>> > >>> I tried to use the 4-echo MEMPRAGE dura detection for > mris_make_surfaces, but I'm not sure if it worked. The terminal output, > including commands, is attached. It was run with version > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. > >>> > >>> On the original recon, in the rh, there is a segment of dura marked as > grey inside the pial line, at 94 111 169. The surfaces did not appear to > change substantially after I reran mris_make_surfaces with the -dura flag > specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You > can see the before and after for yourself on the attached screenshots, or > if you have NMR access, here: > >>> /space/ficus/6/users/SNEF_edits/OB01_orig/ > >>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ > >>> > >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura > did correct a different defect? > >>> 7 non-cortical segments detected > >>> only using segment with 1900 vertices > >>> > >>> Any help would be appreciated, because we have over 130 brains and the > fewer manual corrections, the better! > >>> > >>> Thanks, > >>> -Kayle > >>> > >>> > >>> > >>> > >>> From: Douglas Greve > >>> Date: Thu, May 9, 2013 at 8:44 PM > >>> Subject: Re: [Freesurfer] Working with MEMPRAGE > >>> To: freesurfer@nmr.mgh.harvard.edu > >>> > >>> > >>> > >>> the dcmunpack command is right. You should make sure to analyze only > the > >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig > >>> doug > >>> > >>> > >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: > >>>> Hi Kayle > >>>> > >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. > >>>> > >>>> cheers > >>>> Bruce > >>>> On Thu, > >>>> 9 May 2013, Kayle Sawyer wrote: > >>>> > >>>>> Hi all, > >>>>> > >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have > been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we > instead specify the multiecho scans for recon-all, do we need to give any > additional parameters (e.g. the number of echoes) for it to utilize the 4 > echoes to detect dura and refine pial surfaces in mris_make_surfaces, as > described below? Or would we have to run recon-all with the RMS, then after > it finishes re-run mris_make_surfaces manually with the -dura flag to > refine the pial surface? > >>>>> > >>>>> Also, I'd like to make sure we are using dcmunpack properly. We take > the > >>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso > run > >>>
Re: [Freesurfer] Working with MEMPRAGE
I wont question it, but this is my first multi echo brain and it's the most beautiful i've ever seen. so crisp. On May 13, 2013, at 3:55 PM, Bruce Fischl wrote: > I'm surprised it would work well if they are not float. You'll lose a lot of > precision > On Mon, 13 May 2013, Jonathan Holt wrote: > >> I'll definitely do that next time... >> >> although it didn't seem to pose any noticeable issues this time around? >> >> jon >> On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: >> >>> p.s. make sure that the echoes are in float format, not uchar/int/short >>> (you need to use -odt float in the mri_convert command line) >>> On Mon, 13 May 2013, Bruce Fischl wrote: >>> >>>> you can use file->aux-surfaces->load aux main surface (or something like >>>> that). Or use freeview. >>>> >>>> cheers >>>> Bruce >>>> On Mon, 13 May 2013, Jonathan Holt wrote: >>>> >>>>> Bruce, >>>>> >>>>> how is it that I might load multiple surfaces, loading lh after having >>>>> loaded rh makes the other disappear. this is loading manually, not from >>>>> the command line >>>>> On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> last question promise. Successfully completed mris_make_surfaces for >>>>>> both hemispheres. in my day-to-day editing I open tkmedit thusly: >>>>>> >>>>>> tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz >>>>>> -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface >>>>>> $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg >>>>>> >>>>>> this works for mprage subjects. In evaluating and possibly editing >>>>>> MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as >>>>>> there seem to be many more this time around. >>>>>> >>>>>> best, >>>>>> jon >>>>>> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >>>>>> >>>>>>> Hi Kayle >>>>>>> >>>>>>> it's been a long time since I wrote that code and we've only run it a >>>>>>> few >>>>>>> times. If you upload your subject directory I'll take a look >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> On Sat, 11 May >>>>>>> 2013, Kayle Sawyer wrote: >>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I tried to use the 4-echo MEMPRAGE dura detection for >>>>>>>> mris_make_surfaces, but I'm not sure if it worked. The terminal >>>>>>>> output, including commands, is attached. It was run with version >>>>>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>>>>>>> >>>>>>>> On the original recon, in the rh, there is a segment of dura marked as >>>>>>>> grey inside the pial line, at 94 111 169. The surfaces did not appear >>>>>>>> to change substantially after I reran mris_make_surfaces with the >>>>>>>> -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri >>>>>>>> directory. You can see the before and after for yourself on the >>>>>>>> attached screenshots, or if you have NMR access, here: >>>>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>>>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>>>>>>> >>>>>>>> I saw this output from mris_make_surfaces for the rh, so maybe -dura >>>>>>>> did correct a different defect? >>>>>>>> 7 non-cortical segments detected >>>>>>>> only using segment with 1900 vertices >>>>>>>> >>>>>>>> Any help would be appreciated, because we have over 130 brains and the >>>>>>>> fewer manual corrections, the better! >>>>>>>> >>>>>>>> Thanks, >>>>>>>> -Kayle >>>>>>>> >>>>>>>> >>>>>>>>
Re: [Freesurfer] Working with MEMPRAGE
I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote: > I'll definitely do that next time... > > although it didn't seem to pose any noticeable issues this time around? > > jon > On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: > >> p.s. make sure that the echoes are in float format, not uchar/int/short (you >> need to use -odt float in the mri_convert command line) >> On Mon, 13 May 2013, Bruce Fischl wrote: >> >>> you can use file->aux-surfaces->load aux main surface (or something like >>> that). Or use freeview. >>> >>> cheers >>> Bruce >>> On Mon, 13 May 2013, Jonathan Holt wrote: >>> >>>> Bruce, >>>> >>>> how is it that I might load multiple surfaces, loading lh after having >>>> loaded rh makes the other disappear. this is loading manually, not from >>>> the command line >>>> On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: >>>> >>>>> Hi all, >>>>> >>>>> last question promise. Successfully completed mris_make_surfaces for both >>>>> hemispheres. in my day-to-day editing I open tkmedit thusly: >>>>> >>>>> tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz >>>>> -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface >>>>> $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg >>>>> >>>>> this works for mprage subjects. In evaluating and possibly editing >>>>> MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as >>>>> there seem to be many more this time around. >>>>> >>>>> best, >>>>> jon >>>>> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >>>>> >>>>>> Hi Kayle >>>>>> >>>>>> it's been a long time since I wrote that code and we've only run it a few >>>>>> times. If you upload your subject directory I'll take a look >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Sat, 11 May >>>>>> 2013, Kayle Sawyer wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> I tried to use the 4-echo MEMPRAGE dura detection for >>>>>>> mris_make_surfaces, but I'm not sure if it worked. The terminal output, >>>>>>> including commands, is attached. It was run with version >>>>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>>>>>> >>>>>>> On the original recon, in the rh, there is a segment of dura marked as >>>>>>> grey inside the pial line, at 94 111 169. The surfaces did not appear >>>>>>> to change substantially after I reran mris_make_surfaces with the -dura >>>>>>> flag specifying the 4-echo MEMPRAGE, which I placed in the mri >>>>>>> directory. You can see the before and after for yourself on the >>>>>>> attached screenshots, or if you have NMR access, here: >>>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>>>>>> >>>>>>> I saw this output from mris_make_surfaces for the rh, so maybe -dura >>>>>>> did correct a different defect? >>>>>>> 7 non-cortical segments detected >>>>>>> only using segment with 1900 vertices >>>>>>> >>>>>>> Any help would be appreciated, because we have over 130 brains and the >>>>>>> fewer manual corrections, the better! >>>>>>> >>>>>>> Thanks, >>>>>>> -Kayle >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> From: Douglas Greve >>>>>>> Date: Thu, May 9, 2013 at 8:44 PM >>>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>> >>>>>>> >>>>>>> >>>>>>> the dcmunpack command is right. You should make sure to analyze only the >>>>>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>&g
Re: [Freesurfer] Working with MEMPRAGE
I'll definitely do that next time... although it didn't seem to pose any noticeable issues this time around? jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: > p.s. make sure that the echoes are in float format, not uchar/int/short (you > need to use -odt float in the mri_convert command line) > On Mon, 13 May 2013, Bruce Fischl wrote: > >> you can use file->aux-surfaces->load aux main surface (or something like >> that). Or use freeview. >> >> cheers >> Bruce >> On Mon, 13 May 2013, Jonathan Holt wrote: >> >>> Bruce, >>> >>> how is it that I might load multiple surfaces, loading lh after having >>> loaded rh makes the other disappear. this is loading manually, not from the >>> command line >>> On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: >>> >>>> Hi all, >>>> >>>> last question promise. Successfully completed mris_make_surfaces for both >>>> hemispheres. in my day-to-day editing I open tkmedit thusly: >>>> >>>> tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz >>>> -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface >>>> $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg >>>> >>>> this works for mprage subjects. In evaluating and possibly editing >>>> MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as >>>> there seem to be many more this time around. >>>> >>>> best, >>>> jon >>>> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >>>> >>>>> Hi Kayle >>>>> >>>>> it's been a long time since I wrote that code and we've only run it a few >>>>> times. If you upload your subject directory I'll take a look >>>>> >>>>> cheers >>>>> Bruce >>>>> On Sat, 11 May >>>>> 2013, Kayle Sawyer wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I tried to use the 4-echo MEMPRAGE dura detection for >>>>>> mris_make_surfaces, but I'm not sure if it worked. The terminal output, >>>>>> including commands, is attached. It was run with version >>>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>>>>> >>>>>> On the original recon, in the rh, there is a segment of dura marked as >>>>>> grey inside the pial line, at 94 111 169. The surfaces did not appear to >>>>>> change substantially after I reran mris_make_surfaces with the -dura >>>>>> flag specifying the 4-echo MEMPRAGE, which I placed in the mri >>>>>> directory. You can see the before and after for yourself on the attached >>>>>> screenshots, or if you have NMR access, here: >>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>>>>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>>>>> >>>>>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >>>>>> correct a different defect? >>>>>> 7 non-cortical segments detected >>>>>> only using segment with 1900 vertices >>>>>> >>>>>> Any help would be appreciated, because we have over 130 brains and the >>>>>> fewer manual corrections, the better! >>>>>> >>>>>> Thanks, >>>>>> -Kayle >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> From: Douglas Greve >>>>>> Date: Thu, May 9, 2013 at 8:44 PM >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>> >>>>>> >>>>>> >>>>>> the dcmunpack command is right. You should make sure to analyze only the >>>>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>>>> doug >>>>>> >>>>>> >>>>>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>>>>> Hi Kayle >>>>>>> >>>>>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> On Thu, >>>>>>> 9 May 2013,
Re: [Freesurfer] Working with MEMPRAGE
p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote: > you can use file->aux-surfaces->load aux main surface (or something like > that). Or use freeview. > > cheers > Bruce > On Mon, 13 May 2013, Jonathan Holt wrote: > >> Bruce, >> >> how is it that I might load multiple surfaces, loading lh after having >> loaded rh makes the other disappear. this is loading manually, not from the >> command line >> On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: >> >>> Hi all, >>> >>> last question promise. Successfully completed mris_make_surfaces for both >>> hemispheres. in my day-to-day editing I open tkmedit thusly: >>> >>> tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz >>> -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface >>> $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg >>> >>> this works for mprage subjects. In evaluating and possibly editing MEMPRAGE >>> subjects, which surfaces should I have opened in tkmedit, as there seem to >>> be many more this time around. >>> >>> best, >>> jon >>> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >>> >>>> Hi Kayle >>>> >>>> it's been a long time since I wrote that code and we've only run it a few >>>> times. If you upload your subject directory I'll take a look >>>> >>>> cheers >>>> Bruce >>>> On Sat, 11 May >>>> 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, >>>>> but I'm not sure if it worked. The terminal output, including commands, >>>>> is attached. It was run with version >>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>>>> >>>>> On the original recon, in the rh, there is a segment of dura marked as >>>>> grey inside the pial line, at 94 111 169. The surfaces did not appear to >>>>> change substantially after I reran mris_make_surfaces with the -dura flag >>>>> specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You >>>>> can see the before and after for yourself on the attached screenshots, or >>>>> if you have NMR access, here: >>>>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>>>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>>>> >>>>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >>>>> correct a different defect? >>>>> 7 non-cortical segments detected >>>>> only using segment with 1900 vertices >>>>> >>>>> Any help would be appreciated, because we have over 130 brains and the >>>>> fewer manual corrections, the better! >>>>> >>>>> Thanks, >>>>> -Kayle >>>>> >>>>> >>>>> >>>>> >>>>> From: Douglas Greve >>>>> Date: Thu, May 9, 2013 at 8:44 PM >>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>> >>>>> >>>>> >>>>> the dcmunpack command is right. You should make sure to analyze only the >>>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>>> doug >>>>> >>>>> >>>>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>>>> Hi Kayle >>>>>> >>>>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Thu, >>>>>> 9 May 2013, Kayle Sawyer wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have >>>>>>> been using the MEMPRAGE RMS scans and discarding the multiecho scans. >>>>>>> If we instead specify the multiecho scans for recon-all, do we need to >>>>>>> give any additional parameters (e.g. the number of echoes) for it to >>>>>>> utilize the 4 echoes to detect dura and refine pial surface
Re: [Freesurfer] Working with MEMPRAGE
you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: > Bruce, > > how is it that I might load multiple surfaces, loading lh after having loaded > rh makes the other disappear. this is loading manually, not from the command > line > On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > >> Hi all, >> >> last question promise. Successfully completed mris_make_surfaces for both >> hemispheres. in my day-to-day editing I open tkmedit thusly: >> >> tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface >> $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface >> $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg >> >> this works for mprage subjects. In evaluating and possibly editing MEMPRAGE >> subjects, which surfaces should I have opened in tkmedit, as there seem to >> be many more this time around. >> >> best, >> jon >> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: >> >>> Hi Kayle >>> >>> it's been a long time since I wrote that code and we've only run it a few >>> times. If you upload your subject directory I'll take a look >>> >>> cheers >>> Bruce >>> On Sat, 11 May >>> 2013, Kayle Sawyer wrote: >>> >>>> Hi all, >>>> >>>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, >>>> but I'm not sure if it worked. The terminal output, including commands, is >>>> attached. It was run with version >>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>>> >>>> On the original recon, in the rh, there is a segment of dura marked as >>>> grey inside the pial line, at 94 111 169. The surfaces did not appear to >>>> change substantially after I reran mris_make_surfaces with the -dura flag >>>> specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You >>>> can see the before and after for yourself on the attached screenshots, or >>>> if you have NMR access, here: >>>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>>> >>>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >>>> correct a different defect? >>>> 7 non-cortical segments detected >>>> only using segment with 1900 vertices >>>> >>>> Any help would be appreciated, because we have over 130 brains and the >>>> fewer manual corrections, the better! >>>> >>>> Thanks, >>>> -Kayle >>>> >>>> >>>> >>>> >>>> From: Douglas Greve >>>> Date: Thu, May 9, 2013 at 8:44 PM >>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> >>>> >>>> >>>> the dcmunpack command is right. You should make sure to analyze only the >>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>> doug >>>> >>>> >>>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>>> Hi Kayle >>>>> >>>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, >>>>> 9 May 2013, Kayle Sawyer wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have >>>>>> been using the MEMPRAGE RMS scans and discarding the multiecho scans. If >>>>>> we instead specify the multiecho scans for recon-all, do we need to give >>>>>> any additional parameters (e.g. the number of echoes) for it to utilize >>>>>> the 4 echoes to detect dura and refine pial surfaces in >>>>>> mris_make_surfaces, as described below? Or would we have to run >>>>>> recon-all with the RMS, then after it finishes re-run mris_make_surfaces >>>>>> manually with the -dura flag to refine the pial surface? >>>>>> >>>>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>>>> number] 3danat mgz 001.mgz" so the multi echo scan
Re: [Freesurfer] Working with MEMPRAGE
Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > Hi all, > > last question promise. Successfully completed mris_make_surfaces for both > hemispheres. in my day-to-day editing I open tkmedit thusly: > > tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface > $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface > $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg > > this works for mprage subjects. In evaluating and possibly editing MEMPRAGE > subjects, which surfaces should I have opened in tkmedit, as there seem to be > many more this time around. > > best, > jon > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > >> Hi Kayle >> >> it's been a long time since I wrote that code and we've only run it a few >> times. If you upload your subject directory I'll take a look >> >> cheers >> Bruce >> On Sat, 11 May >> 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, >>> but I'm not sure if it worked. The terminal output, including commands, is >>> attached. It was run with version >>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>> >>> On the original recon, in the rh, there is a segment of dura marked as grey >>> inside the pial line, at 94 111 169. The surfaces did not appear to change >>> substantially after I reran mris_make_surfaces with the -dura flag >>> specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You >>> can see the before and after for yourself on the attached screenshots, or >>> if you have NMR access, here: >>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>> >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >>> correct a different defect? >>> 7 non-cortical segments detected >>> only using segment with 1900 vertices >>> >>> Any help would be appreciated, because we have over 130 brains and the >>> fewer manual corrections, the better! >>> >>> Thanks, >>> -Kayle >>> >>> >>> >>> >>> From: Douglas Greve >>> Date: Thu, May 9, 2013 at 8:44 PM >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> the dcmunpack command is right. You should make sure to analyze only the >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>> doug >>> >>> >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> Hi Kayle >>>> >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>> >>>> cheers >>>> Bruce >>>> On Thu, >>>> 9 May 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>>>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>>>> instead specify the multiecho scans for recon-all, do we need to give any >>>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>>> described below? Or would we have to run recon-all with the RMS, then >>>>> after it finishes re-run mris_make_surfaces manually with the -dura flag >>>>> to refine the pial surface? >>>>> >>>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>>> file, and the RMS gets put into a separate mgz file. >>>>> Thanks, >>>>> -Kayle >>>>> >>>>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>>>> Message: 35 >>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>> From: Bruce Fischl >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: Jonathan Holt
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon there shouldn't be more surfaces I don't think - the ?h.white and ?h.pial should still be the ones you look at Bruce On Mon, 13 May 2013, Jonathan Holt wrote: > Hi all, > > last question promise. Successfully completed mris_make_surfaces for both > hemispheres. in my day-to-day editing I open tkmedit thusly: > > tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface > $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface > $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg > > this works for mprage subjects. In evaluating and possibly editing MEMPRAGE > subjects, which surfaces should I have opened in tkmedit, as there seem to be > many more this time around. > > best, > jon > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > >> Hi Kayle >> >> it's been a long time since I wrote that code and we've only run it a few >> times. If you upload your subject directory I'll take a look >> >> cheers >> Bruce >> On Sat, 11 May >> 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, >>> but I'm not sure if it worked. The terminal output, including commands, is >>> attached. It was run with version >>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>> >>> On the original recon, in the rh, there is a segment of dura marked as grey >>> inside the pial line, at 94 111 169. The surfaces did not appear to change >>> substantially after I reran mris_make_surfaces with the -dura flag >>> specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You >>> can see the before and after for yourself on the attached screenshots, or >>> if you have NMR access, here: >>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>> >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >>> correct a different defect? >>> 7 non-cortical segments detected >>> only using segment with 1900 vertices >>> >>> Any help would be appreciated, because we have over 130 brains and the >>> fewer manual corrections, the better! >>> >>> Thanks, >>> -Kayle >>> >>> >>> >>> >>> From: Douglas Greve >>> Date: Thu, May 9, 2013 at 8:44 PM >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> the dcmunpack command is right. You should make sure to analyze only the >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>> doug >>> >>> >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> Hi Kayle >>>> >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>> >>>> cheers >>>> Bruce >>>> On Thu, >>>> 9 May 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>>>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>>>> instead specify the multiecho scans for recon-all, do we need to give any >>>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>>> described below? Or would we have to run recon-all with the RMS, then >>>>> after it finishes re-run mris_make_surfaces manually with the -dura flag >>>>> to refine the pial surface? >>>>> >>>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>>> file, and the RMS gets put into a separate mgz file. >>>>> Thanks, >>>>> -Kayle >>>>> >>>>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>>>> Message: 35 >>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>> From: Bruce Fischl >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: Jonathan Holt >>>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>&g
Re: [Freesurfer] Working with MEMPRAGE
Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > Hi Kayle > > it's been a long time since I wrote that code and we've only run it a few > times. If you upload your subject directory I'll take a look > > cheers > Bruce > On Sat, 11 May > 2013, Kayle Sawyer wrote: > >> Hi all, >> >> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, >> but I'm not sure if it worked. The terminal output, including commands, is >> attached. It was run with version >> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >> >> On the original recon, in the rh, there is a segment of dura marked as grey >> inside the pial line, at 94 111 169. The surfaces did not appear to change >> substantially after I reran mris_make_surfaces with the -dura flag >> specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can >> see the before and after for yourself on the attached screenshots, or if you >> have NMR access, here: >> /space/ficus/6/users/SNEF_edits/OB01_orig/ >> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >> >> I saw this output from mris_make_surfaces for the rh, so maybe -dura did >> correct a different defect? >> 7 non-cortical segments detected >> only using segment with 1900 vertices >> >> Any help would be appreciated, because we have over 130 brains and the fewer >> manual corrections, the better! >> >> Thanks, >> -Kayle >> >> >> >> >> From: Douglas Greve >> Date: Thu, May 9, 2013 at 8:44 PM >> Subject: Re: [Freesurfer] Working with MEMPRAGE >> To: freesurfer@nmr.mgh.harvard.edu >> >> >> >> the dcmunpack command is right. You should make sure to analyze only the >> RMS in recon-all (ie , that is the only volume that goes into mri/orig >> doug >> >> >> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>> Hi Kayle >>> >>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>> >>> cheers >>> Bruce >>> On Thu, >>> 9 May 2013, Kayle Sawyer wrote: >>> >>>> Hi all, >>>> >>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>>> instead specify the multiecho scans for recon-all, do we need to give any >>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>> described below? Or would we have to run recon-all with the RMS, then >>>> after it finishes re-run mris_make_surfaces manually with the -dura flag >>>> to refine the pial surface? >>>> >>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>> file, and the RMS gets put into a separate mgz file. >>>> Thanks, >>>> -Kayle >>>> >>>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>>> Message: 35 >>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>> From: Bruce Fischl >>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>> To: Jonathan Holt >>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>> Message-ID: >>>>> >>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>> >>>>> it needs to be: >>>>> >>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>>>> >>>>> note the "4" which tells it how many echoes to read >>>>> >>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>> >>>>>> I input: >>>>>> >>>>>> mri
Re: [Freesurfer] Working with MEMPRAGE
Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: > Hi all, > > I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but > I'm not sure if it worked. The terminal output, including commands, is > attached. It was run with version > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. > > On the original recon, in the rh, there is a segment of dura marked as grey > inside the pial line, at 94 111 169. The surfaces did not appear to change > substantially after I reran mris_make_surfaces with the -dura flag specifying > the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the > before and after for yourself on the attached screenshots, or if you have NMR > access, here: > /space/ficus/6/users/SNEF_edits/OB01_orig/ > /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ > > I saw this output from mris_make_surfaces for the rh, so maybe -dura did > correct a different defect? > 7 non-cortical segments detected > only using segment with 1900 vertices > > Any help would be appreciated, because we have over 130 brains and the fewer > manual corrections, the better! > > Thanks, > -Kayle > > > > > From: Douglas Greve > Date: Thu, May 9, 2013 at 8:44 PM > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: freesurfer@nmr.mgh.harvard.edu > > > > the dcmunpack command is right. You should make sure to analyze only the > RMS in recon-all (ie , that is the only volume that goes into mri/orig > doug > > > On 5/9/13 6:48 PM, Bruce Fischl wrote: >> Hi Kayle >> >> you would run recon-all on the RMS, then run the dura stuff posthoc. >> >> cheers >> Bruce >> On Thu, >> 9 May 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>> instead specify the multiecho scans for recon-all, do we need to give any >>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>> described below? Or would we have to run recon-all with the RMS, then after >>> it finishes re-run mris_make_surfaces manually with the -dura flag to >>> refine the pial surface? >>> >>> Also, I'd like to make sure we are using dcmunpack properly. We take the >> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >> file, and the RMS gets put into a separate mgz file. >>> Thanks, >>> -Kayle >>> >>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>> Message: 35 >>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>> From: Bruce Fischl >>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>> To: Jonathan Holt >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Message-ID: >>>> >>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>> >>>> it needs to be: >>>> >>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>>> >>>> note the "4" which tells it how many echoes to read >>>> >>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>> >>>>> I input: >>>>> >>>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>>>> >>>>> it returns: >>>>> >>>>> detecting dura using 0 echos from memprage_echo%d.mgz >>>>> >>>>> >>>>> Should I execute the command in the same directory as the mgz's? Should >>>>> they be set up or placed in a specific directory? I also, as with >>>>> recon-all, exported the proper subject directory beforehand. >>>>> >>>>> >>>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>>>> >>>>>> can you send me the full command line? It should say 4 echoes, not 0 >>>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Thanks Bruce, >>>>>>> >>>>>>> should the hemisphere's be processed separately, or how do I sig
Re: [Freesurfer] Working with MEMPRAGE
echoes) for it to >>>> utilize the 4 >>>> echoes to detect >>>> dura and refine >>>> pial surfaces in >>>> mris_make_surfaces, >>>> as described below? >>>> Or would we have to >>>> run recon-all with >>>> the RMS, then after >>>> it finishes re-run >>>> mris_make_surfaces >>>> manually with the >>>> -dura flag to >>>> refine the pial >>>> surface? >>>> >>>> Also, I'd like to >>>> make sure we are >>>> using dcmunpack >>>> properly. We take >>>> the >>>> >>>> scan.info file and parse it >>>> like this: "-run >>>> [MEMPRAGE_4e_p2_1mm_iso run >>>> number] 3danat mgz 001.mgz" so >>>> the multi echo scan gets put >>>> into one mgz >>>> file, and the RMS gets put into >>>> a separate mgz file. >>>> Thanks, >>>> -Kayle >>>> >>>> On May 9, 2013, at >>>> 12:00 PM, >>>> freesurfer-requ...@nmr.mgh.harvard.edu >>>> wrote: >>>> Message: >>>> 35 >>>> Date: >>>> Thu, 9 >>>> May >>>> 2013 >>>> 10:44:23 >>>> -0400 >>>> (EDT) >>>> From: >>>> Bruce >>>> Fischl >>>> >>>> Subject: >>>> Re: >>>> [Freesurfer] >>>> Working >>>> with >>>> MEMPRAGE >>>> To: >>>> Jonathan >>>> Holt >>>> >>>> Cc: >>>> freesurfer@nmr.mgh.harvard.edu >>>> Message-ID: >>>> >>>> >>>> >>>> Content-Type: >>>> TEXT/PLAIN; >>>> format=flowed; >>>> charset=US-ASCII >>>> >>>> it >>>> needs >>>> to be: >>>> >>>> mris_make_surfaces >>>> -dura >>>> memprage_echo%d.mgz >>>> 4 >>>> subjid >>>> lh >>>> >>>> note >>>> the "4" >>>> which >>>> tells >>>> it how >>>> many &
Re: [Freesurfer] Working with MEMPRAGE
n after >>> it finishes re-run >>> mris_make_surfaces >>> manually with the >>> -dura flag to >>> refine the pial >>> surface? >>> >>> Also, I'd like to >>> make sure we are >>> using dcmunpack >>> properly. We take >>> the >>> >>> scan.info file and parse it >>> like this: "-run >>> [MEMPRAGE_4e_p2_1mm_iso run >>> number] 3danat mgz 001.mgz" so >>> the multi echo scan gets put >>> into one mgz >>> file, and the RMS gets put into >>> a separate mgz file. >>> Thanks, >>> -Kayle >>> >>> On May 9, 2013, at >>> 12:00 PM, >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> wrote: >>> Message: >>> 35 >>> Date: >>> Thu, 9 >>> May >>> 2013 >>> 10:44:23 >>> -0400 >>> (EDT) >>> From: >>> Bruce >>> Fischl >>> >>> Subject: >>> Re: >>> [Freesurfer] >>> Working >>> with >>> MEMPRAGE >>> To: >>> Jonathan >>> Holt >>> >>> Cc: >>> freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> >>> >>> >>> Content-Type: >>> TEXT/PLAIN; >>> format=flowed; >>> charset=US-ASCII >>> >>> it >>> needs >>> to be: >>> >>> mris_make_surfaces >>> -dura >>> memprage_echo%d.mgz >>> 4 >>> subjid >>> lh >>> >>> note >>> the "4" >>> which >>> tells >>> it how >>> many >>> echoes >>> to read >>> >>> On Thu, >>> 9 May >>> 2013, >>> Jonathan >>> Holt >>> wrote: >>> >>> I >>> input: >>> >>> mris_make_surfaces >>> -dura >>> memprage_echo%d.mgz >>> subjid >>>
Re: [Freesurfer] Working with MEMPRAGE
the RMS, then after >>> it finishes re-run >>> mris_make_surfaces >>> manually with the >>> -dura flag to >>> refine the pial >>> surface? >>> >>> Also, I'd like to >>> make sure we are >>> using dcmunpack >>> properly. We take >>> the >>> >>>scan.info file and parse it >>>like this: "-run >>>[MEMPRAGE_4e_p2_1mm_iso run >>>number] 3danat mgz 001.mgz" so >>>the multi echo scan gets put >>>into one mgz >>>file, and the RMS gets put into >>> a separate mgz file. >>> Thanks, >>> -Kayle >>> >>> On May 9, 2013, at >>> 12:00 PM, >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> wrote: >>>Message: >>>35 >>>Date: >>>Thu, 9 >>>May >>>2013 >>>10:44:23 >>>-0400 >>>(EDT) >>>From: >>>Bruce >>>Fischl >>> >>>Subject: >>>Re: >>>[Freesurfer] >>>Working >>>with >>>MEMPRAGE >>>To: >>>Jonathan >>>Holt >>> >>>Cc: >>>freesurfer@nmr.mgh.harvard.edu >>>Message-ID: >>> >>> >>> >>>Content-Type: >>>TEXT/PLAIN; >>>format=flowed; >>>charset=US-ASCII >>> >>>it >>>needs >>>to be: >>> >>>mris_make_surfaces >>>-dura >>>memprage_echo%d.mgz >>>4 >>>subjid >>>lh >>> >>>note >>>the "4" >>>which >>>tells >>>it how >>>many >>>echoes >>>to read >>> >>>On Thu, >>>9 May >>>2013, >>>Jonathan >>>Holt >>>wrote: >>> >>> I >>> input: >>> >>> mris_make_surfaces >>> -dura >>>
Re: [Freesurfer] Working with MEMPRAGE
the >> >>scan.info file and parse it >>like this: "-run >>[MEMPRAGE_4e_p2_1mm_iso run >>number] 3danat mgz 001.mgz" so >>the multi echo scan gets put >>into one mgz >>file, and the RMS gets put into >>a separate mgz file. >> Thanks, >> -Kayle >> >> On May 9, 2013, at >> 12:00 PM, >> freesurfer-requ...@nmr.mgh.harvard.edu >> wrote: >> Message: >> 35 >> Date: >>Thu, 9 >>May >>2013 >>10:44:23 >>-0400 >>(EDT) >>From: >>Bruce >>Fischl >> >>Subject: >>Re: >>[Freesurfer] >>Working >>with >>MEMPRAGE >>To: >>Jonathan >>Holt >> >>Cc: >>freesurfer@nmr.mgh.harvard.edu >>Message-ID: >> >> >> >>Content-Type: >>TEXT/PLAIN; >>format=flowed; >>charset=US-ASCII >> >>it >>needs >>to be: >> >>mris_make_surfaces >>-dura >>memprage_echo%d.mgz >>4 >>subjid >>lh >> >>note >>the "4" >>which >>tells >>it how >>many >>echoes >>to read >> >>On Thu, >>9 May >>2013, >>Jonathan >>Holt >>wrote: >> >> I >> input: >> >> mris_make_surfaces >> -dura >> memprage_echo%d.mgz >> subjid >> lh >> >> it >> returns: >> >> detecting >> dura >> using >> 0 >> echos >> from >> memprage_echo%d.mgz >> >> Should >> I >> execute >> the >> command >>
Re: [Freesurfer] Working with MEMPRAGE
-0400
(EDT)
From:
Bruce
Fischl
Subject:
Re:
[Freesurfer]
Working
with
MEMPRAGE
To:
Jonathan
Holt
Cc:
freesurfer@nmr.mgh.harvard.edu
Message-ID:
   Â
Content-Type:
TEXT/PLAIN;
format=flowed;
charset=US-ASCII
it
needs
to be:
mris_make_surfaces
-dura
memprage_echo%d.mgz
4
subjid
lh
note
the "4"
which
tells
it how
many
echoes
to read
On Thu,
9 May
2013,
Jonathan
Holt
wrote:
I
input:
mris_make_surfaces
-dura
memprage_echo%d.mgz
subjid
lh
it
returns:
detecting
dura
using
0
echos
from
memprage_echo%d.mgz
Should
I
execute
the
command
in
the
same
directory
as
the
mgz's?
Should
they
be
set
up
or
placed
in
a
specific
directory?
I
also,
as
with
recon-all,
exported
the
proper
subject
directory
beforehand.
On
May
9,
2013,
at
10:37
AM,
Bruce
Fischl
wrot
Re: [Freesurfer] Working with MEMPRAGE
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh it's entirely possible I'm specifying the wrong mgz? After running recon-all on the RMS the usual directories were created, etc... including 001.mgz which is in s_MEMPRAGE/mri/orig. On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt wrote: > $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer > $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh > > it's entirely possible I'm specifying the wrong mgz? After running > recon-all on the RMS the usual directories were created, etc... including > 001.mgz which is in s_MEMPRAGE/mri/orig. > > > On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl > wrote: > >> can you send details about the steps you carried out including full >> command lines? >> >> On Fri, 10 May 2013, Jonathan Holt wrote: >> >> I've gotten as far as running the mris_make_surfaces on the RMS, but >>> after running for a bit it stopped with this error >>> >>> mghRead (file/path/s_MEMPRAGE/mri/**0010.mgz -1): coult not open file >>> mris_make_surfaces: could not read 0th echo for dura localization from >>> file/path/s_MEMPRAGE/mri/0010.**mgz >>> >>> for reference, the RMS file name is 001.mgz >>> >>> jon >>> On May 9, 2013, at 8:44 PM, Douglas Greve wrote: >>> >>> >>>> the dcmunpack command is right. You should make sure to analyze only the >>>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>>> doug >>>> >>>> >>>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> >>>>> Hi Kayle >>>>> >>>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, >>>>> 9 May 2013, Kayle Sawyer wrote: >>>>> >>>>> Hi all, >>>>>> >>>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have >>>>>> been using the MEMPRAGE RMS scans and discarding the multiecho scans. If >>>>>> we >>>>>> instead specify the multiecho scans for recon-all, do we need to give any >>>>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>>>> described below? Or would we have to run recon-all with the RMS, then >>>>>> after >>>>>> it finishes re-run mris_make_surfaces manually with the -dura flag to >>>>>> refine the pial surface? >>>>>> >>>>>> Also, I'd like to make sure we are using dcmunpack properly. We take >>>>>> the >>>>>> >>>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso >>>>> run >>>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one >>>>> mgz >>>>> file, and the RMS gets put into a separate mgz file. >>>>> >>>>>> Thanks, >>>>>> -Kayle >>>>>> >>>>>> On May 9, 2013, at 12:00 PM, >>>>>> freesurfer-requ...@nmr.mgh.**harvard.eduwrote: >>>>>> >>>>>>> Message: 35 >>>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>>> From: Bruce Fischl >>>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>>> To: Jonathan Holt >>>>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>>>> Message-ID: >>>>>>> >>>>>> mgh.harvard.edu >>>>>>> > >>>>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>>>> >>>>>>> it needs to be: >>>>>>> >>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>>>>>> >>>>>>> note the "4" which tells it how many echoes to read >>>>>>> >>>>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>>>> >>>>>>> I input: >>>>>>>> >>>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>>>>>>> >>>>&g
Re: [Freesurfer] Working with MEMPRAGE
can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote: > I've gotten as far as running the mris_make_surfaces on the RMS, but after > running for a bit it stopped with this error > > mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file > mris_make_surfaces: could not read 0th echo for dura localization from > file/path/s_MEMPRAGE/mri/0010.mgz > > for reference, the RMS file name is 001.mgz > > jon > On May 9, 2013, at 8:44 PM, Douglas Greve wrote: > >> >> the dcmunpack command is right. You should make sure to analyze only the >> RMS in recon-all (ie , that is the only volume that goes into mri/orig >> doug >> >> >> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>> Hi Kayle >>> >>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>> >>> cheers >>> Bruce >>> On Thu, >>> 9 May 2013, Kayle Sawyer wrote: >>> >>>> Hi all, >>>> >>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>>> instead specify the multiecho scans for recon-all, do we need to give any >>>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>>> described below? Or would we have to run recon-all with the RMS, then >>>> after it finishes re-run mris_make_surfaces manually with the -dura flag >>>> to refine the pial surface? >>>> >>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>> file, and the RMS gets put into a separate mgz file. >>>> Thanks, >>>> -Kayle >>>> >>>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>>> Message: 35 >>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>> From: Bruce Fischl >>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>> To: Jonathan Holt >>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>> Message-ID: >>>>> >>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>> >>>>> it needs to be: >>>>> >>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>>>> >>>>> note the "4" which tells it how many echoes to read >>>>> >>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>> >>>>>> I input: >>>>>> >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>>>>> >>>>>> it returns: >>>>>> >>>>>> detecting dura using 0 echos from memprage_echo%d.mgz >>>>>> >>>>>> >>>>>> Should I execute the command in the same directory as the mgz's? Should >>>>>> they be set up or placed in a specific directory? I also, as with >>>>>> recon-all, exported the proper subject directory beforehand. >>>>>> >>>>>> >>>>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>>>>> >>>>>>> can you send me the full command line? It should say 4 echoes, not 0 >>>>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>>>> >>>>>>>> Thanks Bruce, >>>>>>>> >>>>>>>> should the hemisphere's be processed separately, or how do I signify >>>>>>>> lh and rh simultaneously? >>>>>>>> >>>>>>>> Also, should the fact that after running mris_make_surfaces, it says >>>>>>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>>>>>>> I've got 4 different echos, all mgzs in the directory. I have a >>>>>>>> feeling I'm doing this incorrectly. >>>>>>>> >>>>>>>> jon >>>>>>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>>>>>> >>>>>>>&
Re: [Freesurfer] Working with MEMPRAGE
I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz for reference, the RMS file name is 001.mgz jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote: > > the dcmunpack command is right. You should make sure to analyze only the > RMS in recon-all (ie , that is the only volume that goes into mri/orig > doug > > > On 5/9/13 6:48 PM, Bruce Fischl wrote: >> Hi Kayle >> >> you would run recon-all on the RMS, then run the dura stuff posthoc. >> >> cheers >> Bruce >> On Thu, >> 9 May 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >>> instead specify the multiecho scans for recon-all, do we need to give any >>> additional parameters (e.g. the number of echoes) for it to utilize the 4 >>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >>> described below? Or would we have to run recon-all with the RMS, then after >>> it finishes re-run mris_make_surfaces manually with the -dura flag to >>> refine the pial surface? >>> >>> Also, I'd like to make sure we are using dcmunpack properly. We take the >> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >> file, and the RMS gets put into a separate mgz file. >>> Thanks, >>> -Kayle >>> >>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>>> Message: 35 >>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>> From: Bruce Fischl >>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>> To: Jonathan Holt >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Message-ID: >>>> >>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>> >>>> it needs to be: >>>> >>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>>> >>>> note the "4" which tells it how many echoes to read >>>> >>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>> >>>>> I input: >>>>> >>>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>>>> >>>>> it returns: >>>>> >>>>> detecting dura using 0 echos from memprage_echo%d.mgz >>>>> >>>>> >>>>> Should I execute the command in the same directory as the mgz's? Should >>>>> they be set up or placed in a specific directory? I also, as with >>>>> recon-all, exported the proper subject directory beforehand. >>>>> >>>>> >>>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>>>> >>>>>> can you send me the full command line? It should say 4 echoes, not 0 >>>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Thanks Bruce, >>>>>>> >>>>>>> should the hemisphere's be processed separately, or how do I signify lh >>>>>>> and rh simultaneously? >>>>>>> >>>>>>> Also, should the fact that after running mris_make_surfaces, it says >>>>>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>>>>>> I've got 4 different echos, all mgzs in the directory. I have a feeling >>>>>>> I'm doing this incorrectly. >>>>>>> >>>>>>> jon >>>>>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>>>>> >>>>>>>> Hi Jon >>>>>>>> >>>>>>>> yes, the subject and hemi need to be defined (they are required >>>>>>>> parameters) >>>>>>>> Bruce >>>>>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>>>>> >>>>>>>>> Hi all, >>>>>>>>> combed through the mail archives to figure out how to work with multi >>
Re: [Freesurfer] Working with MEMPRAGE
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: > Hi Kayle > > you would run recon-all on the RMS, then run the dura stuff posthoc. > > cheers > Bruce > On Thu, > 9 May 2013, Kayle Sawyer wrote: > >> Hi all, >> >> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >> instead specify the multiecho scans for recon-all, do we need to give any >> additional parameters (e.g. the number of echoes) for it to utilize the 4 >> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >> described below? Or would we have to run recon-all with the RMS, then after >> it finishes re-run mris_make_surfaces manually with the -dura flag to refine >> the pial surface? >> >> Also, I'd like to make sure we are using dcmunpack properly. We take the > scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run > number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz > file, and the RMS gets put into a separate mgz file. >> Thanks, >> -Kayle >> >> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>> Message: 35 >>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>> From: Bruce Fischl >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: Jonathan Holt >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> >>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>> >>> it needs to be: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>> >>> note the "4" which tells it how many echoes to read >>> >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> >>>> I input: >>>> >>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>>> >>>> it returns: >>>> >>>> detecting dura using 0 echos from memprage_echo%d.mgz >>>> >>>> >>>> Should I execute the command in the same directory as the mgz's? Should >>>> they be set up or placed in a specific directory? I also, as with >>>> recon-all, exported the proper subject directory beforehand. >>>> >>>> >>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>>> >>>>> can you send me the full command line? It should say 4 echoes, not 0 >>>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>>> >>>>>> Thanks Bruce, >>>>>> >>>>>> should the hemisphere's be processed separately, or how do I signify lh >>>>>> and rh simultaneously? >>>>>> >>>>>> Also, should the fact that after running mris_make_surfaces, it says >>>>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>>>>> I've got 4 different echos, all mgzs in the directory. I have a feeling >>>>>> I'm doing this incorrectly. >>>>>> >>>>>> jon >>>>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>>>> >>>>>>> Hi Jon >>>>>>> >>>>>>> yes, the subject and hemi need to be defined (they are required >>>>>>> parameters) >>>>>>> Bruce >>>>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>>>> >>>>>>>> Hi all, >>>>>>>> combed through the mail archives to figure out how to work with multi >>>>>>>> echo >>>>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>>>> commands is the appropriate >>>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>>>>>>> hemispheres need to be specified as per the 1st line? >>>>>>>> jon >>>>>>>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ 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.
Re: [Freesurfer] Working with MEMPRAGE
Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: > Hi all, > > Can the MEMPRAGE be specified in recon-all with the -i flag? We have been > using the MEMPRAGE RMS scans and discarding the multiecho scans. If we > instead specify the multiecho scans for recon-all, do we need to give any > additional parameters (e.g. the number of echoes) for it to utilize the 4 > echoes to detect dura and refine pial surfaces in mris_make_surfaces, as > described below? Or would we have to run recon-all with the RMS, then after > it finishes re-run mris_make_surfaces manually with the -dura flag to refine > the pial surface? > > Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. > > Thanks, > -Kayle > > On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >> Message: 35 >> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >> From: Bruce Fischl >> Subject: Re: [Freesurfer] Working with MEMPRAGE >> To: Jonathan Holt >> Cc: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> >> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >> >> it needs to be: >> >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >> >> note the "4" which tells it how many echoes to read >> >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> I input: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>> >>> it returns: >>> >>> detecting dura using 0 echos from memprage_echo%d.mgz >>> >>> >>> Should I execute the command in the same directory as the mgz's? Should >>> they be set up or placed in a specific directory? I also, as with >>> recon-all, exported the proper subject directory beforehand. >>> >>> >>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>> >>>> can you send me the full command line? It should say 4 echoes, not 0 >>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>> >>>>> Thanks Bruce, >>>>> >>>>> should the hemisphere's be processed separately, or how do I signify lh >>>>> and rh simultaneously? >>>>> >>>>> Also, should the fact that after running mris_make_surfaces, it says >>>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>>>> I've got 4 different echos, all mgzs in the directory. I have a feeling >>>>> I'm doing this incorrectly. >>>>> >>>>> jon >>>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>>> >>>>>> Hi Jon >>>>>> >>>>>> yes, the subject and hemi need to be defined (they are required >>>>>> parameters) >>>>>> Bruce >>>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Hi all, >>>>>>> combed through the mail archives to figure out how to work with multi >>>>>>> echo >>>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>>> commands is the appropriate >>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>>>>>> hemispheres need to be specified as per the 1st line? >>>>>>> jon >>>>>>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Working with MEMPRAGE
Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should they >> be set up or placed in a specific directory? I also, as with recon-all, >> exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> >>>> Thanks Bruce, >>>> >>>> should the hemisphere's be processed separately, or how do I signify lh >>>> and rh simultaneously? >>>> >>>> Also, should the fact that after running mris_make_surfaces, it says >>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've >>>> got 4 different echos, all mgzs in the directory. I have a feeling I'm >>>> doing this incorrectly. >>>> >>>> jon >>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>> >>>>> Hi Jon >>>>> >>>>> yes, the subject and hemi need to be defined (they are required >>>>> parameters) >>>>> Bruce >>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>> >>>>>> Hi all, >>>>>> combed through the mail archives to figure out how to work with multi >>>>>> echo >>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>> commands is the appropriate >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>>>>> hemispheres need to be specified as per the 1st line? >>>>>> jon >>>>>> ___ 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.
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon you need to run recon-all all the way through, then run the command I sent you with the echoes in the mri dir cheers Bruce On Thu, 9 May 2013, Jonathan Holt wrote: > No, > > I believe my PI simply ran mri_convert on the 4 nii's, > > Clearly there is a better approach? > > jon > On May 9, 2013, at 11:04 AM, Bruce Fischl wrote: > >> Did you run recon-all? It will create filled.mgz in the subject/mri dir >> >> >> >> On May 9, 2013, at 11:00 AM, Jonathan Holt wrote: >> >>> That was my suspicion, I've got them in the wrong folder. None of them are >>> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and >>> nothing else. >>> >>> Also the exact error has it looking in >>> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz >>> >>> as opposed to /example/directory/subjects/subjid/mri/filled.mgz >>> >>> I can rename subject directory if need be. >>> >>> >>> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: >>> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: > Oh, simple mistake! > > However, now it spit's an error saying I need filled.mgz? > > > On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: > >> it needs to be: >> >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >> >> note the "4" which tells it how many echoes to read >> >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> I input: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>> >>> it returns: >>> >>> detecting dura using 0 echos from memprage_echo%d.mgz >>> >>> >>> Should I execute the command in the same directory as the mgz's? Should >>> they be set up or placed in a specific directory? I also, as with >>> recon-all, exported the proper subject directory beforehand. >>> >>> >>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>> can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: > Thanks Bruce, > > should the hemisphere's be processed separately, or how do I signify > lh and rh simultaneously? > > Also, should the fact that after running mris_make_surfaces, it says > "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? > I've got 4 different echos, all mgzs in the directory. I have a > feeling I'm doing this incorrectly. > > jon > On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > >> Hi Jon >> >> yes, the subject and hemi need to be defined (they are required >> parameters) >> Bruce >> On Wed, 8 May 2013, Jonathan Holt wrote: >> >>> Hi all, >>> combed through the mail archives to figure out how to work with >>> multi echo >>> mprage, found what I need but I wanted to confirm which of these two >>> commands is the appropriate >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>> hemispheres need to be specified as per the 1st line? >>> jon >>> >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>> >>> >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/l
Re: [Freesurfer] Working with MEMPRAGE
No, I believe my PI simply ran mri_convert on the 4 nii's, Clearly there is a better approach? jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote: > Did you run recon-all? It will create filled.mgz in the subject/mri dir > > > > On May 9, 2013, at 11:00 AM, Jonathan Holt wrote: > >> That was my suspicion, I've got them in the wrong folder. None of them are >> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and >> nothing else. >> >> Also the exact error has it looking in >> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz >> >> as opposed to /example/directory/subjects/subjid/mri/filled.mgz >> >> I can rename subject directory if need be. >> >> >> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: >> >>> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in >>> the subject's mri dir >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should >> they be set up or placed in a specific directory? I also, as with >> recon-all, exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > Hi Jon > > yes, the subject and hemi need to be defined (they are required > parameters) > Bruce > On Wed, 8 May 2013, Jonathan Holt wrote: > >> Hi all, >> combed through the mail archives to figure out how to work with >> multi echo >> mprage, found what I need but I wanted to confirm which of these two >> commands is the appropriate >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >> hemispheres need to be specified as per the 1st line? >> jon >> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
Did you run recon-all? It will create filled.mgz in the subject/mri dir On May 9, 2013, at 11:00 AM, Jonathan Holt wrote: > That was my suspicion, I've got them in the wrong folder. None of them are > 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and > nothing else. > > Also the exact error has it looking in > /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz > > as opposed to /example/directory/subjects/subjid/mri/filled.mgz > > I can rename subject directory if need be. > > > On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: > >> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in >> the subject's mri dir >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> Oh, simple mistake! >>> >>> However, now it spit's an error saying I need filled.mgz? >>> >>> >>> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: >>> it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the "4" which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: > I input: > > mris_make_surfaces -dura memprage_echo%d.mgz subjid lh > > it returns: > > detecting dura using 0 echos from memprage_echo%d.mgz > > > Should I execute the command in the same directory as the mgz's? Should > they be set up or placed in a specific directory? I also, as with > recon-all, exported the proper subject directory beforehand. > > > On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > >> can you send me the full command line? It should say 4 echoes, not 0 >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> Thanks Bruce, >>> >>> should the hemisphere's be processed separately, or how do I signify lh >>> and rh simultaneously? >>> >>> Also, should the fact that after running mris_make_surfaces, it says >>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>> I've got 4 different echos, all mgzs in the directory. I have a feeling >>> I'm doing this incorrectly. >>> >>> jon >>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>> Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: > Hi all, > combed through the mail archives to figure out how to work with multi > echo > mprage, found what I need but I wanted to confirm which of these two > commands is the appropriate > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh > mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and > hemispheres need to be specified as per the 1st line? > jon > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > > > >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: > is your SUBJECTS_DIR set properly? You need to put the memprage echoes in > the subject's mri dir > On Thu, 9 May 2013, Jonathan Holt wrote: > >> Oh, simple mistake! >> >> However, now it spit's an error saying I need filled.mgz? >> >> >> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: >> >>> it needs to be: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >>> >>> note the "4" which tells it how many echoes to read >>> >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > can you send me the full command line? It should say 4 echoes, not 0 > On Thu, 9 May 2013, Jonathan Holt wrote: > >> Thanks Bruce, >> >> should the hemisphere's be processed separately, or how do I signify lh >> and rh simultaneously? >> >> Also, should the fact that after running mris_make_surfaces, it says >> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >> I've got 4 different echos, all mgzs in the directory. I have a feeling >> I'm doing this incorrectly. >> >> jon >> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >> >>> Hi Jon >>> >>> yes, the subject and hemi need to be defined (they are required >>> parameters) >>> Bruce >>> On Wed, 8 May 2013, Jonathan Holt wrote: >>> Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: > Oh, simple mistake! > > However, now it spit's an error saying I need filled.mgz? > > > On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: > >> it needs to be: >> >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >> >> note the "4" which tells it how many echoes to read >> >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> I input: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>> >>> it returns: >>> >>> detecting dura using 0 echos from memprage_echo%d.mgz >>> >>> >>> Should I execute the command in the same directory as the mgz's? Should >>> they be set up or placed in a specific directory? I also, as with >>> recon-all, exported the proper subject directory beforehand. >>> >>> >>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>> can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: > Thanks Bruce, > > should the hemisphere's be processed separately, or how do I signify lh > and rh simultaneously? > > Also, should the fact that after running mris_make_surfaces, it says > "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? > I've got 4 different echos, all mgzs in the directory. I have a feeling > I'm doing this incorrectly. > > jon > On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > >> Hi Jon >> >> yes, the subject and hemi need to be defined (they are required >> parameters) >> Bruce >> On Wed, 8 May 2013, Jonathan Holt wrote: >> >>> Hi all, >>> combed through the mail archives to figure out how to work with multi >>> echo >>> mprage, found what I need but I wanted to confirm which of these two >>> commands is the appropriate >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>> hemispheres need to be specified as per the 1st line? >>> jon >>> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> >>> >>> >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should they >> be set up or placed in a specific directory? I also, as with recon-all, >> exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > Hi Jon > > yes, the subject and hemi need to be defined (they are required > parameters) > Bruce > On Wed, 8 May 2013, Jonathan Holt wrote: > >> Hi all, >> combed through the mail archives to figure out how to work with multi >> echo >> mprage, found what I need but I wanted to confirm which of these two >> commands is the appropriate >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >> hemispheres need to be specified as per the 1st line? >> jon >> > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the "4" which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: > I input: > > mris_make_surfaces -dura memprage_echo%d.mgz subjid lh > > it returns: > > detecting dura using 0 echos from memprage_echo%d.mgz > > > Should I execute the command in the same directory as the mgz's? Should they > be set up or placed in a specific directory? I also, as with recon-all, > exported the proper subject directory beforehand. > > > On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > >> can you send me the full command line? It should say 4 echoes, not 0 >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> Thanks Bruce, >>> >>> should the hemisphere's be processed separately, or how do I signify lh and >>> rh simultaneously? >>> >>> Also, should the fact that after running mris_make_surfaces, it says >>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've >>> got 4 different echos, all mgzs in the directory. I have a feeling I'm >>> doing this incorrectly. >>> >>> jon >>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>> Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: > Hi all, > combed through the mail archives to figure out how to work with multi echo > mprage, found what I need but I wanted to confirm which of these two > commands is the appropriate > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh > mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and > hemispheres need to be specified as per the 1st line? > jon > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > can you send me the full command line? It should say 4 echoes, not 0 > On Thu, 9 May 2013, Jonathan Holt wrote: > >> Thanks Bruce, >> >> should the hemisphere's be processed separately, or how do I signify lh and >> rh simultaneously? >> >> Also, should the fact that after running mris_make_surfaces, it says >> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've >> got 4 different echos, all mgzs in the directory. I have a feeling I'm doing >> this incorrectly. >> >> jon >> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >> >>> Hi Jon >>> >>> yes, the subject and hemi need to be defined (they are required parameters) >>> Bruce >>> On Wed, 8 May 2013, Jonathan Holt wrote: >>> Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: > Thanks Bruce, > > should the hemisphere's be processed separately, or how do I signify lh and > rh simultaneously? > > Also, should the fact that after running mris_make_surfaces, it says > "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've > got 4 different echos, all mgzs in the directory. I have a feeling I'm doing > this incorrectly. > > jon > On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > >> Hi Jon >> >> yes, the subject and hemi need to be defined (they are required parameters) >> Bruce >> On Wed, 8 May 2013, Jonathan Holt wrote: >> >>> Hi all, >>> combed through the mail archives to figure out how to work with multi echo >>> mprage, found what I need but I wanted to confirm which of these two >>> commands is the appropriate >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres >>> need to be specified as per the 1st line? >>> jon >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > Hi Jon > > yes, the subject and hemi need to be defined (they are required parameters) > Bruce > On Wed, 8 May 2013, Jonathan Holt wrote: > >> Hi all, >> combed through the mail archives to figure out how to work with multi echo >> mprage, found what I need but I wanted to confirm which of these two >> commands is the appropriate >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres >> need to be specified as per the 1st line? >> jon >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: > Hi all, > combed through the mail archives to figure out how to work with multi echo > mprage, found what I need but I wanted to confirm which of these two > commands is the appropriate > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh > > mris_make_surfaces -dura memprage_echo%d.mgz > > do the subjid and hemispheres need to be specified as per the 1st line? > > jon > > > > > ___ 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.
